Starting phenix.real_space_refine
on Mon Jul 28 13:53:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vtl_21381/07_2025/6vtl_21381.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vtl_21381/07_2025/6vtl_21381.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vtl_21381/07_2025/6vtl_21381.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vtl_21381/07_2025/6vtl_21381.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vtl_21381/07_2025/6vtl_21381.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vtl_21381/07_2025/6vtl_21381.cif"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.024
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      81      5.16       5
     C    6591      2.51       5
     N    1674      2.21       5
     O    1896      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10242
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 446, 3386
          Classifications: {'peptide': 446}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 425}
          Unresolved non-hydrogen bonds: 191
          Unresolved non-hydrogen angles: 238
          Unresolved non-hydrogen dihedrals: 157
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 134
    Chain: "A"
      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
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 7.57, per 1000 atoms: 0.74
  Number of scatterers: 10242
  At special positions: 0
  Unit cell: (94.608, 97.2, 129.6, 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      81     16.00
     O    1896      8.00
     N    1674      7.00
     C    6591      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=21, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  94 " - pdb=" SG  CYS A 195 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 173 " - pdb=" SG  CYS A 180 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 366 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 309 " - pdb=" SG  CYS A 362 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 322 " - pdb=" SG  CYS A 344 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 324 " - pdb=" SG  CYS A 336 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  94 " - pdb=" SG  CYS C 195 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  94 " - pdb=" SG  CYS B 195 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 173 " - pdb=" SG  CYS C 180 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 173 " - pdb=" SG  CYS B 180 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 366 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 366 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 309 " - pdb=" SG  CYS C 362 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 309 " - pdb=" SG  CYS B 362 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 313 " - pdb=" SG  CYS C 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 322 " - pdb=" SG  CYS C 344 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 322 " - pdb=" SG  CYS B 344 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 324 " - pdb=" SG  CYS C 336 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 324 " - pdb=" SG  CYS B 336 " 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
    NAG-ASN
      " NAG A 601 " - " ASN A 394 "
      " NAG A 602 " - " ASN A 367 "
      " NAG B 601 " - " ASN B 394 "
      " NAG B 602 " - " ASN B 367 "
      " NAG C 601 " - " ASN C 394 "
      " NAG C 602 " - " ASN C 367 "
  Time building additional restraints: 2.52
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2508

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 15 sheets defined
      41.3% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 24
      removed outlier: 3.653A  pdb=" N   SER A  24 " --> pdb=" O   GLN A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 35
    Processing helix  chain 'A' and resid 41 through 53
      removed outlier: 4.149A  pdb=" N   VAL A  45 " --> pdb=" O   SER A  41 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   CYS A  50 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 71
      removed outlier: 3.671A  pdb=" N   VAL A  61 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASN A  64 " --> pdb=" O   LEU A  60 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ARG A  65 " --> pdb=" O   VAL A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 112
      removed outlier: 3.628A  pdb=" N   ALA A 112 " --> pdb=" O   ASP A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 141
      removed outlier: 3.731A  pdb=" N   ILE A 138 " --> pdb=" O   LYS A 134 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LEU A 139 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ASP A 141 " --> pdb=" O   GLU A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 162
    Processing helix  chain 'A' and resid 165 through 170
    Processing helix  chain 'A' and resid 181 through 185
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.778A  pdb=" N   TYR A 230 " --> pdb=" O   GLN A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 263
      removed outlier: 3.622A  pdb=" N   GLY A 263 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 323
      removed outlier: 3.698A  pdb=" N   ARG A 310 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ARG A 316 " --> pdb=" O   ASP A 312 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   TYR A 317 " --> pdb=" O   CYS A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 344
      removed outlier: 3.716A  pdb=" N   GLU A 343 " --> pdb=" O   GLU A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 354
      removed outlier: 3.933A  pdb=" N   ASP A 350 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   PHE A 351 " --> pdb=" O   PRO A 347 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 360
      removed outlier: 3.718A  pdb=" N   CYS A 360 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 384
      No H-bonds generated for 'chain 'A' and resid 382 through 384'
    Processing helix  chain 'A' and resid 385 through 392
      removed outlier: 3.744A  pdb=" N   LYS A 391 " --> pdb=" O   LYS A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 403
      removed outlier: 3.866A  pdb=" N   GLY A 401 " --> pdb=" O   GLU A 397 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   GLU A 402 " --> pdb=" O   GLN A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 432
    Processing helix  chain 'A' and resid 434 through 442
      removed outlier: 3.962A  pdb=" N   LEU A 440 " --> pdb=" O   GLY A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 460
      removed outlier: 3.548A  pdb=" N   VAL A 449 " --> pdb=" O   SER A 445 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   GLU A 458 " --> pdb=" O   ASP A 454 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 24
      removed outlier: 3.653A  pdb=" N   SER C  24 " --> pdb=" O   GLN C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 35
    Processing helix  chain 'C' and resid 41 through 53
      removed outlier: 4.149A  pdb=" N   VAL C  45 " --> pdb=" O   SER C  41 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   CYS C  50 " --> pdb=" O   VAL C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 71
      removed outlier: 3.671A  pdb=" N   VAL C  61 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASN C  64 " --> pdb=" O   LEU C  60 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG C  65 " --> pdb=" O   VAL C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 112
      removed outlier: 3.627A  pdb=" N   ALA C 112 " --> pdb=" O   ASP C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 141
      removed outlier: 3.731A  pdb=" N   ILE C 138 " --> pdb=" O   LYS C 134 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LEU C 139 " --> pdb=" O   GLN C 135 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ASP C 141 " --> pdb=" O   GLU C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 162
    Processing helix  chain 'C' and resid 165 through 170
    Processing helix  chain 'C' and resid 181 through 185
    Processing helix  chain 'C' and resid 226 through 230
      removed outlier: 3.776A  pdb=" N   TYR C 230 " --> pdb=" O   GLN C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 258 through 263
      removed outlier: 3.622A  pdb=" N   GLY C 263 " --> pdb=" O   ILE C 259 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 305 through 323
      removed outlier: 3.697A  pdb=" N   ARG C 310 " --> pdb=" O   ILE C 306 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ARG C 316 " --> pdb=" O   ASP C 312 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   TYR C 317 " --> pdb=" O   CYS C 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 344
      removed outlier: 3.717A  pdb=" N   GLU C 343 " --> pdb=" O   GLU C 339 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 344 through 354
      removed outlier: 3.933A  pdb=" N   ASP C 350 " --> pdb=" O   ASP C 346 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   PHE C 351 " --> pdb=" O   PRO C 347 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU C 352 " --> pdb=" O   ALA C 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 356 through 360
      removed outlier: 3.720A  pdb=" N   CYS C 360 " --> pdb=" O   ASN C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 382 through 384
      No H-bonds generated for 'chain 'C' and resid 382 through 384'
    Processing helix  chain 'C' and resid 385 through 392
      removed outlier: 3.745A  pdb=" N   LYS C 391 " --> pdb=" O   LYS C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 396 through 403
      removed outlier: 3.866A  pdb=" N   GLY C 401 " --> pdb=" O   GLU C 397 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLU C 402 " --> pdb=" O   GLN C 398 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 426 through 432
    Processing helix  chain 'C' and resid 434 through 442
      removed outlier: 3.962A  pdb=" N   LEU C 440 " --> pdb=" O   GLY C 436 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 445 through 460
      removed outlier: 3.549A  pdb=" N   VAL C 449 " --> pdb=" O   SER C 445 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLU C 458 " --> pdb=" O   ASP C 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 24
      removed outlier: 3.652A  pdb=" N   SER B  24 " --> pdb=" O   GLN B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 35
    Processing helix  chain 'B' and resid 41 through 53
      removed outlier: 4.149A  pdb=" N   VAL B  45 " --> pdb=" O   SER B  41 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   CYS B  50 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 71
      removed outlier: 3.671A  pdb=" N   VAL B  61 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ASN B  64 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ARG B  65 " --> pdb=" O   VAL B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 112
      removed outlier: 3.627A  pdb=" N   ALA B 112 " --> pdb=" O   ASP B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 141
      removed outlier: 3.732A  pdb=" N   ILE B 138 " --> pdb=" O   LYS B 134 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU B 139 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASP B 141 " --> pdb=" O   GLU B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 162
    Processing helix  chain 'B' and resid 165 through 170
    Processing helix  chain 'B' and resid 181 through 185
    Processing helix  chain 'B' and resid 226 through 230
      removed outlier: 3.777A  pdb=" N   TYR B 230 " --> pdb=" O   GLN B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 263
      removed outlier: 3.622A  pdb=" N   GLY B 263 " --> pdb=" O   ILE B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 323
      removed outlier: 3.698A  pdb=" N   ARG B 310 " --> pdb=" O   ILE B 306 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ARG B 316 " --> pdb=" O   ASP B 312 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   TYR B 317 " --> pdb=" O   CYS B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 344
      removed outlier: 3.716A  pdb=" N   GLU B 343 " --> pdb=" O   GLU B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 354
      removed outlier: 3.933A  pdb=" N   ASP B 350 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   PHE B 351 " --> pdb=" O   PRO B 347 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU B 352 " --> pdb=" O   ALA B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 360
      removed outlier: 3.719A  pdb=" N   CYS B 360 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 384
      No H-bonds generated for 'chain 'B' and resid 382 through 384'
    Processing helix  chain 'B' and resid 385 through 392
      removed outlier: 3.745A  pdb=" N   LYS B 391 " --> pdb=" O   LYS B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 403
      removed outlier: 3.867A  pdb=" N   GLY B 401 " --> pdb=" O   GLU B 397 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLU B 402 " --> pdb=" O   GLN B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 432
    Processing helix  chain 'B' and resid 434 through 442
      removed outlier: 3.961A  pdb=" N   LEU B 440 " --> pdb=" O   GLY B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 460
      removed outlier: 3.548A  pdb=" N   VAL B 449 " --> pdb=" O   SER B 445 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   GLU B 458 " --> pdb=" O   ASP B 454 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 82
      removed outlier: 8.526A  pdb=" N   ASN A 415 " --> pdb=" O   CYS A 276 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   GLU A 278 " --> pdb=" O   ASN A 415 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   PHE A 270 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   VAL A 406 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   PHE A 410 " --> pdb=" O   VAL A 274 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LEU A 405 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 82
      removed outlier: 8.526A  pdb=" N   ASN A 415 " --> pdb=" O   CYS A 276 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   GLU A 278 " --> pdb=" O   ASN A 415 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLN A 277 " --> pdb=" O   GLY A 372 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87
    Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 190
      removed outlier: 6.842A  pdb=" N   LYS A 194 " --> pdb=" O   ASN A  95 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   ASN A  95 " --> pdb=" O   LYS A 194 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   HIS A 251 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE A 246 " --> pdb=" O   VAL A 266 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 175
    Processing sheet with id=AA6, first strand: chain 'C' and resid 74 through 82
      removed outlier: 8.527A  pdb=" N   ASN C 415 " --> pdb=" O   CYS C 276 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   GLU C 278 " --> pdb=" O   ASN C 415 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   PHE C 270 " --> pdb=" O   ILE C 404 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   VAL C 406 " --> pdb=" O   PHE C 270 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE C 410 " --> pdb=" O   VAL C 274 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU C 405 " --> pdb=" O   LEU C 223 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 74 through 82
      removed outlier: 8.527A  pdb=" N   ASN C 415 " --> pdb=" O   CYS C 276 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   GLU C 278 " --> pdb=" O   ASN C 415 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLN C 277 " --> pdb=" O   GLY C 372 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 86 through 87
    Processing sheet with id=AA9, first strand: chain 'C' and resid 186 through 190
      removed outlier: 6.843A  pdb=" N   LYS C 194 " --> pdb=" O   ASN C  95 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   ASN C  95 " --> pdb=" O   LYS C 194 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   HIS C 251 " --> pdb=" O   ALA C  90 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE C 246 " --> pdb=" O   VAL C 266 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 174 through 175
    Processing sheet with id=AB2, first strand: chain 'B' and resid 74 through 82
      removed outlier: 8.526A  pdb=" N   ASN B 415 " --> pdb=" O   CYS B 276 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   GLU B 278 " --> pdb=" O   ASN B 415 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   PHE B 270 " --> pdb=" O   ILE B 404 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   VAL B 406 " --> pdb=" O   PHE B 270 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE B 410 " --> pdb=" O   VAL B 274 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LEU B 405 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 74 through 82
      removed outlier: 8.526A  pdb=" N   ASN B 415 " --> pdb=" O   CYS B 276 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   GLU B 278 " --> pdb=" O   ASN B 415 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLN B 277 " --> pdb=" O   GLY B 372 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 86 through 87
    Processing sheet with id=AB5, first strand: chain 'B' and resid 186 through 190
      removed outlier: 6.843A  pdb=" N   LYS B 194 " --> pdb=" O   ASN B  95 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   ASN B  95 " --> pdb=" O   LYS B 194 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   HIS B 251 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE B 246 " --> pdb=" O   VAL B 266 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 174 through 175

    426 hydrogen bonds defined for protein.
    1179 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: 3.40

  Time building geometry restraints manager: 3.08 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: 3300
        1.35 -     1.47: 2614
        1.47 -     1.59: 4457
        1.59 -     1.72: 0
        1.72 -     1.84: 111
  Bond restraints: 10482
  Sorted by residual:
  bond pdb=" C1  NAG B 601 "
       pdb=" O5  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 3.93e+00
  bond pdb=" C1  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.88e+00
  bond pdb=" C1  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.82e+00
  bond pdb=" CB  GLU A 137 "
       pdb=" CG  GLU A 137 "
    ideal  model  delta    sigma   weight residual
    1.520  1.574 -0.054 3.00e-02 1.11e+03 3.30e+00
  bond pdb=" CB  GLU C 137 "
       pdb=" CG  GLU C 137 "
    ideal  model  delta    sigma   weight residual
    1.520  1.574 -0.054 3.00e-02 1.11e+03 3.22e+00
  ... (remaining 10477 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 13845
        2.07 -     4.14: 348
        4.14 -     6.21: 47
        6.21 -     8.28: 13
        8.28 -    10.35: 3
  Bond angle restraints: 14256
  Sorted by residual:
  angle pdb=" CA  GLY C 245 "
        pdb=" C   GLY C 245 "
        pdb=" N   ILE C 246 "
      ideal   model   delta    sigma   weight residual
     114.23  117.83   -3.60 8.80e-01 1.29e+00 1.67e+01
  angle pdb=" CA  GLY A 245 "
        pdb=" C   GLY A 245 "
        pdb=" N   ILE A 246 "
      ideal   model   delta    sigma   weight residual
     114.23  117.80   -3.57 8.80e-01 1.29e+00 1.65e+01
  angle pdb=" CA  GLY B 245 "
        pdb=" C   GLY B 245 "
        pdb=" N   ILE B 246 "
      ideal   model   delta    sigma   weight residual
     114.23  117.75   -3.52 8.80e-01 1.29e+00 1.60e+01
  angle pdb=" CA  CYS B 180 "
        pdb=" CB  CYS B 180 "
        pdb=" SG  CYS B 180 "
      ideal   model   delta    sigma   weight residual
     114.40  122.23   -7.83 2.30e+00 1.89e-01 1.16e+01
  angle pdb=" CA  CYS C 180 "
        pdb=" CB  CYS C 180 "
        pdb=" SG  CYS C 180 "
      ideal   model   delta    sigma   weight residual
     114.40  122.17   -7.77 2.30e+00 1.89e-01 1.14e+01
  ... (remaining 14251 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 5735
       17.86 -    35.71: 517
       35.71 -    53.57: 72
       53.57 -    71.43: 3
       71.43 -    89.28: 18
  Dihedral angle restraints: 6345
    sinusoidal: 2436
      harmonic: 3909
  Sorted by residual:
  dihedral pdb=" CB  CYS B 313 "
           pdb=" SG  CYS B 313 "
           pdb=" SG  CYS B 360 "
           pdb=" CB  CYS B 360 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  178.30  -85.30     1      1.00e+01 1.00e-02 8.81e+01
  dihedral pdb=" CB  CYS C 313 "
           pdb=" SG  CYS C 313 "
           pdb=" SG  CYS C 360 "
           pdb=" CB  CYS C 360 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  178.30  -85.30     1      1.00e+01 1.00e-02 8.81e+01
  dihedral pdb=" CB  CYS A 313 "
           pdb=" SG  CYS A 313 "
           pdb=" SG  CYS A 360 "
           pdb=" CB  CYS A 360 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  178.28  -85.28     1      1.00e+01 1.00e-02 8.81e+01
  ... (remaining 6342 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 870
       0.030 -    0.061: 431
       0.061 -    0.091: 185
       0.091 -    0.121: 92
       0.121 -    0.152: 39
  Chirality restraints: 1617
  Sorted by residual:
  chirality pdb=" CA  CYS B 366 "
            pdb=" N   CYS B 366 "
            pdb=" C   CYS B 366 "
            pdb=" CB  CYS B 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.75e-01
  chirality pdb=" CA  CYS A 366 "
            pdb=" N   CYS A 366 "
            pdb=" C   CYS A 366 "
            pdb=" CB  CYS A 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.60e-01
  chirality pdb=" CB  ILE B 125 "
            pdb=" CA  ILE B 125 "
            pdb=" CG1 ILE B 125 "
            pdb=" CG2 ILE B 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.56e-01
  ... (remaining 1614 not shown)

  Planarity restraints: 1845
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 125 "    0.044 5.00e-02 4.00e+02   6.76e-02 7.31e+00
        pdb=" N   PRO B 126 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 126 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 126 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 125 "   -0.044 5.00e-02 4.00e+02   6.75e-02 7.30e+00
        pdb=" N   PRO C 126 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO C 126 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C 126 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 125 "    0.044 5.00e-02 4.00e+02   6.73e-02 7.24e+00
        pdb=" N   PRO A 126 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 126 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 126 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1842 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.82: 3312
        2.82 -     3.34: 8710
        3.34 -     3.86: 16794
        3.86 -     4.38: 19292
        4.38 -     4.90: 32481
  Nonbonded interactions: 80589
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B  95 "
            pdb=" OH  TYR B 230 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OD1 ASN C  95 "
            pdb=" OH  TYR C 230 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OD1 ASN A  95 "
            pdb=" OH  TYR A 230 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" NE1 TRP A  47 "
            pdb=" OD2 ASP C 454 "
     model   vdw
     2.332 3.120
  nonbonded pdb=" O   SER A  36 "
            pdb=" NH2 ARG A  44 "
     model   vdw
     2.349 3.120
  ... (remaining 80584 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.270
  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:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.090
  Find NCS groups from input model:        0.180
  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:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7018
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      :  0.004   0.054  10509  Z= 0.193
  Angle     :  0.803  10.354  14316  Z= 0.426
  Chirality :  0.048   0.152   1617
  Planarity :  0.006   0.068   1839
  Dihedral  : 13.731  89.283   3774
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.96 (0.18), residues: 1332
  helix: -4.73 (0.10), residues: 447
  sheet: -3.46 (0.29), residues: 237
  loop : -1.95 (0.21), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  47 
 HIS   0.003   0.001   HIS A  29 
 PHE   0.013   0.001   PHE A 264 
 TYR   0.011   0.001   TYR B 416 
 ARG   0.003   0.000   ARG A  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00079 (    6)
  link_NAG-ASN         : angle       1.29645 (   18)
  hydrogen bonds       : bond        0.29192 (  387)
  hydrogen bonds       : angle      10.83466 ( 1179)
  SS BOND              : bond        0.00682 (   21)
  SS BOND              : angle       2.08597 (   42)
  covalent geometry    : bond        0.00412 (10482)
  covalent geometry    : angle       0.79560 (14256)

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 1.063 
Fit side-chains
REVERT: A   57 LEU cc_start: 0.8200 (tp) cc_final: 0.7795 (tp)
REVERT: A  139 LEU cc_start: 0.6892 (tt) cc_final: 0.6520 (mp)
REVERT: A  277 GLN cc_start: 0.8650 (tp40) cc_final: 0.8074 (tp40)
REVERT: A  329 MET cc_start: 0.8640 (mtt) cc_final: 0.8308 (mtp)
REVERT: C   57 LEU cc_start: 0.8258 (tp) cc_final: 0.7811 (tp)
REVERT: C  277 GLN cc_start: 0.8609 (tp40) cc_final: 0.8099 (tp40)
REVERT: C  329 MET cc_start: 0.8585 (mtt) cc_final: 0.8110 (mtp)
REVERT: B   57 LEU cc_start: 0.8149 (tp) cc_final: 0.7942 (tp)
REVERT: B  101 PHE cc_start: 0.7788 (t80) cc_final: 0.7349 (t80)
REVERT: B  139 LEU cc_start: 0.6813 (tt) cc_final: 0.6426 (mp)
REVERT: B  277 GLN cc_start: 0.8632 (tp40) cc_final: 0.8093 (tp40)
REVERT: B  329 MET cc_start: 0.8598 (mtt) cc_final: 0.8180 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2073
  time to fit residues: 47.9547
Evaluate side-chains
  103 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    4.9990
   chunk 100 optimal weight:   20.0000
   chunk 55 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 67 optimal weight:    0.8980
   chunk 53 optimal weight:    0.1980
   chunk 103 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 119 optimal weight:   10.0000
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 217 ASN
** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 ASN
** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.161485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.125283 restraints weight = 19598.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.127474 restraints weight = 11717.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.129023 restraints weight = 8826.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10509  Z= 0.210
  Angle     :  0.649   7.421  14316  Z= 0.337
  Chirality :  0.043   0.157   1617
  Planarity :  0.005   0.053   1839
  Dihedral  :  5.177  17.353   1572
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.70 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.74 (0.21), residues: 1332
  helix: -3.43 (0.16), residues: 447
  sheet: -2.71 (0.29), residues: 285
  loop : -1.31 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B  47 
 HIS   0.006   0.002   HIS B 251 
 PHE   0.011   0.001   PHE C 158 
 TYR   0.017   0.002   TYR C 416 
 ARG   0.003   0.000   ARG C 100 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00295 (    6)
  link_NAG-ASN         : angle       1.40650 (   18)
  hydrogen bonds       : bond        0.04492 (  387)
  hydrogen bonds       : angle       6.53964 ( 1179)
  SS BOND              : bond        0.00255 (   21)
  SS BOND              : angle       1.28334 (   42)
  covalent geometry    : bond        0.00473 (10482)
  covalent geometry    : angle       0.64419 (14256)

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 2.412 
Fit side-chains
REVERT: A   57 LEU cc_start: 0.8261 (tp) cc_final: 0.7954 (tp)
REVERT: A  139 LEU cc_start: 0.7242 (tt) cc_final: 0.6715 (mp)
REVERT: A  277 GLN cc_start: 0.8641 (tp40) cc_final: 0.8139 (tp40)
REVERT: A  329 MET cc_start: 0.8658 (mtt) cc_final: 0.8410 (mtp)
REVERT: C   57 LEU cc_start: 0.8278 (tp) cc_final: 0.7941 (tp)
REVERT: C  277 GLN cc_start: 0.8636 (tp40) cc_final: 0.8179 (tp-100)
REVERT: C  329 MET cc_start: 0.8567 (mtt) cc_final: 0.8186 (mtp)
REVERT: B   57 LEU cc_start: 0.8280 (tp) cc_final: 0.7939 (tp)
REVERT: B  101 PHE cc_start: 0.7900 (t80) cc_final: 0.7618 (t80)
REVERT: B  277 GLN cc_start: 0.8658 (tp40) cc_final: 0.8378 (tp40)
REVERT: B  283 TYR cc_start: 0.8230 (m-80) cc_final: 0.7899 (m-80)
REVERT: B  329 MET cc_start: 0.8613 (mtt) cc_final: 0.8341 (mtp)
  outliers start: 22
  outliers final: 13
  residues processed: 127
  average time/residue: 0.2091
  time to fit residues: 41.1414
Evaluate side-chains
  114 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 1.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  364 MET
Chi-restraints excluded: chain C residue  380 ILE
Chi-restraints excluded: chain C residue  389 LEU
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  389 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 88 optimal weight:    8.9990
   chunk 58 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 78 optimal weight:   20.0000
   chunk 103 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 54 optimal weight:    0.3980
   chunk 99 optimal weight:    9.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 398 GLN
C 398 GLN
B 398 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.160506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.117831 restraints weight = 20435.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.121982 restraints weight = 10931.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.124571 restraints weight = 7681.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10509  Z= 0.171
  Angle     :  0.588   6.514  14316  Z= 0.296
  Chirality :  0.042   0.179   1617
  Planarity :  0.004   0.046   1839
  Dihedral  :  4.841  15.894   1572
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 13.08 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.22), residues: 1332
  helix: -2.45 (0.20), residues: 441
  sheet: -2.64 (0.28), residues: 285
  loop : -1.12 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  47 
 HIS   0.004   0.001   HIS B 251 
 PHE   0.009   0.001   PHE B 264 
 TYR   0.019   0.001   TYR C 416 
 ARG   0.003   0.000   ARG C 100 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00199 (    6)
  link_NAG-ASN         : angle       1.59903 (   18)
  hydrogen bonds       : bond        0.03712 (  387)
  hydrogen bonds       : angle       5.84421 ( 1179)
  SS BOND              : bond        0.00330 (   21)
  SS BOND              : angle       1.01208 (   42)
  covalent geometry    : bond        0.00383 (10482)
  covalent geometry    : angle       0.58397 (14256)

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 1.216 
Fit side-chains
REVERT: A   57 LEU cc_start: 0.8242 (tp) cc_final: 0.7926 (tp)
REVERT: A  329 MET cc_start: 0.8603 (mtt) cc_final: 0.8212 (mtp)
REVERT: C   57 LEU cc_start: 0.8273 (tp) cc_final: 0.7937 (tp)
REVERT: C  329 MET cc_start: 0.8477 (mtt) cc_final: 0.8131 (mtp)
REVERT: C  416 TYR cc_start: 0.8595 (p90) cc_final: 0.8363 (p90)
REVERT: B   57 LEU cc_start: 0.8296 (tp) cc_final: 0.7961 (tp)
REVERT: B  101 PHE cc_start: 0.7970 (t80) cc_final: 0.7704 (t80)
REVERT: B  277 GLN cc_start: 0.8668 (tp40) cc_final: 0.8320 (tp40)
REVERT: B  329 MET cc_start: 0.8550 (mtt) cc_final: 0.8182 (mtp)
  outliers start: 32
  outliers final: 22
  residues processed: 133
  average time/residue: 0.1783
  time to fit residues: 37.6133
Evaluate side-chains
  130 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  180 CYS
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue  180 CYS
Chi-restraints excluded: chain C residue  246 ILE
Chi-restraints excluded: chain C residue  364 MET
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  380 ILE
Chi-restraints excluded: chain C residue  418 THR
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  180 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  418 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 111 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 131 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
C 217 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.170507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.133740 restraints weight = 19760.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.135958 restraints weight = 11543.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.137580 restraints weight = 8966.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10509  Z= 0.127
  Angle     :  0.555   8.043  14316  Z= 0.276
  Chirality :  0.041   0.182   1617
  Planarity :  0.004   0.044   1839
  Dihedral  :  4.576  15.310   1572
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.85 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.22), residues: 1332
  helix: -1.85 (0.21), residues: 447
  sheet: -2.76 (0.28), residues: 267
  loop : -0.90 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  47 
 HIS   0.003   0.001   HIS C 251 
 PHE   0.010   0.001   PHE B 264 
 TYR   0.016   0.001   TYR B 416 
 ARG   0.002   0.000   ARG C 100 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00140 (    6)
  link_NAG-ASN         : angle       1.59113 (   18)
  hydrogen bonds       : bond        0.03233 (  387)
  hydrogen bonds       : angle       5.53260 ( 1179)
  SS BOND              : bond        0.00128 (   21)
  SS BOND              : angle       0.80798 (   42)
  covalent geometry    : bond        0.00288 (10482)
  covalent geometry    : angle       0.55105 (14256)

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 1.098 
Fit side-chains
REVERT: C   57 LEU cc_start: 0.8221 (tp) cc_final: 0.8008 (tp)
REVERT: C  329 MET cc_start: 0.8562 (mtt) cc_final: 0.8361 (mtp)
REVERT: B   57 LEU cc_start: 0.8243 (tp) cc_final: 0.8012 (tp)
REVERT: B  101 PHE cc_start: 0.7893 (t80) cc_final: 0.7661 (t80)
REVERT: B  277 GLN cc_start: 0.8617 (tp40) cc_final: 0.8341 (tp40)
  outliers start: 28
  outliers final: 18
  residues processed: 136
  average time/residue: 0.1920
  time to fit residues: 40.8072
Evaluate side-chains
  122 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 2.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  180 CYS
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  180 CYS
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  364 MET
Chi-restraints excluded: chain C residue  405 LEU
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  180 CYS
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  405 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 112 optimal weight:    0.9990
   chunk 100 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 88 optimal weight:   10.0000
   chunk 115 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 105 optimal weight:    0.6980
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 = 0.4632 r_free = 0.4632 target = 0.169942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.126040 restraints weight = 20834.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.129888 restraints weight = 11973.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.132512 restraints weight = 8713.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10509  Z= 0.162
  Angle     :  0.587   8.978  14316  Z= 0.286
  Chirality :  0.042   0.176   1617
  Planarity :  0.004   0.043   1839
  Dihedral  :  4.581  16.699   1572
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 15.54 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.23), residues: 1332
  helix: -1.34 (0.23), residues: 453
  sheet: -2.57 (0.28), residues: 285
  loop : -0.82 (0.27), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  47 
 HIS   0.004   0.001   HIS B 251 
 PHE   0.009   0.001   PHE B 264 
 TYR   0.032   0.001   TYR C 416 
 ARG   0.004   0.000   ARG A  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00131 (    6)
  link_NAG-ASN         : angle       1.59811 (   18)
  hydrogen bonds       : bond        0.03194 (  387)
  hydrogen bonds       : angle       5.46751 ( 1179)
  SS BOND              : bond        0.00303 (   21)
  SS BOND              : angle       0.88222 (   42)
  covalent geometry    : bond        0.00370 (10482)
  covalent geometry    : angle       0.58330 (14256)

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 106
  time to evaluate  : 1.352 
Fit side-chains
REVERT: A   78 LEU cc_start: 0.9027 (mm) cc_final: 0.8803 (mm)
REVERT: C   57 LEU cc_start: 0.8250 (tp) cc_final: 0.7992 (tp)
REVERT: C  329 MET cc_start: 0.8466 (mtt) cc_final: 0.8139 (mtp)
REVERT: B   57 LEU cc_start: 0.8254 (tp) cc_final: 0.7955 (tp)
REVERT: B   78 LEU cc_start: 0.9032 (mm) cc_final: 0.8794 (mm)
REVERT: B  101 PHE cc_start: 0.7973 (t80) cc_final: 0.7720 (t80)
REVERT: B  277 GLN cc_start: 0.8635 (tp40) cc_final: 0.8246 (tp40)
  outliers start: 34
  outliers final: 30
  residues processed: 131
  average time/residue: 0.2420
  time to fit residues: 51.0440
Evaluate side-chains
  133 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  180 CYS
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  180 CYS
Chi-restraints excluded: chain C residue  262 LEU
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  364 MET
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  380 ILE
Chi-restraints excluded: chain C residue  405 LEU
Chi-restraints excluded: chain C residue  418 THR
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  180 CYS
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  418 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   chunk 55 optimal weight:   20.0000
   chunk 80 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 108 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0060
   chunk 103 optimal weight:    1.9990
   chunk 102 optimal weight:    7.9990
   overall best weight:    0.9800

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

Flipped N/Q/H residues before XYZ refinement:
C 111 HIS
B 111 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.170792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.134454 restraints weight = 19764.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.136872 restraints weight = 11611.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.138270 restraints weight = 9048.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.4290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10509  Z= 0.115
  Angle     :  0.552   7.390  14316  Z= 0.270
  Chirality :  0.041   0.176   1617
  Planarity :  0.004   0.042   1839
  Dihedral  :  4.359  15.261   1572
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 15.83 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.23), residues: 1332
  helix: -0.92 (0.23), residues: 453
  sheet: -2.72 (0.28), residues: 273
  loop : -0.74 (0.27), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  47 
 HIS   0.002   0.001   HIS C 251 
 PHE   0.010   0.001   PHE B 264 
 TYR   0.024   0.001   TYR C 416 
 ARG   0.005   0.000   ARG C  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00121 (    6)
  link_NAG-ASN         : angle       1.54949 (   18)
  hydrogen bonds       : bond        0.02963 (  387)
  hydrogen bonds       : angle       5.29392 ( 1179)
  SS BOND              : bond        0.00162 (   21)
  SS BOND              : angle       0.72711 (   42)
  covalent geometry    : bond        0.00259 (10482)
  covalent geometry    : angle       0.54936 (14256)

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 1.096 
Fit side-chains
REVERT: A   78 LEU cc_start: 0.9024 (mm) cc_final: 0.8787 (mm)
REVERT: B   78 LEU cc_start: 0.9030 (mm) cc_final: 0.8776 (mm)
REVERT: B  101 PHE cc_start: 0.7896 (t80) cc_final: 0.7674 (t80)
REVERT: B  277 GLN cc_start: 0.8601 (tp40) cc_final: 0.8370 (tp40)
  outliers start: 33
  outliers final: 28
  residues processed: 130
  average time/residue: 0.1601
  time to fit residues: 33.7959
Evaluate side-chains
  129 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  180 CYS
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  180 CYS
Chi-restraints excluded: chain C residue  246 ILE
Chi-restraints excluded: chain C residue  262 LEU
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  364 MET
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  180 CYS
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  405 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 115 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 125 optimal weight:    2.9990
   chunk 38 optimal weight:    0.1980
   chunk 73 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 130 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 54 optimal weight:    8.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
C 111 HIS
B 111 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.171019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.127560 restraints weight = 21041.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.131578 restraints weight = 11926.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.134156 restraints weight = 8628.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.4221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10509  Z= 0.130
  Angle     :  0.564   8.259  14316  Z= 0.274
  Chirality :  0.041   0.179   1617
  Planarity :  0.004   0.041   1839
  Dihedral  :  4.293  15.272   1572
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 15.73 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.23), residues: 1332
  helix: -0.64 (0.24), residues: 459
  sheet: -2.36 (0.28), residues: 285
  loop : -0.66 (0.27), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  47 
 HIS   0.003   0.001   HIS B 251 
 PHE   0.009   0.001   PHE B 264 
 TYR   0.021   0.001   TYR C 416 
 ARG   0.003   0.000   ARG C  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00111 (    6)
  link_NAG-ASN         : angle       1.52923 (   18)
  hydrogen bonds       : bond        0.02936 (  387)
  hydrogen bonds       : angle       5.22022 ( 1179)
  SS BOND              : bond        0.00171 (   21)
  SS BOND              : angle       0.85270 (   42)
  covalent geometry    : bond        0.00295 (10482)
  covalent geometry    : angle       0.56103 (14256)

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 104
  time to evaluate  : 1.164 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 LEU cc_start: 0.9023 (mm) cc_final: 0.8777 (mm)
REVERT: A  329 MET cc_start: 0.8358 (mtp) cc_final: 0.8070 (ptp)
REVERT: B   78 LEU cc_start: 0.9036 (mm) cc_final: 0.8738 (mm)
REVERT: B  101 PHE cc_start: 0.7947 (t80) cc_final: 0.7699 (t80)
REVERT: B  277 GLN cc_start: 0.8567 (tp40) cc_final: 0.8188 (tp40)
  outliers start: 37
  outliers final: 33
  residues processed: 132
  average time/residue: 0.1615
  time to fit residues: 34.4711
Evaluate side-chains
  134 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 101
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  180 CYS
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  180 CYS
Chi-restraints excluded: chain C residue  246 ILE
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  364 MET
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  389 LEU
Chi-restraints excluded: chain C residue  405 LEU
Chi-restraints excluded: chain C residue  418 THR
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  180 CYS
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  418 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 118 optimal weight:    7.9990
   chunk 62 optimal weight:    6.9990
   chunk 129 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 97 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0020
   chunk 40 optimal weight:    5.9990
   chunk 49 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 98 optimal weight:    0.0470
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.4886

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
C 111 HIS
B 111 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.172624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.136899 restraints weight = 19804.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.137998 restraints weight = 11284.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.139550 restraints weight = 9469.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.4277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10509  Z= 0.093
  Angle     :  0.556   9.320  14316  Z= 0.266
  Chirality :  0.041   0.180   1617
  Planarity :  0.004   0.041   1839
  Dihedral  :  4.094  15.221   1572
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.01 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.24), residues: 1332
  helix: -0.49 (0.24), residues: 462
  sheet: -2.22 (0.29), residues: 285
  loop : -0.46 (0.28), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  47 
 HIS   0.003   0.001   HIS C 328 
 PHE   0.010   0.001   PHE B 264 
 TYR   0.022   0.001   TYR C 416 
 ARG   0.003   0.000   ARG C  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00120 (    6)
  link_NAG-ASN         : angle       1.45783 (   18)
  hydrogen bonds       : bond        0.02763 (  387)
  hydrogen bonds       : angle       5.08978 ( 1179)
  SS BOND              : bond        0.00130 (   21)
  SS BOND              : angle       0.66617 (   42)
  covalent geometry    : bond        0.00209 (10482)
  covalent geometry    : angle       0.55323 (14256)

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 1.046 
Fit side-chains
REVERT: A   78 LEU cc_start: 0.9003 (mm) cc_final: 0.8720 (mm)
REVERT: B   78 LEU cc_start: 0.9043 (mm) cc_final: 0.8755 (mm)
REVERT: B  101 PHE cc_start: 0.7921 (t80) cc_final: 0.7694 (t80)
REVERT: B  277 GLN cc_start: 0.8489 (tp40) cc_final: 0.8111 (tp40)
  outliers start: 35
  outliers final: 29
  residues processed: 134
  average time/residue: 0.1526
  time to fit residues: 32.9650
Evaluate side-chains
  130 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   99 PHE
Chi-restraints excluded: chain C residue  180 CYS
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  329 MET
Chi-restraints excluded: chain C residue  364 MET
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  418 THR
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  180 CYS
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  418 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 126 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 54 optimal weight:   20.0000
   chunk 23 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 121 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 117 optimal weight:    0.7980
   chunk 99 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
C 111 HIS
B 111 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4706 r_free = 0.4706 target = 0.171043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.134577 restraints weight = 19884.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.136755 restraints weight = 11737.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.138219 restraints weight = 8999.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.4252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10509  Z= 0.147
  Angle     :  0.577   7.642  14316  Z= 0.279
  Chirality :  0.041   0.187   1617
  Planarity :  0.004   0.040   1839
  Dihedral  :  4.208  17.346   1572
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 17.40 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.24), residues: 1332
  helix: -0.41 (0.25), residues: 465
  sheet: -2.24 (0.29), residues: 285
  loop : -0.46 (0.28), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  47 
 HIS   0.004   0.001   HIS B 251 
 PHE   0.008   0.001   PHE B 273 
 TYR   0.017   0.001   TYR C 416 
 ARG   0.003   0.000   ARG C  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00115 (    6)
  link_NAG-ASN         : angle       1.49485 (   18)
  hydrogen bonds       : bond        0.02944 (  387)
  hydrogen bonds       : angle       5.16400 ( 1179)
  SS BOND              : bond        0.00246 (   21)
  SS BOND              : angle       0.91119 (   42)
  covalent geometry    : bond        0.00335 (10482)
  covalent geometry    : angle       0.57377 (14256)

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 103
  time to evaluate  : 1.265 
Fit side-chains
REVERT: A   78 LEU cc_start: 0.9031 (mm) cc_final: 0.8749 (mm)
REVERT: C  416 TYR cc_start: 0.8664 (p90) cc_final: 0.8334 (p90)
REVERT: B   78 LEU cc_start: 0.9044 (mm) cc_final: 0.8744 (mm)
REVERT: B  101 PHE cc_start: 0.7955 (t80) cc_final: 0.7722 (t80)
REVERT: B  277 GLN cc_start: 0.8536 (tp40) cc_final: 0.8172 (tp40)
REVERT: B  416 TYR cc_start: 0.8607 (p90) cc_final: 0.8299 (p90)
  outliers start: 34
  outliers final: 31
  residues processed: 129
  average time/residue: 0.1722
  time to fit residues: 35.8489
Evaluate side-chains
  131 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 100
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  180 CYS
Chi-restraints excluded: chain C residue  246 ILE
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  364 MET
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  405 LEU
Chi-restraints excluded: chain C residue  418 THR
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  180 CYS
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  418 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 110 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 108 optimal weight:    3.9990
   chunk 9 optimal weight:    0.3980
   chunk 32 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9980
   chunk 103 optimal weight:    0.6980
   chunk 82 optimal weight:    6.9990
   chunk 13 optimal weight:    0.0770
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
C 111 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.173398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.138749 restraints weight = 20895.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.140736 restraints weight = 14928.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.142224 restraints weight = 12397.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.4308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10509  Z= 0.099
  Angle     :  0.563   7.819  14316  Z= 0.270
  Chirality :  0.041   0.183   1617
  Planarity :  0.004   0.041   1839
  Dihedral  :  4.068  15.046   1572
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.99 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.24), residues: 1332
  helix: -0.33 (0.25), residues: 468
  sheet: -2.15 (0.29), residues: 285
  loop : -0.26 (0.28), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  47 
 HIS   0.003   0.001   HIS B 328 
 PHE   0.008   0.001   PHE B 264 
 TYR   0.018   0.001   TYR C 416 
 ARG   0.003   0.000   ARG C  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00123 (    6)
  link_NAG-ASN         : angle       1.43203 (   18)
  hydrogen bonds       : bond        0.02822 (  387)
  hydrogen bonds       : angle       5.07872 ( 1179)
  SS BOND              : bond        0.00137 (   21)
  SS BOND              : angle       0.64833 (   42)
  covalent geometry    : bond        0.00221 (10482)
  covalent geometry    : angle       0.56071 (14256)

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

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

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2664 Ramachandran restraints generated.
    1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 1.223 
Fit side-chains
REVERT: A   78 LEU cc_start: 0.9033 (mm) cc_final: 0.8739 (mm)
REVERT: C  416 TYR cc_start: 0.8662 (p90) cc_final: 0.8350 (p90)
REVERT: B   78 LEU cc_start: 0.9034 (mm) cc_final: 0.8733 (mm)
REVERT: B  101 PHE cc_start: 0.7928 (t80) cc_final: 0.7704 (t80)
REVERT: B  277 GLN cc_start: 0.8488 (tp40) cc_final: 0.8119 (tp40)
REVERT: B  416 TYR cc_start: 0.8573 (p90) cc_final: 0.8289 (p90)
  outliers start: 30
  outliers final: 25
  residues processed: 124
  average time/residue: 0.1609
  time to fit residues: 31.8025
Evaluate side-chains
  126 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  364 MET
Chi-restraints excluded: chain C residue  366 CYS
Chi-restraints excluded: chain C residue  418 THR
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  366 CYS
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  418 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 10 optimal weight:    9.9990
   chunk 108 optimal weight:    4.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
C 111 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.170380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.126283 restraints weight = 21015.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.129898 restraints weight = 12077.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.132702 restraints weight = 8825.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10509  Z= 0.163
  Angle     :  0.587   7.542  14316  Z= 0.285
  Chirality :  0.042   0.187   1617
  Planarity :  0.004   0.040   1839
  Dihedral  :  4.228  14.997   1572
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 17.70 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.24), residues: 1332
  helix: -0.14 (0.25), residues: 453
  sheet: -2.28 (0.29), residues: 285
  loop : -0.35 (0.28), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  47 
 HIS   0.005   0.001   HIS B 328 
 PHE   0.008   0.001   PHE B 264 
 TYR   0.018   0.001   TYR A 110 
 ARG   0.003   0.000   ARG C  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00130 (    6)
  link_NAG-ASN         : angle       1.45611 (   18)
  hydrogen bonds       : bond        0.02972 (  387)
  hydrogen bonds       : angle       5.14815 ( 1179)
  SS BOND              : bond        0.00248 (   21)
  SS BOND              : angle       1.03243 (   42)
  covalent geometry    : bond        0.00370 (10482)
  covalent geometry    : angle       0.58300 (14256)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3492.41 seconds
wall clock time: 64 minutes 24.87 seconds (3864.87 seconds total)