Starting phenix.real_space_refine
on Thu May 15 07:46:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ona_16984/05_2025/8ona_16984.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ona_16984/05_2025/8ona_16984.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ona_16984/05_2025/8ona_16984.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ona_16984/05_2025/8ona_16984.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ona_16984/05_2025/8ona_16984.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ona_16984/05_2025/8ona_16984.cif"
  }
  resolution = 3.0
  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=   0.002 sd=   0.035
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     108      5.16       5
     C    8217      2.51       5
     N    2154      2.21       5
     O    2421      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12900
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 523, 4188
          Classifications: {'peptide': 523}
          Link IDs: {'PTRANS': 29, 'TRANS': 493}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 41
          Classifications: {'peptide': 4}
          Link IDs: {'TRANS': 3}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Restraints were copied for chains:
    C, B, D, F
  Time building chain proxies: 8.20, per 1000 atoms: 0.64
  Number of scatterers: 12900
  At special positions: 0
  Unit cell: (107.31, 104.244, 133.882, 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     108     16.00
     O    2421      8.00
     N    2154      7.00
     C    8217      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=24, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  80 " - pdb=" SG  CYS A 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 172 " - pdb=" SG  CYS A 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 300 " - pdb=" SG  CYS A 405 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 318 " - pdb=" SG  CYS A 401 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 322 " - pdb=" SG  CYS A 399 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 331 " - pdb=" SG  CYS A 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS A 350 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 360 " - pdb=" SG  CYS A 368 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  80 " - pdb=" SG  CYS C 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  80 " - pdb=" SG  CYS B 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 172 " - pdb=" SG  CYS C 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 172 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 300 " - pdb=" SG  CYS C 405 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 300 " - pdb=" SG  CYS B 405 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 318 " - pdb=" SG  CYS C 401 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 318 " - pdb=" SG  CYS B 401 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 322 " - pdb=" SG  CYS C 399 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 322 " - pdb=" SG  CYS B 399 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 331 " - pdb=" SG  CYS C 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 331 " - pdb=" SG  CYS B 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 333 " - pdb=" SG  CYS C 350 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 333 " - pdb=" SG  CYS B 350 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 360 " - pdb=" SG  CYS C 368 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 360 " - pdb=" SG  CYS B 368 " 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=3, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 180 "
      " NAG A 602 " - " ASN A 299 "
      " NAG A 603 " - " ASN A 392 "
      " NAG A 604 " - " ASN A 444 "
      " NAG A 605 " - " ASN A 460 "
      " NAG B 601 " - " ASN B 180 "
      " NAG B 602 " - " ASN B 299 "
      " NAG B 603 " - " ASN B 392 "
      " NAG B 604 " - " ASN B 444 "
      " NAG B 605 " - " ASN B 460 "
      " NAG C 601 " - " ASN C 180 "
      " NAG C 602 " - " ASN C 299 "
      " NAG C 603 " - " ASN C 392 "
      " NAG C 604 " - " ASN C 444 "
      " NAG C 605 " - " ASN C 460 "
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.40
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2988

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 9 sheets defined
      49.6% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 14
    Processing helix  chain 'A' and resid 17 through 24
      removed outlier: 4.449A  pdb=" N   LYS A  21 " --> pdb=" O   HIS A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 58
    Processing helix  chain 'A' and resid 86 through 100
    Processing helix  chain 'A' and resid 102 through 107
      removed outlier: 3.546A  pdb=" N   ILE A 107 " --> pdb=" O   PHE A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 124
      removed outlier: 3.663A  pdb=" N   LYS A 124 " --> pdb=" O   LYS A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 133
    Processing helix  chain 'A' and resid 136 through 144
    Processing helix  chain 'A' and resid 145 through 153
      removed outlier: 3.675A  pdb=" N   PHE A 149 " --> pdb=" O   SER A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 159
    Processing helix  chain 'A' and resid 180 through 184
    Processing helix  chain 'A' and resid 314 through 332
      removed outlier: 3.657A  pdb=" N   CYS A 318 " --> pdb=" O   ARG A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 362
    Processing helix  chain 'A' and resid 365 through 390
      removed outlier: 4.224A  pdb=" N   THR A 390 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 398
    Processing helix  chain 'A' and resid 423 through 435
    Processing helix  chain 'A' and resid 438 through 444
      removed outlier: 3.665A  pdb=" N   PHE A 443 " --> pdb=" O   ASN A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 447
      No H-bonds generated for 'chain 'A' and resid 445 through 447'
    Processing helix  chain 'A' and resid 448 through 459
    Processing helix  chain 'A' and resid 460 through 462
      No H-bonds generated for 'chain 'A' and resid 460 through 462'
    Processing helix  chain 'A' and resid 463 through 468
    Processing helix  chain 'A' and resid 493 through 509
    Processing helix  chain 'A' and resid 512 through 529
    Processing helix  chain 'B' and resid 3 through 14
    Processing helix  chain 'B' and resid 17 through 24
      removed outlier: 4.450A  pdb=" N   LYS B  21 " --> pdb=" O   HIS B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 58
    Processing helix  chain 'B' and resid 86 through 100
    Processing helix  chain 'B' and resid 102 through 107
      removed outlier: 3.546A  pdb=" N   ILE B 107 " --> pdb=" O   PHE B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 124
      removed outlier: 3.663A  pdb=" N   LYS B 124 " --> pdb=" O   LYS B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 133
    Processing helix  chain 'B' and resid 136 through 144
    Processing helix  chain 'B' and resid 145 through 153
      removed outlier: 3.676A  pdb=" N   PHE B 149 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 159
    Processing helix  chain 'B' and resid 180 through 184
    Processing helix  chain 'B' and resid 314 through 332
      removed outlier: 3.658A  pdb=" N   CYS B 318 " --> pdb=" O   ARG B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 362
    Processing helix  chain 'B' and resid 365 through 390
      removed outlier: 4.224A  pdb=" N   THR B 390 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 398
    Processing helix  chain 'B' and resid 423 through 435
    Processing helix  chain 'B' and resid 438 through 444
      removed outlier: 3.665A  pdb=" N   PHE B 443 " --> pdb=" O   ASN B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 447
      No H-bonds generated for 'chain 'B' and resid 445 through 447'
    Processing helix  chain 'B' and resid 448 through 459
    Processing helix  chain 'B' and resid 460 through 462
      No H-bonds generated for 'chain 'B' and resid 460 through 462'
    Processing helix  chain 'B' and resid 463 through 468
    Processing helix  chain 'B' and resid 493 through 509
    Processing helix  chain 'B' and resid 512 through 529
    Processing helix  chain 'C' and resid 3 through 14
    Processing helix  chain 'C' and resid 17 through 24
      removed outlier: 4.450A  pdb=" N   LYS C  21 " --> pdb=" O   HIS C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 58
    Processing helix  chain 'C' and resid 86 through 100
    Processing helix  chain 'C' and resid 102 through 107
      removed outlier: 3.546A  pdb=" N   ILE C 107 " --> pdb=" O   PHE C 104 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 124
      removed outlier: 3.663A  pdb=" N   LYS C 124 " --> pdb=" O   LYS C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 133
    Processing helix  chain 'C' and resid 136 through 144
    Processing helix  chain 'C' and resid 145 through 153
      removed outlier: 3.675A  pdb=" N   PHE C 149 " --> pdb=" O   SER C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 159
    Processing helix  chain 'C' and resid 180 through 184
    Processing helix  chain 'C' and resid 314 through 332
      removed outlier: 3.657A  pdb=" N   CYS C 318 " --> pdb=" O   ARG C 314 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 357 through 362
    Processing helix  chain 'C' and resid 365 through 390
      removed outlier: 4.224A  pdb=" N   THR C 390 " --> pdb=" O   LYS C 386 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 392 through 398
    Processing helix  chain 'C' and resid 423 through 435
    Processing helix  chain 'C' and resid 438 through 444
      removed outlier: 3.665A  pdb=" N   PHE C 443 " --> pdb=" O   ASN C 440 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 445 through 447
      No H-bonds generated for 'chain 'C' and resid 445 through 447'
    Processing helix  chain 'C' and resid 448 through 459
    Processing helix  chain 'C' and resid 460 through 462
      No H-bonds generated for 'chain 'C' and resid 460 through 462'
    Processing helix  chain 'C' and resid 463 through 468
    Processing helix  chain 'C' and resid 493 through 509
    Processing helix  chain 'C' and resid 512 through 529
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68
    Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 178
      removed outlier: 6.455A  pdb=" N   ILE A 222 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   CYS A 172 " --> pdb=" O   SER A 220 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   SER A 220 " --> pdb=" O   CYS A 172 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   TYR A 174 " --> pdb=" O   GLY A 218 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   GLY A 218 " --> pdb=" O   TYR A 174 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   PHE A 279 " --> pdb=" O   PHE A 471 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 189
      removed outlier: 6.458A  pdb=" N   ASN A 195 " --> pdb=" O   ASN A  81 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   ASN A  81 " --> pdb=" O   ASN A 195 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 68
    Processing sheet with id=AA5, first strand: chain 'B' and resid 177 through 178
      removed outlier: 6.455A  pdb=" N   ILE B 222 " --> pdb=" O   VAL B 170 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   CYS B 172 " --> pdb=" O   SER B 220 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   SER B 220 " --> pdb=" O   CYS B 172 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   TYR B 174 " --> pdb=" O   GLY B 218 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   GLY B 218 " --> pdb=" O   TYR B 174 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   PHE B 279 " --> pdb=" O   PHE B 471 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 189
      removed outlier: 6.457A  pdb=" N   ASN B 195 " --> pdb=" O   ASN B  81 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   ASN B  81 " --> pdb=" O   ASN B 195 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 61 through 68
    Processing sheet with id=AA8, first strand: chain 'C' and resid 177 through 178
      removed outlier: 6.454A  pdb=" N   ILE C 222 " --> pdb=" O   VAL C 170 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   CYS C 172 " --> pdb=" O   SER C 220 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   SER C 220 " --> pdb=" O   CYS C 172 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   TYR C 174 " --> pdb=" O   GLY C 218 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   GLY C 218 " --> pdb=" O   TYR C 174 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   PHE C 279 " --> pdb=" O   PHE C 471 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 189
      removed outlier: 6.458A  pdb=" N   ASN C 195 " --> pdb=" O   ASN C  81 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   ASN C  81 " --> pdb=" O   ASN C 195 " (cutoff:3.500A)

    670 hydrogen bonds defined for protein.
    1893 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: 3.69

  Time building geometry restraints manager: 3.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3176
        1.33 -     1.45: 2854
        1.45 -     1.58: 7035
        1.58 -     1.70: 0
        1.70 -     1.82: 162
  Bond restraints: 13227
  Sorted by residual:
  bond pdb=" N   GLN B  13 "
       pdb=" CA  GLN B  13 "
    ideal  model  delta    sigma   weight residual
    1.456  1.504 -0.048 1.18e-02 7.18e+03 1.65e+01
  bond pdb=" N   GLN C  13 "
       pdb=" CA  GLN C  13 "
    ideal  model  delta    sigma   weight residual
    1.456  1.503 -0.048 1.18e-02 7.18e+03 1.62e+01
  bond pdb=" N   GLN A  13 "
       pdb=" CA  GLN A  13 "
    ideal  model  delta    sigma   weight residual
    1.456  1.503 -0.047 1.18e-02 7.18e+03 1.61e+01
  bond pdb=" C   ASP A   5 "
       pdb=" O   ASP A   5 "
    ideal  model  delta    sigma   weight residual
    1.235  1.277 -0.042 1.26e-02 6.30e+03 1.10e+01
  bond pdb=" C   ASP B   5 "
       pdb=" O   ASP B   5 "
    ideal  model  delta    sigma   weight residual
    1.235  1.277 -0.041 1.26e-02 6.30e+03 1.07e+01
  ... (remaining 13222 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 17275
        1.81 -     3.61: 529
        3.61 -     5.42: 85
        5.42 -     7.23: 15
        7.23 -     9.04: 6
  Bond angle restraints: 17910
  Sorted by residual:
  angle pdb=" C   GLU C  12 "
        pdb=" N   GLN C  13 "
        pdb=" CA  GLN C  13 "
      ideal   model   delta    sigma   weight residual
     122.73  113.82    8.91 1.61e+00 3.86e-01 3.06e+01
  angle pdb=" C   GLU B  12 "
        pdb=" N   GLN B  13 "
        pdb=" CA  GLN B  13 "
      ideal   model   delta    sigma   weight residual
     122.73  113.83    8.90 1.61e+00 3.86e-01 3.05e+01
  angle pdb=" C   GLU A  12 "
        pdb=" N   GLN A  13 "
        pdb=" CA  GLN A  13 "
      ideal   model   delta    sigma   weight residual
     122.73  113.86    8.87 1.61e+00 3.86e-01 3.03e+01
  angle pdb=" C   GLN C  13 "
        pdb=" N   THR C  14 "
        pdb=" CA  THR C  14 "
      ideal   model   delta    sigma   weight residual
     122.64  113.60    9.04 1.70e+00 3.46e-01 2.83e+01
  angle pdb=" C   GLN A  13 "
        pdb=" N   THR A  14 "
        pdb=" CA  THR A  14 "
      ideal   model   delta    sigma   weight residual
     122.64  113.62    9.02 1.70e+00 3.46e-01 2.81e+01
  ... (remaining 17905 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.80: 7277
       15.80 -    31.59: 694
       31.59 -    47.39: 150
       47.39 -    63.18: 27
       63.18 -    78.98: 21
  Dihedral angle restraints: 8169
    sinusoidal: 3540
      harmonic: 4629
  Sorted by residual:
  dihedral pdb=" CA  MET A  16 "
           pdb=" C   MET A  16 "
           pdb=" N   HIS A  17 "
           pdb=" CA  HIS A  17 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.21  -19.79     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  MET B  16 "
           pdb=" C   MET B  16 "
           pdb=" N   HIS B  17 "
           pdb=" CA  HIS B  17 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.22  -19.78     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  MET C  16 "
           pdb=" C   MET C  16 "
           pdb=" N   HIS C  17 "
           pdb=" CA  HIS C  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.24  -19.76     0      5.00e+00 4.00e-02 1.56e+01
  ... (remaining 8166 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1733
       0.081 -    0.162: 199
       0.162 -    0.243: 9
       0.243 -    0.324: 3
       0.324 -    0.404: 6
  Chirality restraints: 1950
  Sorted by residual:
  chirality pdb=" CA  ARG C 102 "
            pdb=" N   ARG C 102 "
            pdb=" C   ARG C 102 "
            pdb=" CB  ARG C 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.09e+00
  chirality pdb=" CA  ARG A 102 "
            pdb=" N   ARG A 102 "
            pdb=" C   ARG A 102 "
            pdb=" CB  ARG A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.07e+00
  chirality pdb=" CA  ARG B 102 "
            pdb=" N   ARG B 102 "
            pdb=" C   ARG B 102 "
            pdb=" CB  ARG B 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.02e+00
  ... (remaining 1947 not shown)

  Planarity restraints: 2322
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 248 "   -0.014 2.00e-02 2.50e+03   2.88e-02 8.30e+00
        pdb=" C   ALA C 248 "    0.050 2.00e-02 2.50e+03
        pdb=" O   ALA C 248 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   VAL C 249 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 248 "   -0.014 2.00e-02 2.50e+03   2.88e-02 8.28e+00
        pdb=" C   ALA A 248 "    0.050 2.00e-02 2.50e+03
        pdb=" O   ALA A 248 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   VAL A 249 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 248 "   -0.014 2.00e-02 2.50e+03   2.86e-02 8.19e+00
        pdb=" C   ALA B 248 "    0.050 2.00e-02 2.50e+03
        pdb=" O   ALA B 248 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   VAL B 249 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 2319 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 4302
        2.84 -     3.35: 12172
        3.35 -     3.87: 21415
        3.87 -     4.38: 25047
        4.38 -     4.90: 42554
  Nonbonded interactions: 105490
  Sorted by model distance:
  nonbonded pdb=" O   PRO C  20 "
            pdb=" OD1 ASN C  24 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   PRO B  20 "
            pdb=" OD1 ASN B  24 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   PRO A  20 "
            pdb=" OD1 ASN A  24 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OE1 GLN A  48 "
            pdb=" OE1 GLN A 504 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" OE1 GLN C  48 "
            pdb=" OE1 GLN C 504 "
     model   vdw
     2.362 3.040
  ... (remaining 105485 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.540
  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:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     29.950
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
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      :  0.005   0.104  13269  Z= 0.312
  Angle     :  0.750   9.037  18003  Z= 0.436
  Chirality :  0.052   0.404   1950
  Planarity :  0.004   0.029   2307
  Dihedral  : 13.104  78.976   5109
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  7.49 %
    Favored  : 92.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.21), residues: 1563
  helix:  0.16 (0.19), residues: 684
  sheet:  1.09 (0.30), residues: 279
  loop :  0.59 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  34 
 HIS   0.005   0.001   HIS B 376 
 PHE   0.024   0.001   PHE A  33 
 TYR   0.014   0.002   TYR B 414 
 ARG   0.003   0.000   ARG B 102 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00215 (   15)
  link_NAG-ASN         : angle       2.68325 (   45)
  hydrogen bonds       : bond        0.13738 (  670)
  hydrogen bonds       : angle       6.15669 ( 1893)
  SS BOND              : bond        0.00228 (   24)
  SS BOND              : angle       0.78473 (   48)
  covalent geometry    : bond        0.00444 (13227)
  covalent geometry    : angle       0.73838 (17910)
  Misc. bond           : bond        0.10386 (    3)

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

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

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  499 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 493
  time to evaluate  : 1.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7599 (ttt) cc_final: 0.7225 (ttt)
REVERT: A   49 MET cc_start: 0.6342 (ttt) cc_final: 0.6038 (ttp)
REVERT: A   61 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7667 (ttmm)
REVERT: A  100 ASP cc_start: 0.7278 (t0) cc_final: 0.6722 (t0)
REVERT: A  111 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7675 (mt-10)
REVERT: A  120 LYS cc_start: 0.7799 (mttt) cc_final: 0.7550 (tppp)
REVERT: A  138 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7445 (mt-10)
REVERT: A  203 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7346 (mm-30)
REVERT: A  232 LYS cc_start: 0.8380 (mttt) cc_final: 0.8086 (mttm)
REVERT: A  271 GLU cc_start: 0.7437 (pt0) cc_final: 0.7225 (pt0)
REVERT: A  288 ARG cc_start: 0.7311 (mtp85) cc_final: 0.6768 (mtm-85)
REVERT: A  290 ASN cc_start: 0.7792 (m110) cc_final: 0.7591 (m-40)
REVERT: A  302 ASP cc_start: 0.7303 (p0) cc_final: 0.6937 (p0)
REVERT: A  303 LYS cc_start: 0.7634 (mtmt) cc_final: 0.7370 (mtmt)
REVERT: A  380 LYS cc_start: 0.6968 (mtpt) cc_final: 0.6720 (mtpt)
REVERT: A  388 LYS cc_start: 0.7247 (mtpp) cc_final: 0.7018 (mtpp)
REVERT: A  409 SER cc_start: 0.7501 (m) cc_final: 0.7062 (t)
REVERT: A  411 ASP cc_start: 0.7684 (m-30) cc_final: 0.7285 (m-30)
REVERT: A  438 LYS cc_start: 0.8094 (mttt) cc_final: 0.7818 (mttp)
REVERT: A  440 ASN cc_start: 0.7226 (p0) cc_final: 0.6602 (t0)
REVERT: A  465 GLU cc_start: 0.7711 (tp30) cc_final: 0.7496 (tp30)
REVERT: A  470 ASP cc_start: 0.7746 (m-30) cc_final: 0.7252 (m-30)
REVERT: B   10 PHE cc_start: 0.6376 (t80) cc_final: 0.6023 (t80)
REVERT: B   21 LYS cc_start: 0.7265 (tppp) cc_final: 0.6955 (mmtt)
REVERT: B   33 PHE cc_start: 0.7398 (t80) cc_final: 0.7149 (t80)
REVERT: B   44 MET cc_start: 0.7439 (ttt) cc_final: 0.6852 (ttt)
REVERT: B   60 PRO cc_start: 0.7894 (Cg_endo) cc_final: 0.7633 (Cg_exo)
REVERT: B   61 LYS cc_start: 0.8018 (ttmt) cc_final: 0.7513 (mtpp)
REVERT: B   62 LYS cc_start: 0.6305 (ttpp) cc_final: 0.6079 (tttp)
REVERT: B  100 ASP cc_start: 0.7176 (t0) cc_final: 0.6607 (t70)
REVERT: B  135 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7224 (mt-10)
REVERT: B  138 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7296 (mp0)
REVERT: B  141 GLN cc_start: 0.8124 (mm110) cc_final: 0.7877 (mm110)
REVERT: B  156 GLU cc_start: 0.7726 (tt0) cc_final: 0.7498 (tt0)
REVERT: B  171 ASN cc_start: 0.8276 (t0) cc_final: 0.8056 (m-40)
REVERT: B  203 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7255 (mm-30)
REVERT: B  232 LYS cc_start: 0.8211 (mttt) cc_final: 0.7902 (mttp)
REVERT: B  244 GLU cc_start: 0.7871 (tp30) cc_final: 0.7668 (tp30)
REVERT: B  288 ARG cc_start: 0.7142 (mtp85) cc_final: 0.6751 (mtm110)
REVERT: B  301 SER cc_start: 0.6940 (t) cc_final: 0.6600 (p)
REVERT: B  303 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7312 (mtpp)
REVERT: B  308 ASP cc_start: 0.7746 (m-30) cc_final: 0.7514 (p0)
REVERT: B  310 THR cc_start: 0.8384 (p) cc_final: 0.7780 (t)
REVERT: B  311 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6481 (mm-30)
REVERT: B  329 GLU cc_start: 0.7453 (tt0) cc_final: 0.7140 (tt0)
REVERT: B  353 ASP cc_start: 0.7528 (p0) cc_final: 0.7230 (p0)
REVERT: B  380 LYS cc_start: 0.7046 (mtpt) cc_final: 0.6841 (mtpt)
REVERT: B  402 PHE cc_start: 0.7967 (m-80) cc_final: 0.7636 (m-80)
REVERT: B  425 GLU cc_start: 0.7451 (tp30) cc_final: 0.7138 (mm-30)
REVERT: B  440 ASN cc_start: 0.7348 (p0) cc_final: 0.7120 (m-40)
REVERT: B  462 SER cc_start: 0.8231 (m) cc_final: 0.7773 (p)
REVERT: B  465 GLU cc_start: 0.7664 (tp30) cc_final: 0.7462 (tp30)
REVERT: B  466 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7040 (mm-30)
REVERT: B  492 TYR cc_start: 0.7852 (t80) cc_final: 0.7159 (t80)
REVERT: B  518 GLU cc_start: 0.7175 (tp30) cc_final: 0.6958 (tp30)
REVERT: C    7 MET cc_start: 0.6814 (ttm) cc_final: 0.6596 (ttm)
REVERT: C   10 PHE cc_start: 0.6183 (t80) cc_final: 0.5851 (t80)
REVERT: C   33 PHE cc_start: 0.7353 (t80) cc_final: 0.7052 (t80)
REVERT: C   61 LYS cc_start: 0.7886 (ttmt) cc_final: 0.7547 (ttmm)
REVERT: C   66 GLU cc_start: 0.7472 (pt0) cc_final: 0.6812 (pm20)
REVERT: C   99 GLU cc_start: 0.7502 (tt0) cc_final: 0.7237 (tt0)
REVERT: C  100 ASP cc_start: 0.7379 (t0) cc_final: 0.6845 (t70)
REVERT: C  120 LYS cc_start: 0.7695 (mttt) cc_final: 0.7408 (ttmm)
REVERT: C  138 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7464 (mp0)
REVERT: C  142 GLU cc_start: 0.7499 (tt0) cc_final: 0.7223 (tt0)
REVERT: C  156 GLU cc_start: 0.7688 (tt0) cc_final: 0.7267 (pm20)
REVERT: C  178 ARG cc_start: 0.7384 (ttm170) cc_final: 0.7000 (ttp-170)
REVERT: C  181 LYS cc_start: 0.7705 (mtmm) cc_final: 0.7236 (mtpp)
REVERT: C  232 LYS cc_start: 0.8394 (mttt) cc_final: 0.8033 (mttp)
REVERT: C  249 VAL cc_start: 0.8242 (m) cc_final: 0.8012 (m)
REVERT: C  288 ARG cc_start: 0.7201 (mtp85) cc_final: 0.6772 (mtm110)
REVERT: C  303 LYS cc_start: 0.7695 (mtmt) cc_final: 0.7369 (mtmt)
REVERT: C  346 ASN cc_start: 0.7610 (m-40) cc_final: 0.7362 (m-40)
REVERT: C  441 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7062 (mm-30)
REVERT: C  462 SER cc_start: 0.8179 (m) cc_final: 0.7817 (t)
REVERT: C  463 ASN cc_start: 0.7933 (t0) cc_final: 0.7243 (t0)
REVERT: C  465 GLU cc_start: 0.7788 (tp30) cc_final: 0.7518 (tp30)
REVERT: C  466 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7265 (mm-30)
REVERT: C  470 ASP cc_start: 0.7767 (m-30) cc_final: 0.7556 (m-30)
REVERT: C  480 ASP cc_start: 0.7265 (m-30) cc_final: 0.6881 (m-30)
REVERT: C  487 GLN cc_start: 0.7708 (tt0) cc_final: 0.7374 (tt0)
REVERT: C  492 TYR cc_start: 0.7659 (t80) cc_final: 0.6990 (t80)
REVERT: C  494 ARG cc_start: 0.6765 (ttp-110) cc_final: 0.6553 (ttp-110)
  outliers start: 6
  outliers final: 0
  residues processed: 496
  average time/residue: 1.3552
  time to fit residues: 723.0115
Evaluate side-chains
  396 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 396
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    0.9990
   chunk 118 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 122 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 141 optimal weight:    5.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  24 ASN
A 297 HIS
A 495 ASN
B  48 GLN
B 173 HIS
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 496 GLN
C  48 GLN
C  91 ASN
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 290 ASN
C 297 HIS
C 319 GLN
C 324 GLN
C 482 ASN
C 496 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.121266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.108257 restraints weight = 17229.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 1.94
r_work: 0.3249 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.083  13269  Z= 0.218
  Angle     :  0.731  15.445  18003  Z= 0.371
  Chirality :  0.048   0.261   1950
  Planarity :  0.005   0.041   2307
  Dihedral  :  5.328  36.993   2040
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 13.49 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  1.07 (0.21), residues: 1563
  helix:  0.88 (0.20), residues: 690
  sheet:  0.91 (0.28), residues: 279
  loop :  0.63 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 349 
 HIS   0.006   0.001   HIS B 260 
 PHE   0.024   0.002   PHE B 431 
 TYR   0.016   0.002   TYR A 414 
 ARG   0.006   0.001   ARG C 351 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00684 (   15)
  link_NAG-ASN         : angle       2.21865 (   45)
  hydrogen bonds       : bond        0.04530 (  670)
  hydrogen bonds       : angle       4.80782 ( 1893)
  SS BOND              : bond        0.00515 (   24)
  SS BOND              : angle       3.81690 (   48)
  covalent geometry    : bond        0.00512 (13227)
  covalent geometry    : angle       0.69721 (17910)
  Misc. bond           : bond        0.00118 (    3)

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

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

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  462 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 424
  time to evaluate  : 1.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.8772 (tptt) cc_final: 0.8482 (mmtp)
REVERT: A   44 MET cc_start: 0.7761 (ttt) cc_final: 0.7507 (ttt)
REVERT: A   49 MET cc_start: 0.7381 (ttt) cc_final: 0.7154 (ttp)
REVERT: A   62 LYS cc_start: 0.7913 (ttpp) cc_final: 0.7696 (tttp)
REVERT: A  102 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7909 (mtm-85)
REVERT: A  203 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7534 (mm-30)
REVERT: A  301 SER cc_start: 0.8552 (t) cc_final: 0.8148 (p)
REVERT: A  302 ASP cc_start: 0.7770 (p0) cc_final: 0.7487 (p0)
REVERT: A  336 VAL cc_start: 0.8412 (p) cc_final: 0.8098 (t)
REVERT: A  373 MET cc_start: 0.8080 (mmp) cc_final: 0.7821 (mmm)
REVERT: A  380 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7593 (mtpt)
REVERT: A  438 LYS cc_start: 0.8552 (mttt) cc_final: 0.8335 (mttm)
REVERT: A  440 ASN cc_start: 0.7500 (p0) cc_final: 0.7177 (t0)
REVERT: A  465 GLU cc_start: 0.7882 (tp30) cc_final: 0.7645 (tp30)
REVERT: A  466 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7948 (mm-30)
REVERT: A  470 ASP cc_start: 0.8057 (m-30) cc_final: 0.7696 (m-30)
REVERT: A  521 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8163 (tm-30)
REVERT: B   15 THR cc_start: 0.7988 (p) cc_final: 0.7723 (p)
REVERT: B   44 MET cc_start: 0.7815 (ttt) cc_final: 0.7462 (ttt)
REVERT: B   49 MET cc_start: 0.7473 (ttt) cc_final: 0.6756 (tmm)
REVERT: B   61 LYS cc_start: 0.8467 (ttmt) cc_final: 0.8240 (ttpp)
REVERT: B   62 LYS cc_start: 0.7952 (ttpp) cc_final: 0.7737 (tttp)
REVERT: B  121 LYS cc_start: 0.8522 (ttpp) cc_final: 0.8230 (tttm)
REVERT: B  135 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7748 (mt-10)
REVERT: B  156 GLU cc_start: 0.8048 (tt0) cc_final: 0.7784 (tt0)
REVERT: B  203 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7513 (mm-30)
REVERT: B  244 GLU cc_start: 0.7727 (tp30) cc_final: 0.7478 (tp30)
REVERT: B  303 LYS cc_start: 0.8668 (mtmt) cc_final: 0.8317 (mtpp)
REVERT: B  329 GLU cc_start: 0.8233 (tt0) cc_final: 0.8011 (tt0)
REVERT: B  363 THR cc_start: 0.8385 (m) cc_final: 0.8091 (t)
REVERT: B  370 GLN cc_start: 0.8196 (mt0) cc_final: 0.7709 (mm110)
REVERT: B  380 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7656 (mtpt)
REVERT: B  441 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7207 (mp0)
REVERT: B  466 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7701 (mm-30)
REVERT: B  492 TYR cc_start: 0.8684 (t80) cc_final: 0.8142 (t80)
REVERT: B  521 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8252 (tm-30)
REVERT: C   51 GLU cc_start: 0.7325 (tp30) cc_final: 0.7038 (tm-30)
REVERT: C   61 LYS cc_start: 0.8252 (ttmt) cc_final: 0.8016 (ttmm)
REVERT: C   62 LYS cc_start: 0.7984 (ttpp) cc_final: 0.7709 (ttmm)
REVERT: C  141 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8513 (mm-40)
REVERT: C  142 GLU cc_start: 0.8171 (tt0) cc_final: 0.7916 (tt0)
REVERT: C  156 GLU cc_start: 0.8001 (tt0) cc_final: 0.7757 (tt0)
REVERT: C  229 MET cc_start: 0.8840 (pmm) cc_final: 0.8531 (pmm)
REVERT: C  288 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7923 (mtm-85)
REVERT: C  301 SER cc_start: 0.8477 (t) cc_final: 0.8196 (p)
REVERT: C  346 ASN cc_start: 0.8051 (m-40) cc_final: 0.7792 (m-40)
REVERT: C  380 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7790 (mtpp)
REVERT: C  432 ASP cc_start: 0.8370 (t70) cc_final: 0.8081 (t0)
REVERT: C  438 LYS cc_start: 0.8522 (mttt) cc_final: 0.8213 (mttm)
REVERT: C  462 SER cc_start: 0.8747 (m) cc_final: 0.8404 (t)
REVERT: C  463 ASN cc_start: 0.8702 (t0) cc_final: 0.8114 (t0)
REVERT: C  465 GLU cc_start: 0.7974 (tp30) cc_final: 0.7763 (tp30)
REVERT: C  466 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7898 (mm-30)
REVERT: C  470 ASP cc_start: 0.8008 (m-30) cc_final: 0.7781 (m-30)
REVERT: C  492 TYR cc_start: 0.8626 (t80) cc_final: 0.8373 (t80)
REVERT: C  521 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8049 (tm-30)
  outliers start: 38
  outliers final: 13
  residues processed: 445
  average time/residue: 1.3341
  time to fit residues: 640.3023
Evaluate side-chains
  403 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 388
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 PHE
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   57 PHE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  391 LYS
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain C residue   46 CYS
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue  141 GLN
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  363 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 10 optimal weight:    0.1980
   chunk 39 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 152 optimal weight:    4.9990
   chunk 69 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 134 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 154 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 297 HIS
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 GLN
B 482 ASN
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 482 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.123154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.110053 restraints weight = 17532.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.97
r_work: 0.3280 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13269  Z= 0.140
  Angle     :  0.624   8.837  18003  Z= 0.318
  Chirality :  0.045   0.263   1950
  Planarity :  0.005   0.053   2307
  Dihedral  :  5.186  33.778   2040
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 16.63 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  1.31 (0.21), residues: 1563
  helix:  1.32 (0.20), residues: 690
  sheet:  0.82 (0.28), residues: 279
  loop :  0.55 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  34 
 HIS   0.004   0.001   HIS A 297 
 PHE   0.028   0.001   PHE A  33 
 TYR   0.015   0.001   TYR B 118 
 ARG   0.004   0.000   ARG B 383 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00555 (   15)
  link_NAG-ASN         : angle       1.94149 (   45)
  hydrogen bonds       : bond        0.04206 (  670)
  hydrogen bonds       : angle       4.55120 ( 1893)
  SS BOND              : bond        0.00531 (   24)
  SS BOND              : angle       2.38561 (   48)
  covalent geometry    : bond        0.00308 (13227)
  covalent geometry    : angle       0.60528 (17910)
  Misc. bond           : bond        0.00051 (    3)

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

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

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  427 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 388
  time to evaluate  : 1.369 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 THR cc_start: 0.8096 (p) cc_final: 0.7885 (p)
REVERT: A   44 MET cc_start: 0.7705 (ttt) cc_final: 0.7415 (ttt)
REVERT: A   49 MET cc_start: 0.7374 (ttt) cc_final: 0.6980 (tmm)
REVERT: A  102 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.7998 (mtm-85)
REVERT: A  203 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7574 (mm-30)
REVERT: A  288 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7933 (mtm-85)
REVERT: A  301 SER cc_start: 0.8444 (t) cc_final: 0.8101 (p)
REVERT: A  302 ASP cc_start: 0.7776 (p0) cc_final: 0.7496 (p0)
REVERT: A  336 VAL cc_start: 0.8417 (p) cc_final: 0.8147 (t)
REVERT: A  373 MET cc_start: 0.8133 (mmp) cc_final: 0.7885 (mmm)
REVERT: A  380 LYS cc_start: 0.7588 (mtpt) cc_final: 0.7255 (mttp)
REVERT: A  440 ASN cc_start: 0.7420 (p0) cc_final: 0.7203 (t0)
REVERT: A  465 GLU cc_start: 0.7992 (tp30) cc_final: 0.7742 (tp30)
REVERT: A  470 ASP cc_start: 0.8039 (m-30) cc_final: 0.7674 (m-30)
REVERT: A  521 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8036 (tm-30)
REVERT: B   10 PHE cc_start: 0.8113 (t80) cc_final: 0.7899 (t80)
REVERT: B   44 MET cc_start: 0.7735 (ttt) cc_final: 0.7366 (ttt)
REVERT: B   49 MET cc_start: 0.7464 (ttt) cc_final: 0.6781 (tmm)
REVERT: B   62 LYS cc_start: 0.7899 (ttpp) cc_final: 0.7688 (tttp)
REVERT: B  121 LYS cc_start: 0.8495 (ttpp) cc_final: 0.8193 (tttm)
REVERT: B  135 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7623 (mt-10)
REVERT: B  156 GLU cc_start: 0.8027 (tt0) cc_final: 0.7783 (tt0)
REVERT: B  203 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7558 (mm-30)
REVERT: B  244 GLU cc_start: 0.7742 (tp30) cc_final: 0.7539 (tp30)
REVERT: B  293 ILE cc_start: 0.8067 (mm) cc_final: 0.7430 (mt)
REVERT: B  303 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8403 (mtpp)
REVERT: B  329 GLU cc_start: 0.8253 (tt0) cc_final: 0.8050 (tt0)
REVERT: B  370 GLN cc_start: 0.8168 (mt0) cc_final: 0.7708 (mm110)
REVERT: B  441 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7064 (mp0)
REVERT: B  466 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7736 (mm-30)
REVERT: B  492 TYR cc_start: 0.8684 (t80) cc_final: 0.8230 (t80)
REVERT: B  521 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8184 (tm-30)
REVERT: C   10 PHE cc_start: 0.8063 (t80) cc_final: 0.7853 (t80)
REVERT: C   22 VAL cc_start: 0.8850 (t) cc_final: 0.8598 (p)
REVERT: C   61 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7815 (ttmm)
REVERT: C   95 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7964 (mtt180)
REVERT: C  141 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8447 (mm110)
REVERT: C  142 GLU cc_start: 0.8149 (tt0) cc_final: 0.7859 (tt0)
REVERT: C  203 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7384 (mm-30)
REVERT: C  288 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7867 (mtm-85)
REVERT: C  323 MET cc_start: 0.8324 (mtm) cc_final: 0.8118 (mtm)
REVERT: C  346 ASN cc_start: 0.8034 (m-40) cc_final: 0.7768 (m-40)
REVERT: C  355 ASN cc_start: 0.7956 (m-40) cc_final: 0.7678 (p0)
REVERT: C  380 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7752 (mmtp)
REVERT: C  438 LYS cc_start: 0.8520 (mttt) cc_final: 0.8309 (mttt)
REVERT: C  462 SER cc_start: 0.8727 (m) cc_final: 0.8374 (t)
REVERT: C  463 ASN cc_start: 0.8672 (t0) cc_final: 0.8098 (t0)
REVERT: C  466 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7910 (mm-30)
REVERT: C  492 TYR cc_start: 0.8625 (t80) cc_final: 0.8331 (t80)
REVERT: C  521 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7982 (tm-30)
  outliers start: 39
  outliers final: 18
  residues processed: 404
  average time/residue: 1.4014
  time to fit residues: 608.5731
Evaluate side-chains
  394 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 374
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   57 PHE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain B residue  520 LEU
Chi-restraints excluded: chain C residue    7 MET
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   46 CYS
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue  105 SER
Chi-restraints excluded: chain C residue  141 GLN
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain C residue  363 THR
Chi-restraints excluded: chain C residue  384 SER
Chi-restraints excluded: chain C residue  501 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 144 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 124 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 297 HIS
B 482 ASN
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 482 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.122888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.109854 restraints weight = 17379.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 1.94
r_work: 0.3277 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13269  Z= 0.149
  Angle     :  0.637  14.792  18003  Z= 0.324
  Chirality :  0.044   0.263   1950
  Planarity :  0.005   0.058   2307
  Dihedral  :  4.984  28.764   2040
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.70 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.21), residues: 1563
  helix:  1.45 (0.20), residues: 690
  sheet:  0.91 (0.29), residues: 270
  loop :  0.47 (0.26), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  34 
 HIS   0.003   0.001   HIS B 260 
 PHE   0.018   0.001   PHE B 431 
 TYR   0.014   0.001   TYR B 118 
 ARG   0.005   0.000   ARG B 383 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00566 (   15)
  link_NAG-ASN         : angle       1.90604 (   45)
  hydrogen bonds       : bond        0.04119 (  670)
  hydrogen bonds       : angle       4.47874 ( 1893)
  SS BOND              : bond        0.00699 (   24)
  SS BOND              : angle       3.35881 (   48)
  covalent geometry    : bond        0.00341 (13227)
  covalent geometry    : angle       0.60664 (17910)
  Misc. bond           : bond        0.00025 (    3)

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

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

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  419 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 380
  time to evaluate  : 1.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 THR cc_start: 0.8060 (p) cc_final: 0.7842 (p)
REVERT: A   44 MET cc_start: 0.7661 (ttt) cc_final: 0.7368 (ttt)
REVERT: A   49 MET cc_start: 0.7404 (ttt) cc_final: 0.7021 (tmm)
REVERT: A  102 ARG cc_start: 0.8239 (mtm-85) cc_final: 0.7925 (mtm180)
REVERT: A  288 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7844 (mtm-85)
REVERT: A  302 ASP cc_start: 0.7779 (p0) cc_final: 0.7523 (p0)
REVERT: A  336 VAL cc_start: 0.8430 (p) cc_final: 0.8176 (t)
REVERT: A  373 MET cc_start: 0.8113 (mmp) cc_final: 0.7811 (mmm)
REVERT: A  380 LYS cc_start: 0.7452 (mtpt) cc_final: 0.7154 (mttp)
REVERT: A  386 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8318 (mtmt)
REVERT: A  465 GLU cc_start: 0.7927 (tp30) cc_final: 0.7709 (tp30)
REVERT: A  470 ASP cc_start: 0.7973 (m-30) cc_final: 0.7616 (m-30)
REVERT: A  521 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7898 (tm-30)
REVERT: B   44 MET cc_start: 0.7697 (ttt) cc_final: 0.7445 (ttt)
REVERT: B   49 MET cc_start: 0.7529 (ttt) cc_final: 0.7259 (tmm)
REVERT: B  121 LYS cc_start: 0.8483 (ttpp) cc_final: 0.8162 (tttm)
REVERT: B  156 GLU cc_start: 0.8040 (tt0) cc_final: 0.7781 (tt0)
REVERT: B  203 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7531 (mm-30)
REVERT: B  244 GLU cc_start: 0.7735 (tp30) cc_final: 0.7533 (tp30)
REVERT: B  301 SER cc_start: 0.8785 (m) cc_final: 0.8472 (p)
REVERT: B  303 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8373 (mtpp)
REVERT: B  329 GLU cc_start: 0.8204 (tt0) cc_final: 0.7946 (tt0)
REVERT: B  347 ILE cc_start: 0.8531 (tp) cc_final: 0.8304 (tp)
REVERT: B  370 GLN cc_start: 0.8183 (mt0) cc_final: 0.7690 (mm110)
REVERT: B  381 CYS cc_start: 0.6517 (m) cc_final: 0.6088 (t)
REVERT: B  440 ASN cc_start: 0.7388 (p0) cc_final: 0.7034 (p0)
REVERT: B  441 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7237 (mp0)
REVERT: B  463 ASN cc_start: 0.8629 (t0) cc_final: 0.8198 (t0)
REVERT: B  466 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7753 (mm-30)
REVERT: B  492 TYR cc_start: 0.8693 (t80) cc_final: 0.8231 (t80)
REVERT: B  521 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: C   10 PHE cc_start: 0.8153 (t80) cc_final: 0.7796 (t80)
REVERT: C   22 VAL cc_start: 0.8819 (t) cc_final: 0.8602 (p)
REVERT: C  141 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8469 (mm110)
REVERT: C  203 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7414 (mm-30)
REVERT: C  288 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7806 (mtm-85)
REVERT: C  293 ILE cc_start: 0.8017 (mm) cc_final: 0.7687 (mt)
REVERT: C  312 ARG cc_start: 0.8217 (ttp80) cc_final: 0.8005 (ttp-170)
REVERT: C  323 MET cc_start: 0.8274 (mtm) cc_final: 0.8063 (mtm)
REVERT: C  346 ASN cc_start: 0.8084 (m-40) cc_final: 0.7804 (m-40)
REVERT: C  355 ASN cc_start: 0.7958 (m-40) cc_final: 0.7678 (p0)
REVERT: C  363 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7942 (p)
REVERT: C  462 SER cc_start: 0.8731 (m) cc_final: 0.8384 (t)
REVERT: C  463 ASN cc_start: 0.8682 (t0) cc_final: 0.8108 (t0)
REVERT: C  466 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7932 (mm-30)
REVERT: C  521 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7944 (tm-30)
  outliers start: 39
  outliers final: 17
  residues processed: 396
  average time/residue: 1.3743
  time to fit residues: 585.5523
Evaluate side-chains
  382 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 361
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   57 PHE
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain B residue  462 SER
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain C residue    7 MET
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue  105 SER
Chi-restraints excluded: chain C residue  141 GLN
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain C residue  363 THR
Chi-restraints excluded: chain C residue  384 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 128 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 91 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 297 HIS
** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 482 ASN
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 482 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.120468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107689 restraints weight = 17628.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 1.89
r_work: 0.3282 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13269  Z= 0.148
  Angle     :  0.605  13.174  18003  Z= 0.308
  Chirality :  0.044   0.259   1950
  Planarity :  0.005   0.058   2307
  Dihedral  :  4.841  26.765   2040
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.20 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.21), residues: 1563
  helix:  1.55 (0.20), residues: 690
  sheet:  0.83 (0.29), residues: 273
  loop :  0.44 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 508 
 HIS   0.005   0.001   HIS B 297 
 PHE   0.025   0.001   PHE B  33 
 TYR   0.014   0.001   TYR B 118 
 ARG   0.006   0.000   ARG B 178 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00536 (   15)
  link_NAG-ASN         : angle       1.83624 (   45)
  hydrogen bonds       : bond        0.04011 (  670)
  hydrogen bonds       : angle       4.44071 ( 1893)
  SS BOND              : bond        0.00460 (   24)
  SS BOND              : angle       2.60381 (   48)
  covalent geometry    : bond        0.00340 (13227)
  covalent geometry    : angle       0.58399 (17910)
  Misc. bond           : bond        0.00032 (    3)

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

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

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  402 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 365
  time to evaluate  : 1.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 THR cc_start: 0.8044 (p) cc_final: 0.7829 (p)
REVERT: A   44 MET cc_start: 0.7618 (ttt) cc_final: 0.7309 (ttt)
REVERT: A   49 MET cc_start: 0.7418 (ttt) cc_final: 0.7102 (tmm)
REVERT: A  102 ARG cc_start: 0.8240 (mtm-85) cc_final: 0.7952 (mtm180)
REVERT: A  203 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7659 (mm-30)
REVERT: A  288 ARG cc_start: 0.8183 (mtp85) cc_final: 0.7954 (mtp180)
REVERT: A  302 ASP cc_start: 0.7793 (p0) cc_final: 0.7538 (p0)
REVERT: A  373 MET cc_start: 0.8140 (mmp) cc_final: 0.7867 (mmm)
REVERT: A  380 LYS cc_start: 0.7329 (mtpt) cc_final: 0.7094 (mttp)
REVERT: A  393 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.8038 (m)
REVERT: A  465 GLU cc_start: 0.7920 (tp30) cc_final: 0.7689 (tp30)
REVERT: A  470 ASP cc_start: 0.7961 (m-30) cc_final: 0.7669 (m-30)
REVERT: A  521 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7870 (tm-30)
REVERT: B   44 MET cc_start: 0.7678 (ttt) cc_final: 0.7439 (ttt)
REVERT: B  121 LYS cc_start: 0.8505 (ttpp) cc_final: 0.8163 (tttm)
REVERT: B  156 GLU cc_start: 0.8055 (tt0) cc_final: 0.7802 (tt0)
REVERT: B  203 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7547 (mm-30)
REVERT: B  213 GLU cc_start: 0.7826 (pt0) cc_final: 0.7516 (pt0)
REVERT: B  301 SER cc_start: 0.8757 (m) cc_final: 0.8450 (p)
REVERT: B  303 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8397 (mtpp)
REVERT: B  329 GLU cc_start: 0.8169 (tt0) cc_final: 0.7911 (tt0)
REVERT: B  347 ILE cc_start: 0.8529 (tp) cc_final: 0.8312 (tp)
REVERT: B  370 GLN cc_start: 0.8142 (mt0) cc_final: 0.7659 (mm110)
REVERT: B  380 LYS cc_start: 0.7497 (mtpt) cc_final: 0.7185 (mmtp)
REVERT: B  440 ASN cc_start: 0.7336 (p0) cc_final: 0.7009 (p0)
REVERT: B  441 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7283 (mp0)
REVERT: B  463 ASN cc_start: 0.8609 (t0) cc_final: 0.8190 (t0)
REVERT: B  466 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7724 (mm-30)
REVERT: B  492 TYR cc_start: 0.8696 (t80) cc_final: 0.8219 (t80)
REVERT: B  521 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8232 (tm-30)
REVERT: C   10 PHE cc_start: 0.8175 (t80) cc_final: 0.7860 (t80)
REVERT: C   46 CYS cc_start: 0.7637 (m) cc_final: 0.7367 (t)
REVERT: C  141 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8462 (mm110)
REVERT: C  203 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7429 (mm-30)
REVERT: C  288 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7816 (mtm180)
REVERT: C  323 MET cc_start: 0.8282 (mtm) cc_final: 0.8072 (mtm)
REVERT: C  346 ASN cc_start: 0.8076 (m-40) cc_final: 0.7797 (m-40)
REVERT: C  355 ASN cc_start: 0.7918 (m-40) cc_final: 0.7687 (p0)
REVERT: C  363 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.7942 (p)
REVERT: C  462 SER cc_start: 0.8738 (m) cc_final: 0.8389 (t)
REVERT: C  463 ASN cc_start: 0.8686 (t0) cc_final: 0.8091 (t0)
REVERT: C  466 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7925 (mm-30)
REVERT: C  516 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7929 (mm)
REVERT: C  521 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7894 (tm-30)
  outliers start: 37
  outliers final: 16
  residues processed: 376
  average time/residue: 1.4017
  time to fit residues: 566.0581
Evaluate side-chains
  372 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 351
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   57 PHE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain C residue    7 MET
Chi-restraints excluded: chain C residue   15 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue  141 GLN
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain C residue  363 THR
Chi-restraints excluded: chain C residue  480 ASP
Chi-restraints excluded: chain C residue  516 LEU
Chi-restraints excluded: chain C residue  529 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 95 optimal weight:    0.9980
   chunk 154 optimal weight:    1.9990
   chunk 135 optimal weight:    1.9990
   chunk 136 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 151 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0570
   chunk 13 optimal weight:    0.5980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A 297 HIS
B 152 ASN
** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 482 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.123823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.110706 restraints weight = 17691.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.97
r_work: 0.3289 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13269  Z= 0.128
  Angle     :  0.616  16.540  18003  Z= 0.312
  Chirality :  0.043   0.254   1950
  Planarity :  0.005   0.057   2307
  Dihedral  :  4.689  26.457   2040
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 19.70 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.21), residues: 1563
  helix:  1.63 (0.20), residues: 690
  sheet:  1.00 (0.29), residues: 270
  loop :  0.39 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C 508 
 HIS   0.004   0.001   HIS B 297 
 PHE   0.016   0.001   PHE B 431 
 TYR   0.014   0.001   TYR B 118 
 ARG   0.010   0.000   ARG B 178 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00516 (   15)
  link_NAG-ASN         : angle       1.75960 (   45)
  hydrogen bonds       : bond        0.03814 (  670)
  hydrogen bonds       : angle       4.42967 ( 1893)
  SS BOND              : bond        0.00526 (   24)
  SS BOND              : angle       2.97444 (   48)
  covalent geometry    : bond        0.00293 (13227)
  covalent geometry    : angle       0.59195 (17910)
  Misc. bond           : bond        0.00023 (    3)

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

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

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  398 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 359
  time to evaluate  : 1.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 THR cc_start: 0.8030 (p) cc_final: 0.7821 (p)
REVERT: A   44 MET cc_start: 0.7631 (ttt) cc_final: 0.7332 (ttt)
REVERT: A   49 MET cc_start: 0.7385 (ttt) cc_final: 0.7049 (tmm)
REVERT: A  102 ARG cc_start: 0.8227 (mtm-85) cc_final: 0.7949 (mtm180)
REVERT: A  178 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7775 (mtm-85)
REVERT: A  288 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7885 (mtm180)
REVERT: A  289 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7675 (ttt90)
REVERT: A  302 ASP cc_start: 0.7801 (p0) cc_final: 0.7533 (p0)
REVERT: A  373 MET cc_start: 0.8093 (mmp) cc_final: 0.7819 (mmm)
REVERT: A  380 LYS cc_start: 0.7343 (mtpt) cc_final: 0.7107 (mttp)
REVERT: A  381 CYS cc_start: 0.6658 (OUTLIER) cc_final: 0.6172 (t)
REVERT: A  406 ASP cc_start: 0.7884 (t0) cc_final: 0.7370 (t0)
REVERT: A  462 SER cc_start: 0.8663 (m) cc_final: 0.8257 (p)
REVERT: A  465 GLU cc_start: 0.7948 (tp30) cc_final: 0.7721 (tp30)
REVERT: A  470 ASP cc_start: 0.7932 (m-30) cc_final: 0.7526 (m-30)
REVERT: A  521 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7638 (tm-30)
REVERT: B   44 MET cc_start: 0.7705 (ttt) cc_final: 0.7397 (ttt)
REVERT: B  121 LYS cc_start: 0.8517 (ttpp) cc_final: 0.8142 (tttp)
REVERT: B  156 GLU cc_start: 0.8035 (tt0) cc_final: 0.7789 (tt0)
REVERT: B  178 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7646 (ttm170)
REVERT: B  203 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7543 (mm-30)
REVERT: B  213 GLU cc_start: 0.7810 (pt0) cc_final: 0.7465 (pt0)
REVERT: B  301 SER cc_start: 0.8737 (m) cc_final: 0.8393 (p)
REVERT: B  303 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8352 (mtpp)
REVERT: B  329 GLU cc_start: 0.8155 (tt0) cc_final: 0.7913 (tt0)
REVERT: B  347 ILE cc_start: 0.8509 (tp) cc_final: 0.8285 (tp)
REVERT: B  370 GLN cc_start: 0.8113 (mt0) cc_final: 0.7701 (mm110)
REVERT: B  380 LYS cc_start: 0.7342 (mtpt) cc_final: 0.7015 (mmtp)
REVERT: B  381 CYS cc_start: 0.6556 (m) cc_final: 0.6069 (t)
REVERT: B  438 LYS cc_start: 0.8635 (mttt) cc_final: 0.8383 (mttt)
REVERT: B  440 ASN cc_start: 0.7306 (p0) cc_final: 0.6712 (p0)
REVERT: B  441 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6733 (mp0)
REVERT: B  463 ASN cc_start: 0.8604 (t0) cc_final: 0.8146 (t0)
REVERT: B  466 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7741 (mm-30)
REVERT: B  492 TYR cc_start: 0.8671 (t80) cc_final: 0.8167 (t80)
REVERT: B  521 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8205 (tm-30)
REVERT: C   10 PHE cc_start: 0.8118 (t80) cc_final: 0.7791 (t80)
REVERT: C  141 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8447 (mm110)
REVERT: C  203 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7454 (mm-30)
REVERT: C  288 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7808 (mtm-85)
REVERT: C  293 ILE cc_start: 0.7707 (mt) cc_final: 0.7431 (mt)
REVERT: C  312 ARG cc_start: 0.8200 (ttp80) cc_final: 0.7993 (ttp-170)
REVERT: C  323 MET cc_start: 0.8281 (mtm) cc_final: 0.8067 (mtm)
REVERT: C  346 ASN cc_start: 0.8107 (m-40) cc_final: 0.7819 (m-40)
REVERT: C  355 ASN cc_start: 0.7915 (m-40) cc_final: 0.7685 (p0)
REVERT: C  363 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7917 (p)
REVERT: C  380 LYS cc_start: 0.7982 (mmtp) cc_final: 0.7766 (mmtp)
REVERT: C  462 SER cc_start: 0.8749 (m) cc_final: 0.8392 (t)
REVERT: C  463 ASN cc_start: 0.8685 (t0) cc_final: 0.8055 (t0)
REVERT: C  466 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7962 (mm-30)
REVERT: C  516 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7936 (mm)
REVERT: C  521 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7874 (tm-30)
  outliers start: 39
  outliers final: 19
  residues processed: 374
  average time/residue: 1.4622
  time to fit residues: 587.4844
Evaluate side-chains
  388 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 362
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   57 PHE
Chi-restraints excluded: chain A residue  120 LYS
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  381 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  178 ARG
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain C residue    7 MET
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   46 CYS
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue  141 GLN
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain C residue  363 THR
Chi-restraints excluded: chain C residue  480 ASP
Chi-restraints excluded: chain C residue  501 ILE
Chi-restraints excluded: chain C residue  516 LEU
Chi-restraints excluded: chain C residue  529 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 58 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9990
   chunk 143 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 297 HIS
** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 482 ASN
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 482 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.122879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.109839 restraints weight = 17476.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 1.96
r_work: 0.3285 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13269  Z= 0.146
  Angle     :  0.615  12.676  18003  Z= 0.311
  Chirality :  0.044   0.257   1950
  Planarity :  0.005   0.057   2307
  Dihedral  :  4.654  26.486   2040
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.77 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.21), residues: 1563
  helix:  1.62 (0.20), residues: 690
  sheet:  1.05 (0.29), residues: 270
  loop :  0.39 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  34 
 HIS   0.004   0.001   HIS B 297 
 PHE   0.022   0.001   PHE B  33 
 TYR   0.014   0.001   TYR B 118 
 ARG   0.010   0.000   ARG B 178 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00518 (   15)
  link_NAG-ASN         : angle       1.78968 (   45)
  hydrogen bonds       : bond        0.03854 (  670)
  hydrogen bonds       : angle       4.38978 ( 1893)
  SS BOND              : bond        0.00514 (   24)
  SS BOND              : angle       2.79619 (   48)
  covalent geometry    : bond        0.00340 (13227)
  covalent geometry    : angle       0.59240 (17910)
  Misc. bond           : bond        0.00031 (    3)

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

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

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  414 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 374
  time to evaluate  : 1.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 THR cc_start: 0.8010 (p) cc_final: 0.7808 (p)
REVERT: A   44 MET cc_start: 0.7618 (ttt) cc_final: 0.7316 (ttt)
REVERT: A   49 MET cc_start: 0.7373 (ttt) cc_final: 0.7040 (tmm)
REVERT: A  102 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7956 (mtm180)
REVERT: A  178 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7748 (mtm-85)
REVERT: A  288 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7988 (mtp180)
REVERT: A  302 ASP cc_start: 0.7729 (p0) cc_final: 0.7485 (p0)
REVERT: A  373 MET cc_start: 0.8069 (mmp) cc_final: 0.7813 (mmm)
REVERT: A  381 CYS cc_start: 0.6628 (OUTLIER) cc_final: 0.6147 (t)
REVERT: A  462 SER cc_start: 0.8700 (m) cc_final: 0.8291 (p)
REVERT: A  465 GLU cc_start: 0.7951 (tp30) cc_final: 0.7733 (tp30)
REVERT: A  470 ASP cc_start: 0.7931 (m-30) cc_final: 0.7539 (m-30)
REVERT: A  521 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7640 (tm-30)
REVERT: B   66 GLU cc_start: 0.8070 (pt0) cc_final: 0.7863 (pm20)
REVERT: B  156 GLU cc_start: 0.8045 (tt0) cc_final: 0.7790 (tt0)
REVERT: B  178 ARG cc_start: 0.8076 (mtm-85) cc_final: 0.7705 (mtt180)
REVERT: B  301 SER cc_start: 0.8716 (m) cc_final: 0.8346 (p)
REVERT: B  303 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8322 (mtpp)
REVERT: B  312 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7255 (ttm170)
REVERT: B  326 TYR cc_start: 0.8601 (m-80) cc_final: 0.8013 (m-10)
REVERT: B  329 GLU cc_start: 0.8122 (tt0) cc_final: 0.7887 (tt0)
REVERT: B  347 ILE cc_start: 0.8552 (tp) cc_final: 0.8328 (tp)
REVERT: B  370 GLN cc_start: 0.8097 (mt0) cc_final: 0.7688 (mm110)
REVERT: B  380 LYS cc_start: 0.7366 (mtpt) cc_final: 0.7059 (mmtp)
REVERT: B  438 LYS cc_start: 0.8627 (mttt) cc_final: 0.8405 (mttt)
REVERT: B  440 ASN cc_start: 0.7280 (p0) cc_final: 0.6711 (p0)
REVERT: B  441 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6762 (mp0)
REVERT: B  463 ASN cc_start: 0.8629 (t0) cc_final: 0.8134 (t0)
REVERT: B  466 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7801 (mm-30)
REVERT: B  492 TYR cc_start: 0.8662 (t80) cc_final: 0.8148 (t80)
REVERT: B  521 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8182 (tm-30)
REVERT: C   10 PHE cc_start: 0.8196 (t80) cc_final: 0.7874 (t80)
REVERT: C  110 SER cc_start: 0.8378 (t) cc_final: 0.8101 (p)
REVERT: C  141 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8389 (mm-40)
REVERT: C  203 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7461 (mm-30)
REVERT: C  288 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7794 (mtm-85)
REVERT: C  312 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7989 (ttp-170)
REVERT: C  323 MET cc_start: 0.8277 (mtm) cc_final: 0.8062 (mtm)
REVERT: C  346 ASN cc_start: 0.8080 (m-40) cc_final: 0.7783 (m-40)
REVERT: C  355 ASN cc_start: 0.7915 (m-40) cc_final: 0.7693 (p0)
REVERT: C  363 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7901 (p)
REVERT: C  380 LYS cc_start: 0.8014 (mmtp) cc_final: 0.7808 (mmtp)
REVERT: C  462 SER cc_start: 0.8744 (m) cc_final: 0.8383 (t)
REVERT: C  463 ASN cc_start: 0.8679 (t0) cc_final: 0.8042 (t0)
REVERT: C  466 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7931 (mm-30)
REVERT: C  488 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7776 (mt-10)
REVERT: C  516 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7943 (mm)
REVERT: C  521 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7871 (tm-30)
  outliers start: 40
  outliers final: 24
  residues processed: 393
  average time/residue: 1.3936
  time to fit residues: 588.4693
Evaluate side-chains
  397 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 366
  time to evaluate  : 1.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   57 PHE
Chi-restraints excluded: chain A residue  120 LYS
Chi-restraints excluded: chain A residue  381 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  312 ARG
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain B residue  462 SER
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain C residue    7 MET
Chi-restraints excluded: chain C residue   15 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   57 PHE
Chi-restraints excluded: chain C residue  141 GLN
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain C residue  363 THR
Chi-restraints excluded: chain C residue  480 ASP
Chi-restraints excluded: chain C residue  488 GLU
Chi-restraints excluded: chain C residue  501 ILE
Chi-restraints excluded: chain C residue  516 LEU
Chi-restraints excluded: chain C residue  529 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 143 optimal weight:    0.4980
   chunk 49 optimal weight:    0.9990
   chunk 112 optimal weight:    0.7980
   chunk 96 optimal weight:    0.6980
   chunk 126 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 118 optimal weight:    0.5980
   chunk 105 optimal weight:    0.0570
   chunk 142 optimal weight:    0.7980
   chunk 114 optimal weight:    0.1980
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
A 297 HIS
B 297 HIS
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 482 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.122752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.110009 restraints weight = 17682.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.89
r_work: 0.3313 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13269  Z= 0.121
  Angle     :  0.624  13.766  18003  Z= 0.313
  Chirality :  0.043   0.249   1950
  Planarity :  0.005   0.057   2307
  Dihedral  :  4.568  26.747   2040
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 20.70 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.21), residues: 1563
  helix:  1.71 (0.20), residues: 687
  sheet:  1.10 (0.29), residues: 270
  loop :  0.37 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 508 
 HIS   0.004   0.001   HIS B 297 
 PHE   0.017   0.001   PHE B 431 
 TYR   0.014   0.001   TYR A 118 
 ARG   0.007   0.000   ARG B 178 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00508 (   15)
  link_NAG-ASN         : angle       1.70560 (   45)
  hydrogen bonds       : bond        0.03630 (  670)
  hydrogen bonds       : angle       4.40881 ( 1893)
  SS BOND              : bond        0.00454 (   24)
  SS BOND              : angle       3.15956 (   48)
  covalent geometry    : bond        0.00274 (13227)
  covalent geometry    : angle       0.59791 (17910)
  Misc. bond           : bond        0.00015 (    3)

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

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

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  408 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 371
  time to evaluate  : 1.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 THR cc_start: 0.7921 (p) cc_final: 0.7719 (p)
REVERT: A   44 MET cc_start: 0.7551 (ttt) cc_final: 0.7243 (ttt)
REVERT: A   49 MET cc_start: 0.7335 (ttt) cc_final: 0.6851 (tmm)
REVERT: A  102 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7929 (mtm180)
REVERT: A  178 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7707 (mtm-85)
REVERT: A  288 ARG cc_start: 0.8183 (mtp85) cc_final: 0.7873 (mtm180)
REVERT: A  302 ASP cc_start: 0.7670 (p0) cc_final: 0.7428 (p0)
REVERT: A  370 GLN cc_start: 0.7815 (mm110) cc_final: 0.7470 (mp10)
REVERT: A  373 MET cc_start: 0.8076 (mmp) cc_final: 0.7831 (mmm)
REVERT: A  381 CYS cc_start: 0.6591 (OUTLIER) cc_final: 0.6092 (t)
REVERT: A  462 SER cc_start: 0.8675 (m) cc_final: 0.8261 (p)
REVERT: A  465 GLU cc_start: 0.7948 (tp30) cc_final: 0.7740 (tp30)
REVERT: A  470 ASP cc_start: 0.7907 (m-30) cc_final: 0.7548 (m-30)
REVERT: A  521 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7634 (tm-30)
REVERT: B   22 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8537 (p)
REVERT: B  121 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8237 (tttp)
REVERT: B  156 GLU cc_start: 0.8035 (tt0) cc_final: 0.7785 (tt0)
REVERT: B  178 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7693 (mtt180)
REVERT: B  213 GLU cc_start: 0.7742 (pt0) cc_final: 0.7354 (pt0)
REVERT: B  301 SER cc_start: 0.8694 (m) cc_final: 0.8326 (p)
REVERT: B  303 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8293 (mtpp)
REVERT: B  326 TYR cc_start: 0.8574 (m-80) cc_final: 0.7978 (m-10)
REVERT: B  329 GLU cc_start: 0.8096 (tt0) cc_final: 0.7868 (tt0)
REVERT: B  347 ILE cc_start: 0.8474 (tp) cc_final: 0.8245 (tp)
REVERT: B  370 GLN cc_start: 0.8099 (mt0) cc_final: 0.7693 (mm110)
REVERT: B  380 LYS cc_start: 0.7216 (mtpt) cc_final: 0.6956 (mmtp)
REVERT: B  441 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7497 (mp0)
REVERT: B  463 ASN cc_start: 0.8657 (t0) cc_final: 0.8115 (t0)
REVERT: B  466 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7792 (mm-30)
REVERT: B  492 TYR cc_start: 0.8649 (t80) cc_final: 0.8123 (t80)
REVERT: B  521 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: C   10 PHE cc_start: 0.8147 (t80) cc_final: 0.7828 (t80)
REVERT: C  110 SER cc_start: 0.8379 (t) cc_final: 0.8110 (p)
REVERT: C  141 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8345 (mm-40)
REVERT: C  156 GLU cc_start: 0.7798 (pm20) cc_final: 0.7400 (pm20)
REVERT: C  203 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7592 (mm-30)
REVERT: C  288 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7812 (mtm-85)
REVERT: C  318 CYS cc_start: 0.7826 (t) cc_final: 0.7531 (t)
REVERT: C  323 MET cc_start: 0.8262 (mtm) cc_final: 0.8047 (mtm)
REVERT: C  346 ASN cc_start: 0.8046 (m-40) cc_final: 0.7744 (m-40)
REVERT: C  380 LYS cc_start: 0.7996 (mmtp) cc_final: 0.7779 (mmtp)
REVERT: C  462 SER cc_start: 0.8738 (m) cc_final: 0.8375 (t)
REVERT: C  463 ASN cc_start: 0.8687 (t0) cc_final: 0.8087 (t0)
REVERT: C  466 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7904 (mm-30)
REVERT: C  516 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7949 (mm)
REVERT: C  521 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7793 (tm-30)
REVERT: F  611 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7740 (mtm-85)
  outliers start: 37
  outliers final: 25
  residues processed: 386
  average time/residue: 1.3534
  time to fit residues: 562.8136
Evaluate side-chains
  395 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 364
  time to evaluate  : 1.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   57 PHE
Chi-restraints excluded: chain A residue  381 CYS
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  178 ARG
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain C residue    7 MET
Chi-restraints excluded: chain C residue   15 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   46 CYS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   57 PHE
Chi-restraints excluded: chain C residue  141 GLN
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain C residue  363 THR
Chi-restraints excluded: chain C residue  480 ASP
Chi-restraints excluded: chain C residue  501 ILE
Chi-restraints excluded: chain C residue  516 LEU
Chi-restraints excluded: chain C residue  529 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 86 optimal weight:    3.9990
   chunk 119 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 91 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0570
   chunk 71 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   chunk 105 optimal weight:    0.0370
   overall best weight:    0.4176

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

Flipped N/Q/H residues before XYZ refinement:
A 297 HIS
B 297 HIS
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 482 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.125980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.112892 restraints weight = 17364.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 1.95
r_work: 0.3314 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13269  Z= 0.122
  Angle     :  0.637  12.818  18003  Z= 0.317
  Chirality :  0.043   0.267   1950
  Planarity :  0.005   0.057   2307
  Dihedral  :  4.515  33.194   2040
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 21.20 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  1.59 (0.21), residues: 1563
  helix:  1.73 (0.20), residues: 687
  sheet:  1.10 (0.29), residues: 276
  loop :  0.37 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 219 
 HIS   0.004   0.001   HIS B 297 
 PHE   0.023   0.001   PHE B  33 
 TYR   0.014   0.001   TYR C 118 
 ARG   0.006   0.000   ARG B 178 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00609 (   15)
  link_NAG-ASN         : angle       1.73167 (   45)
  hydrogen bonds       : bond        0.03593 (  670)
  hydrogen bonds       : angle       4.37991 ( 1893)
  SS BOND              : bond        0.00400 (   24)
  SS BOND              : angle       3.12524 (   48)
  covalent geometry    : bond        0.00282 (13227)
  covalent geometry    : angle       0.61131 (17910)
  Misc. bond           : bond        0.00013 (    3)

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

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

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  395 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 364
  time to evaluate  : 1.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7576 (ttt) cc_final: 0.7256 (ttt)
REVERT: A   49 MET cc_start: 0.7273 (ttt) cc_final: 0.6819 (tmm)
REVERT: A  102 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7913 (mtm180)
REVERT: A  178 ARG cc_start: 0.7934 (mtm-85) cc_final: 0.7710 (mtm-85)
REVERT: A  288 ARG cc_start: 0.8198 (mtp85) cc_final: 0.7945 (mtp180)
REVERT: A  289 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7749 (ttt90)
REVERT: A  302 ASP cc_start: 0.7677 (p0) cc_final: 0.7433 (p0)
REVERT: A  352 ASP cc_start: 0.7867 (t0) cc_final: 0.7398 (t0)
REVERT: A  354 ASP cc_start: 0.7617 (m-30) cc_final: 0.7260 (m-30)
REVERT: A  370 GLN cc_start: 0.7804 (mm110) cc_final: 0.7455 (mp10)
REVERT: A  373 MET cc_start: 0.8049 (mmp) cc_final: 0.7806 (mmm)
REVERT: A  406 ASP cc_start: 0.7662 (t0) cc_final: 0.7270 (t0)
REVERT: A  462 SER cc_start: 0.8676 (m) cc_final: 0.8278 (p)
REVERT: A  465 GLU cc_start: 0.7993 (tp30) cc_final: 0.7787 (tp30)
REVERT: A  470 ASP cc_start: 0.7850 (m-30) cc_final: 0.7526 (m-30)
REVERT: A  507 LEU cc_start: 0.8875 (tm) cc_final: 0.8675 (tp)
REVERT: A  521 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7619 (tm-30)
REVERT: B   10 PHE cc_start: 0.7865 (t80) cc_final: 0.7582 (t80)
REVERT: B   22 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8456 (p)
REVERT: B   29 MET cc_start: 0.7098 (ppp) cc_final: 0.6809 (ppp)
REVERT: B  121 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8234 (tttp)
REVERT: B  156 GLU cc_start: 0.8012 (tt0) cc_final: 0.7758 (tt0)
REVERT: B  178 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7777 (mtt180)
REVERT: B  213 GLU cc_start: 0.7720 (pt0) cc_final: 0.7407 (pt0)
REVERT: B  301 SER cc_start: 0.8699 (m) cc_final: 0.8320 (p)
REVERT: B  303 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8305 (mtpp)
REVERT: B  326 TYR cc_start: 0.8555 (m-80) cc_final: 0.8025 (m-10)
REVERT: B  329 GLU cc_start: 0.8083 (tt0) cc_final: 0.7859 (tt0)
REVERT: B  347 ILE cc_start: 0.8433 (tp) cc_final: 0.8208 (tp)
REVERT: B  370 GLN cc_start: 0.8110 (mt0) cc_final: 0.7679 (mm110)
REVERT: B  380 LYS cc_start: 0.7123 (mtpt) cc_final: 0.6895 (mmtp)
REVERT: B  463 ASN cc_start: 0.8613 (t0) cc_final: 0.8080 (t0)
REVERT: B  466 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7819 (mm-30)
REVERT: B  492 TYR cc_start: 0.8639 (t80) cc_final: 0.8051 (t80)
REVERT: B  521 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8153 (tm-30)
REVERT: C   10 PHE cc_start: 0.8168 (t80) cc_final: 0.7883 (t80)
REVERT: C   46 CYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7482 (t)
REVERT: C   62 LYS cc_start: 0.7871 (ttpp) cc_final: 0.7535 (ttpp)
REVERT: C  110 SER cc_start: 0.8368 (t) cc_final: 0.8086 (p)
REVERT: C  141 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8317 (mm-40)
REVERT: C  203 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7592 (mm-30)
REVERT: C  288 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7811 (mtm-85)
REVERT: C  323 MET cc_start: 0.8270 (mtm) cc_final: 0.8046 (mtm)
REVERT: C  346 ASN cc_start: 0.8063 (m-40) cc_final: 0.7731 (m-40)
REVERT: C  462 SER cc_start: 0.8751 (m) cc_final: 0.8384 (t)
REVERT: C  463 ASN cc_start: 0.8677 (t0) cc_final: 0.8043 (t0)
REVERT: C  466 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7894 (mm-30)
REVERT: C  516 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7915 (mm)
REVERT: C  521 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7830 (tm-30)
  outliers start: 31
  outliers final: 21
  residues processed: 376
  average time/residue: 1.3801
  time to fit residues: 558.2758
Evaluate side-chains
  378 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 352
  time to evaluate  : 1.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   57 PHE
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  381 CYS
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain C residue   46 CYS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   57 PHE
Chi-restraints excluded: chain C residue  141 GLN
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain C residue  363 THR
Chi-restraints excluded: chain C residue  480 ASP
Chi-restraints excluded: chain C residue  501 ILE
Chi-restraints excluded: chain C residue  516 LEU
Chi-restraints excluded: chain C residue  529 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 129 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   chunk 41 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 102 optimal weight:    0.5980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 297 HIS
B 440 ASN
** C  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 482 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.123902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.110773 restraints weight = 17440.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.96
r_work: 0.3283 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.3462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13269  Z= 0.160
  Angle     :  0.665  12.270  18003  Z= 0.332
  Chirality :  0.044   0.256   1950
  Planarity :  0.005   0.060   2307
  Dihedral  :  4.564  33.285   2040
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 21.77 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  1.51 (0.21), residues: 1563
  helix:  1.61 (0.20), residues: 687
  sheet:  1.16 (0.29), residues: 276
  loop :  0.33 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 219 
 HIS   0.004   0.001   HIS A 376 
 PHE   0.022   0.001   PHE B  10 
 TYR   0.015   0.001   TYR A 118 
 ARG   0.006   0.000   ARG B 178 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00518 (   15)
  link_NAG-ASN         : angle       1.71839 (   45)
  hydrogen bonds       : bond        0.03954 (  670)
  hydrogen bonds       : angle       4.41382 ( 1893)
  SS BOND              : bond        0.00387 (   24)
  SS BOND              : angle       3.22203 (   48)
  covalent geometry    : bond        0.00376 (13227)
  covalent geometry    : angle       0.63935 (17910)
  Misc. bond           : bond        0.00033 (    3)

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

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

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3126 Ramachandran restraints generated.
    1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  395 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 367
  time to evaluate  : 1.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7603 (ttt) cc_final: 0.7296 (ttt)
REVERT: A   49 MET cc_start: 0.7326 (ttt) cc_final: 0.6868 (tmm)
REVERT: A  102 ARG cc_start: 0.8213 (mtm-85) cc_final: 0.7950 (mtm180)
REVERT: A  178 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7636 (mtm-85)
REVERT: A  213 GLU cc_start: 0.7464 (pt0) cc_final: 0.7217 (pt0)
REVERT: A  288 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7894 (mtm180)
REVERT: A  302 ASP cc_start: 0.7689 (p0) cc_final: 0.7447 (p0)
REVERT: A  352 ASP cc_start: 0.7899 (t0) cc_final: 0.7426 (t0)
REVERT: A  354 ASP cc_start: 0.7656 (m-30) cc_final: 0.7295 (m-30)
REVERT: A  370 GLN cc_start: 0.7800 (mm110) cc_final: 0.7449 (mp10)
REVERT: A  373 MET cc_start: 0.8076 (mmp) cc_final: 0.7844 (mmm)
REVERT: A  470 ASP cc_start: 0.7918 (m-30) cc_final: 0.7507 (m-30)
REVERT: A  507 LEU cc_start: 0.8907 (tm) cc_final: 0.8704 (tp)
REVERT: A  521 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7605 (tm-30)
REVERT: B   22 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8449 (p)
REVERT: B   23 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8020 (pt)
REVERT: B  121 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8206 (tttp)
REVERT: B  156 GLU cc_start: 0.8032 (tt0) cc_final: 0.7787 (tt0)
REVERT: B  178 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7805 (mtt180)
REVERT: B  213 GLU cc_start: 0.7820 (pt0) cc_final: 0.7545 (pt0)
REVERT: B  301 SER cc_start: 0.8697 (m) cc_final: 0.8324 (p)
REVERT: B  303 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8303 (mtpp)
REVERT: B  308 ASP cc_start: 0.7723 (p0) cc_final: 0.7478 (p0)
REVERT: B  326 TYR cc_start: 0.8615 (m-80) cc_final: 0.8164 (m-10)
REVERT: B  329 GLU cc_start: 0.8126 (tt0) cc_final: 0.7904 (tt0)
REVERT: B  347 ILE cc_start: 0.8465 (tp) cc_final: 0.8230 (tp)
REVERT: B  370 GLN cc_start: 0.8132 (mt0) cc_final: 0.7627 (mm110)
REVERT: B  380 LYS cc_start: 0.7192 (mtpt) cc_final: 0.6950 (mmtp)
REVERT: B  463 ASN cc_start: 0.8638 (t0) cc_final: 0.8115 (t0)
REVERT: B  466 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7830 (mm-30)
REVERT: B  480 ASP cc_start: 0.7841 (m-30) cc_final: 0.7270 (p0)
REVERT: B  492 TYR cc_start: 0.8663 (t80) cc_final: 0.8131 (t80)
REVERT: B  521 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8181 (tm-30)
REVERT: C   10 PHE cc_start: 0.8213 (t80) cc_final: 0.7920 (t80)
REVERT: C   46 CYS cc_start: 0.7846 (m) cc_final: 0.7522 (t)
REVERT: C   51 GLU cc_start: 0.7504 (tp30) cc_final: 0.7304 (tm-30)
REVERT: C   62 LYS cc_start: 0.7888 (ttpp) cc_final: 0.7582 (ttpp)
REVERT: C  110 SER cc_start: 0.8379 (t) cc_final: 0.8098 (p)
REVERT: C  141 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8319 (mm-40)
REVERT: C  288 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7803 (mtm-85)
REVERT: C  323 MET cc_start: 0.8309 (mtm) cc_final: 0.8100 (mtm)
REVERT: C  346 ASN cc_start: 0.8062 (m-40) cc_final: 0.7732 (m-40)
REVERT: C  381 CYS cc_start: 0.6495 (m) cc_final: 0.6112 (t)
REVERT: C  462 SER cc_start: 0.8744 (m) cc_final: 0.8382 (t)
REVERT: C  463 ASN cc_start: 0.8675 (t0) cc_final: 0.8037 (t0)
REVERT: C  466 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7913 (mm-30)
REVERT: C  516 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8019 (mm)
REVERT: C  521 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7722 (tm-30)
  outliers start: 28
  outliers final: 21
  residues processed: 378
  average time/residue: 1.4958
  time to fit residues: 608.3997
Evaluate side-chains
  387 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 361
  time to evaluate  : 1.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   57 PHE
Chi-restraints excluded: chain A residue  381 CYS
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  524 ILE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   23 ILE
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue  178 ARG
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  490 GLU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   57 PHE
Chi-restraints excluded: chain C residue  141 GLN
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain C residue  363 THR
Chi-restraints excluded: chain C residue  501 ILE
Chi-restraints excluded: chain C residue  516 LEU
Chi-restraints excluded: chain C residue  529 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 117 optimal weight:    0.9990
   chunk 126 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 144 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 153 optimal weight:    3.9990
   chunk 137 optimal weight:    0.0470
   overall best weight:    0.6880

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

Flipped N/Q/H residues before XYZ refinement:
A 297 HIS
** C  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 482 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.124091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.110997 restraints weight = 17360.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.95
r_work: 0.3295 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13269  Z= 0.139
  Angle     :  0.663  11.658  18003  Z= 0.330
  Chirality :  0.043   0.253   1950
  Planarity :  0.005   0.058   2307
  Dihedral  :  4.507  30.565   2040
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 22.56 %
    Favored  : 75.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  1.53 (0.21), residues: 1563
  helix:  1.63 (0.20), residues: 687
  sheet:  1.24 (0.30), residues: 270
  loop :  0.31 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 219 
 HIS   0.005   0.001   HIS A 376 
 PHE   0.026   0.001   PHE B  33 
 TYR   0.014   0.001   TYR A 118 
 ARG   0.007   0.001   ARG C 383 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00506 (   15)
  link_NAG-ASN         : angle       1.66256 (   45)
  hydrogen bonds       : bond        0.03773 (  670)
  hydrogen bonds       : angle       4.38851 ( 1893)
  SS BOND              : bond        0.00382 (   24)
  SS BOND              : angle       3.06243 (   48)
  covalent geometry    : bond        0.00326 (13227)
  covalent geometry    : angle       0.64027 (17910)
  Misc. bond           : bond        0.00024 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11231.06 seconds
wall clock time: 193 minutes 12.45 seconds (11592.45 seconds total)