Starting phenix.real_space_refine
on Thu Jul 24 11:04:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6y3y_10676/07_2025/6y3y_10676.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6y3y_10676/07_2025/6y3y_10676.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6y3y_10676/07_2025/6y3y_10676.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6y3y_10676/07_2025/6y3y_10676.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6y3y_10676/07_2025/6y3y_10676.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6y3y_10676/07_2025/6y3y_10676.cif"
  }
  resolution = 3.39
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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      26      5.16       5
     C    3778      2.51       5
     N     886      2.21       5
     O    1164      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5854
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2707
          Classifications: {'peptide': 332}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 316}
    Chain: "C"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "D"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          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
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Restraints were copied for chains:
    G, H, J, B, I
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" C1  NAG A 406 " occ=0.81
      ... (12 atoms not shown)
      pdb=" O7  NAG A 406 " occ=0.81
    residue:
      pdb=" C1  NAG A 407 " occ=0.44
      ... (12 atoms not shown)
      pdb=" O7  NAG A 407 " occ=0.44
    residue:
      pdb=" C1  NAG B 406 " occ=0.81
      ... (12 atoms not shown)
      pdb=" O7  NAG B 406 " occ=0.81
    residue:
      pdb=" C1  NAG B 407 " occ=0.44
      ... (12 atoms not shown)
      pdb=" O7  NAG B 407 " occ=0.44
  Time building chain proxies: 5.37, per 1000 atoms: 0.92
  Number of scatterers: 5854
  At special positions: 0
  Unit cell: (105.455, 73.255, 88.55, 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      26     16.00
     O    1164      8.00
     N     886      7.00
     C    3778      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  38 " - pdb=" SG  CYS A  59 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 154 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 180 " - pdb=" SG  CYS A 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 188 " - pdb=" SG  CYS A 219 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 277 " - pdb=" SG  CYS A 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 317 " - pdb=" SG  CYS A 341 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  38 " - pdb=" SG  CYS B  59 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 107 " - pdb=" SG  CYS B 154 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 180 " - pdb=" SG  CYS B 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 188 " - pdb=" SG  CYS B 219 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 277 " - pdb=" SG  CYS B 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 317 " - pdb=" SG  CYS B 341 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA C   3 " - " MAN C   4 "
      " BMA D   3 " - " MAN D   4 "
      " BMA G   3 " - " MAN G   4 "
      " BMA H   3 " - " MAN H   4 "
    ALPHA1-6
      " BMA D   3 " - " MAN D   5 "
      " BMA H   3 " - " MAN H   5 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
      " NAG J   1 " - " NAG J   2 "
    NAG-ASN
      " NAG A 405 " - " ASN A 110 "
      " NAG A 406 " - " ASN A 145 "
      " NAG A 407 " - " ASN A 193 "
      " NAG B 405 " - " ASN B 110 "
      " NAG B 406 " - " ASN B 145 "
      " NAG B 407 " - " ASN B 193 "
      " NAG C   1 " - " ASN A  83 "
      " NAG D   1 " - " ASN A 286 "
      " NAG E   1 " - " ASN A 314 "
      " NAG F   1 " - " ASN A 328 "
      " NAG G   1 " - " ASN B  83 "
      " NAG H   1 " - " ASN B 286 "
      " NAG I   1 " - " ASN B 314 "
      " NAG J   1 " - " ASN B 328 "
  Time building additional restraints: 2.00
  Conformation dependent library (CDL) restraints added in 827.5 milliseconds
  

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1260

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 11 sheets defined
      17.2% alpha, 16.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 37
      removed outlier: 3.738A  pdb=" N   ASP A  37 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 44
      removed outlier: 3.518A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 78
    Processing helix  chain 'A' and resid 113 through 132
    Processing helix  chain 'A' and resid 271 through 276
    Processing helix  chain 'A' and resid 301 through 309
    Processing helix  chain 'A' and resid 310 through 313
      removed outlier: 3.689A  pdb=" N   TYR A 313 " --> pdb=" O   GLY A 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 310 through 313'
    Processing helix  chain 'B' and resid 33 through 37
      removed outlier: 3.737A  pdb=" N   ASP B  37 " --> pdb=" O   SER B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 44
      removed outlier: 3.517A  pdb=" N   LEU B  44 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 78
    Processing helix  chain 'B' and resid 113 through 132
    Processing helix  chain 'B' and resid 271 through 276
    Processing helix  chain 'B' and resid 301 through 309
    Processing helix  chain 'B' and resid 310 through 313
      removed outlier: 3.689A  pdb=" N   TYR B 313 " --> pdb=" O   GLY B 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 310 through 313'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65
      removed outlier: 8.627A  pdb=" N   SER A  65 " --> pdb=" O   TRP A  28 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LEU A  30 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   PHE A  29 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ILE A  91 " --> pdb=" O   GLN A 257 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   VAL A 259 " --> pdb=" O   ILE A  91 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   PHE A  93 " --> pdb=" O   VAL A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87
      removed outlier: 8.426A  pdb=" N   LYS A 243 " --> pdb=" O   PRO A 186 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU A 184 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 168
    Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 176
      removed outlier: 3.733A  pdb=" N   VAL A 173 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 197
      removed outlier: 4.276A  pdb=" N   VAL A 206 " --> pdb=" O   GLY B 208 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   GLY B 208 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   GLY A 208 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   VAL B 206 " --> pdb=" O   GLY A 208 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 318
    Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 65
      removed outlier: 8.627A  pdb=" N   SER B  65 " --> pdb=" O   TRP B  28 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LEU B  30 " --> pdb=" O   SER B  65 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   PHE B  29 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ILE B  91 " --> pdb=" O   GLN B 257 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   VAL B 259 " --> pdb=" O   ILE B  91 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   PHE B  93 " --> pdb=" O   VAL B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87
      removed outlier: 8.426A  pdb=" N   LYS B 243 " --> pdb=" O   PRO B 186 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU B 184 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 165 through 168
    Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 176
      removed outlier: 3.732A  pdb=" N   VAL B 173 " --> pdb=" O   VAL B 231 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 317 through 318

    120 hydrogen bonds defined for protein.
    312 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.52

  Time building geometry restraints manager: 2.22 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1682
        1.34 -     1.46: 1772
        1.46 -     1.58: 2546
        1.58 -     1.70: 0
        1.70 -     1.82: 28
  Bond restraints: 6028
  Sorted by residual:
  bond pdb=" C   PHE A 108 "
       pdb=" N   PRO A 109 "
    ideal  model  delta    sigma   weight residual
    1.334  1.503 -0.169 2.34e-02 1.83e+03 5.20e+01
  bond pdb=" C   PHE B 108 "
       pdb=" N   PRO B 109 "
    ideal  model  delta    sigma   weight residual
    1.334  1.503 -0.169 2.34e-02 1.83e+03 5.20e+01
  bond pdb=" C1  NAG B 405 "
       pdb=" O5  NAG B 405 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.50e+00
  bond pdb=" C1  NAG A 405 "
       pdb=" O5  NAG A 405 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.44e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.42e+00
  ... (remaining 6023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 7885
        2.41 -     4.81: 252
        4.81 -     7.22: 51
        7.22 -     9.63: 6
        9.63 -    12.04: 4
  Bond angle restraints: 8198
  Sorted by residual:
  angle pdb=" C   PHE A 108 "
        pdb=" N   PRO A 109 "
        pdb=" CA  PRO A 109 "
      ideal   model   delta    sigma   weight residual
     119.84  131.88  -12.04 1.25e+00 6.40e-01 9.27e+01
  angle pdb=" C   PHE B 108 "
        pdb=" N   PRO B 109 "
        pdb=" CA  PRO B 109 "
      ideal   model   delta    sigma   weight residual
     119.84  131.84  -12.00 1.25e+00 6.40e-01 9.22e+01
  angle pdb=" CA  PHE A 108 "
        pdb=" C   PHE A 108 "
        pdb=" N   PRO A 109 "
      ideal   model   delta    sigma   weight residual
     118.56  125.78   -7.22 1.31e+00 5.83e-01 3.03e+01
  angle pdb=" CA  PHE B 108 "
        pdb=" C   PHE B 108 "
        pdb=" N   PRO B 109 "
      ideal   model   delta    sigma   weight residual
     118.56  125.74   -7.18 1.31e+00 5.83e-01 3.00e+01
  angle pdb=" CA  PHE B 108 "
        pdb=" C   PHE B 108 "
        pdb=" O   PHE B 108 "
      ideal   model   delta    sigma   weight residual
     119.22  114.87    4.35 1.02e+00 9.61e-01 1.82e+01
  ... (remaining 8193 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.52: 3720
       21.52 -    43.04: 138
       43.04 -    64.56: 20
       64.56 -    86.07: 38
       86.07 -   107.59: 24
  Dihedral angle restraints: 3940
    sinusoidal: 1960
      harmonic: 1980
  Sorted by residual:
  dihedral pdb=" CA  ASN A 168 "
           pdb=" C   ASN A 168 "
           pdb=" N   TYR A 169 "
           pdb=" CA  TYR A 169 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.44  -21.56     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  ASN B 168 "
           pdb=" C   ASN B 168 "
           pdb=" N   TYR B 169 "
           pdb=" CA  TYR B 169 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.47  -21.53     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" CA  SER A 147 "
           pdb=" C   SER A 147 "
           pdb=" N   LEU A 148 "
           pdb=" CA  LEU A 148 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.45   20.55     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 3937 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 780
       0.076 -    0.152: 155
       0.152 -    0.228: 17
       0.228 -    0.305: 8
       0.305 -    0.381: 4
  Chirality restraints: 964
  Sorted by residual:
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN A 328 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.02   -0.38 2.00e-01 2.50e+01 3.62e+00
  chirality pdb=" C1  NAG J   1 "
            pdb=" ND2 ASN B 328 "
            pdb=" C2  NAG J   1 "
            pdb=" O5  NAG J   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.02   -0.38 2.00e-01 2.50e+01 3.62e+00
  chirality pdb=" C1  NAG B 406 "
            pdb=" ND2 ASN B 145 "
            pdb=" C2  NAG B 406 "
            pdb=" O5  NAG B 406 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-01 2.50e+01 2.41e+00
  ... (remaining 961 not shown)

  Planarity restraints: 1006
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 107 "    0.017 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   CYS A 107 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   CYS A 107 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PHE A 108 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 107 "   -0.017 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   CYS B 107 "    0.057 2.00e-02 2.50e+03
        pdb=" O   CYS B 107 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   PHE B 108 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 100 "    0.038 5.00e-02 4.00e+02   5.76e-02 5.31e+00
        pdb=" N   PRO A 101 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 101 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 101 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1003 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1822
        2.82 -     3.34: 4959
        3.34 -     3.86: 10213
        3.86 -     4.38: 11600
        4.38 -     4.90: 20014
  Nonbonded interactions: 48608
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 253 "
            pdb=" OH  TYR B 336 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OH  TYR A 336 "
            pdb=" O   PHE B 253 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OH  TYR A 283 "
            pdb=" O   TYR A 336 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OH  TYR B 283 "
            pdb=" O   TYR B 336 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OG  SER B 319 "
            pdb=" O   GLY B 322 "
     model   vdw
     2.344 3.040
  ... (remaining 48603 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'I'
}

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=0.44 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.910
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.460
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
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      :  0.008   0.169   6074  Z= 0.344
  Angle     :  1.078  12.036   8324  Z= 0.518
  Chirality :  0.067   0.381    964
  Planarity :  0.007   0.058    992
  Dihedral  : 17.088 107.593   2644
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.45 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  4.89 %
    Favored  : 94.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.44 (0.27), residues: 660
  helix: -2.69 (0.36), residues: 102
  sheet: -2.19 (0.39), residues: 172
  loop : -3.54 (0.25), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP B 116 
 HIS   0.004   0.001   HIS B  40 
 PHE   0.026   0.003   PHE B  93 
 TYR   0.025   0.003   TYR B 128 
 ARG   0.004   0.001   ARG B 125 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00496 (   14)
  link_NAG-ASN         : angle       3.40886 (   42)
  link_ALPHA1-6        : bond        0.00112 (    2)
  link_ALPHA1-6        : angle       1.45179 (    6)
  link_BETA1-4         : bond        0.01095 (   14)
  link_BETA1-4         : angle       2.31312 (   42)
  link_ALPHA1-3        : bond        0.00280 (    4)
  link_ALPHA1-3        : angle       1.59151 (   12)
  hydrogen bonds       : bond        0.21892 (  120)
  hydrogen bonds       : angle       9.02188 (  312)
  SS BOND              : bond        0.00312 (   12)
  SS BOND              : angle       0.88053 (   24)
  covalent geometry    : bond        0.00772 ( 6028)
  covalent geometry    : angle       1.04165 ( 8198)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 144
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.7764 (pp20) cc_final: 0.7501 (pp20)
REVERT: A  155 LYS cc_start: 0.7031 (pmtt) cc_final: 0.5975 (tptt)
REVERT: A  316 SER cc_start: 0.8801 (m) cc_final: 0.8558 (p)
REVERT: B   95 GLU cc_start: 0.7764 (pp20) cc_final: 0.7478 (pp20)
REVERT: B  155 LYS cc_start: 0.7056 (pmtt) cc_final: 0.6018 (tptt)
REVERT: B  316 SER cc_start: 0.8775 (m) cc_final: 0.8527 (p)
  outliers start: 2
  outliers final: 2
  residues processed: 146
  average time/residue: 0.2022
  time to fit residues: 37.3293
Evaluate side-chains
  83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain B residue  108 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
A  98 ASN
B  55 HIS
B  98 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.126001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.097778 restraints weight = 9021.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 3.10
r_work: 0.3177 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3198
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3196
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6074  Z= 0.170
  Angle     :  0.791  13.098   8324  Z= 0.367
  Chirality :  0.052   0.384    964
  Planarity :  0.005   0.040    992
  Dihedral  : 15.522  76.606   1434
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  8.47 %
    Favored  : 88.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.46 (0.30), residues: 660
  helix: -1.20 (0.50), residues: 102
  sheet: -1.82 (0.39), residues: 172
  loop : -2.97 (0.28), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 116 
 HIS   0.003   0.001   HIS A  40 
 PHE   0.015   0.002   PHE A  78 
 TYR   0.017   0.002   TYR A 102 
 ARG   0.002   0.000   ARG A 125 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00998 (   14)
  link_NAG-ASN         : angle       4.03919 (   42)
  link_ALPHA1-6        : bond        0.00467 (    2)
  link_ALPHA1-6        : angle       1.81615 (    6)
  link_BETA1-4         : bond        0.00434 (   14)
  link_BETA1-4         : angle       2.18633 (   42)
  link_ALPHA1-3        : bond        0.00921 (    4)
  link_ALPHA1-3        : angle       2.06891 (   12)
  hydrogen bonds       : bond        0.03907 (  120)
  hydrogen bonds       : angle       6.45670 (  312)
  SS BOND              : bond        0.00267 (   12)
  SS BOND              : angle       0.51202 (   24)
  covalent geometry    : bond        0.00386 ( 6028)
  covalent geometry    : angle       0.71922 ( 8198)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.8128 (pp20) cc_final: 0.7830 (pp20)
REVERT: A  197 TYR cc_start: 0.8796 (m-80) cc_final: 0.8361 (m-80)
REVERT: A  316 SER cc_start: 0.8928 (m) cc_final: 0.8640 (p)
REVERT: B   95 GLU cc_start: 0.8080 (pp20) cc_final: 0.7736 (pp20)
REVERT: B  237 PHE cc_start: 0.8417 (m-80) cc_final: 0.8216 (m-80)
REVERT: B  316 SER cc_start: 0.8951 (m) cc_final: 0.8645 (p)
  outliers start: 16
  outliers final: 10
  residues processed: 104
  average time/residue: 0.1733
  time to fit residues: 24.3355
Evaluate side-chains
  90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  113 ASN
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  233 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 47 optimal weight:    0.1980
   chunk 32 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 25 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0270
   overall best weight:    0.5238

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.127265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.100224 restraints weight = 9045.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 3.05
r_work: 0.3234 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6074  Z= 0.135
  Angle     :  0.712  10.725   8324  Z= 0.324
  Chirality :  0.051   0.420    964
  Planarity :  0.005   0.038    992
  Dihedral  : 11.595  60.157   1434
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  9.93 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.32), residues: 660
  helix: -0.45 (0.55), residues: 102
  sheet: -1.57 (0.39), residues: 180
  loop : -2.63 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 116 
 HIS   0.003   0.001   HIS A 299 
 PHE   0.016   0.002   PHE A 329 
 TYR   0.017   0.001   TYR B 197 
 ARG   0.004   0.000   ARG A 340 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00741 (   14)
  link_NAG-ASN         : angle       3.57352 (   42)
  link_ALPHA1-6        : bond        0.00575 (    2)
  link_ALPHA1-6        : angle       1.69564 (    6)
  link_BETA1-4         : bond        0.00574 (   14)
  link_BETA1-4         : angle       1.84757 (   42)
  link_ALPHA1-3        : bond        0.01158 (    4)
  link_ALPHA1-3        : angle       1.49053 (   12)
  hydrogen bonds       : bond        0.03443 (  120)
  hydrogen bonds       : angle       5.72833 (  312)
  SS BOND              : bond        0.00262 (   12)
  SS BOND              : angle       0.37299 (   24)
  covalent geometry    : bond        0.00303 ( 6028)
  covalent geometry    : angle       0.65228 ( 8198)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.8099 (pp20) cc_final: 0.7848 (pp20)
REVERT: A  316 SER cc_start: 0.8990 (m) cc_final: 0.8666 (p)
REVERT: B   95 GLU cc_start: 0.8097 (pp20) cc_final: 0.7854 (pp20)
REVERT: B  316 SER cc_start: 0.8981 (m) cc_final: 0.8651 (p)
  outliers start: 13
  outliers final: 11
  residues processed: 97
  average time/residue: 0.1808
  time to fit residues: 23.5485
Evaluate side-chains
  84 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  233 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
B 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.123655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.096726 restraints weight = 9289.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 3.05
r_work: 0.3171 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   6074  Z= 0.172
  Angle     :  0.689  10.497   8324  Z= 0.323
  Chirality :  0.050   0.410    964
  Planarity :  0.005   0.037    992
  Dihedral  :  9.282  55.307   1434
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.48 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 10.26 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.32), residues: 660
  helix: -0.11 (0.57), residues: 102
  sheet: -1.46 (0.39), residues: 180
  loop : -2.58 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 116 
 HIS   0.003   0.001   HIS A 103 
 PHE   0.017   0.002   PHE B 139 
 TYR   0.017   0.002   TYR A 197 
 ARG   0.002   0.000   ARG A 340 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00630 (   14)
  link_NAG-ASN         : angle       3.41905 (   42)
  link_ALPHA1-6        : bond        0.00668 (    2)
  link_ALPHA1-6        : angle       1.64923 (    6)
  link_BETA1-4         : bond        0.00444 (   14)
  link_BETA1-4         : angle       1.59047 (   42)
  link_ALPHA1-3        : bond        0.01154 (    4)
  link_ALPHA1-3        : angle       1.53219 (   12)
  hydrogen bonds       : bond        0.03435 (  120)
  hydrogen bonds       : angle       5.52288 (  312)
  SS BOND              : bond        0.00307 (   12)
  SS BOND              : angle       0.46809 (   24)
  covalent geometry    : bond        0.00400 ( 6028)
  covalent geometry    : angle       0.63542 ( 8198)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.8156 (pp20) cc_final: 0.7894 (pp20)
REVERT: A  316 SER cc_start: 0.8974 (m) cc_final: 0.8652 (p)
REVERT: A  340 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7896 (mtt-85)
REVERT: B   95 GLU cc_start: 0.8132 (pp20) cc_final: 0.7847 (pp20)
REVERT: B  316 SER cc_start: 0.8987 (m) cc_final: 0.8649 (p)
  outliers start: 23
  outliers final: 18
  residues processed: 97
  average time/residue: 0.1837
  time to fit residues: 24.5640
Evaluate side-chains
  88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  341 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 2 optimal weight:    0.0770
   chunk 54 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0570
   chunk 1 optimal weight:    0.0570
   chunk 15 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 60 optimal weight:    0.3980
   overall best weight:    0.2774

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.126620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.100387 restraints weight = 9021.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 2.99
r_work: 0.3229 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6074  Z= 0.107
  Angle     :  0.651  10.441   8324  Z= 0.300
  Chirality :  0.049   0.402    964
  Planarity :  0.004   0.039    992
  Dihedral  :  8.436  54.549   1434
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.54 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (0.32), residues: 660
  helix: -0.02 (0.57), residues: 102
  sheet: -1.28 (0.40), residues: 180
  loop : -2.49 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 263 
 HIS   0.003   0.001   HIS B 299 
 PHE   0.013   0.001   PHE A 151 
 TYR   0.014   0.001   TYR B 197 
 ARG   0.002   0.000   ARG B 340 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00682 (   14)
  link_NAG-ASN         : angle       3.32712 (   42)
  link_ALPHA1-6        : bond        0.00786 (    2)
  link_ALPHA1-6        : angle       1.39808 (    6)
  link_BETA1-4         : bond        0.00551 (   14)
  link_BETA1-4         : angle       1.49588 (   42)
  link_ALPHA1-3        : bond        0.01134 (    4)
  link_ALPHA1-3        : angle       1.40898 (   12)
  hydrogen bonds       : bond        0.02917 (  120)
  hydrogen bonds       : angle       5.23539 (  312)
  SS BOND              : bond        0.00186 (   12)
  SS BOND              : angle       0.31662 (   24)
  covalent geometry    : bond        0.00230 ( 6028)
  covalent geometry    : angle       0.59802 ( 8198)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.8119 (pp20) cc_final: 0.7900 (pp20)
REVERT: A  316 SER cc_start: 0.9002 (m) cc_final: 0.8656 (p)
REVERT: B   95 GLU cc_start: 0.8127 (pp20) cc_final: 0.7912 (pp20)
REVERT: B  197 TYR cc_start: 0.8740 (m-80) cc_final: 0.8356 (m-80)
REVERT: B  316 SER cc_start: 0.8987 (m) cc_final: 0.8640 (p)
  outliers start: 13
  outliers final: 9
  residues processed: 88
  average time/residue: 0.2703
  time to fit residues: 31.6652
Evaluate side-chains
  77 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  217 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.123128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.096665 restraints weight = 9162.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.99
r_work: 0.3169 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3176
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3176
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   6074  Z= 0.158
  Angle     :  0.666  10.188   8324  Z= 0.310
  Chirality :  0.049   0.395    964
  Planarity :  0.004   0.039    992
  Dihedral  :  8.103  54.754   1434
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.55 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 12.38 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.32), residues: 660
  helix:  0.12 (0.58), residues: 102
  sheet: -1.19 (0.40), residues: 180
  loop : -2.44 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 116 
 HIS   0.002   0.001   HIS A 103 
 PHE   0.015   0.002   PHE A 151 
 TYR   0.016   0.001   TYR A 295 
 ARG   0.003   0.001   ARG B 267 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00637 (   14)
  link_NAG-ASN         : angle       3.23543 (   42)
  link_ALPHA1-6        : bond        0.00764 (    2)
  link_ALPHA1-6        : angle       1.38087 (    6)
  link_BETA1-4         : bond        0.00481 (   14)
  link_BETA1-4         : angle       1.42272 (   42)
  link_ALPHA1-3        : bond        0.01153 (    4)
  link_ALPHA1-3        : angle       1.32249 (   12)
  hydrogen bonds       : bond        0.03111 (  120)
  hydrogen bonds       : angle       5.26468 (  312)
  SS BOND              : bond        0.00260 (   12)
  SS BOND              : angle       0.44556 (   24)
  covalent geometry    : bond        0.00364 ( 6028)
  covalent geometry    : angle       0.61784 ( 8198)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 SER cc_start: 0.8977 (m) cc_final: 0.8661 (p)
REVERT: B  316 SER cc_start: 0.8989 (m) cc_final: 0.8649 (p)
  outliers start: 17
  outliers final: 14
  residues processed: 84
  average time/residue: 0.1694
  time to fit residues: 19.2198
Evaluate side-chains
  81 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  267 ARG
Chi-restraints excluded: chain B residue  273 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 54 optimal weight:    0.0020
   chunk 26 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 5 optimal weight:    0.2980
   chunk 55 optimal weight:    0.0020
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.2996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.125577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.099339 restraints weight = 9145.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 3.01
r_work: 0.3221 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6074  Z= 0.110
  Angle     :  0.650  10.170   8324  Z= 0.304
  Chirality :  0.049   0.390    964
  Planarity :  0.004   0.042    992
  Dihedral  :  7.791  54.740   1434
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 12.54 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.32), residues: 660
  helix:  0.23 (0.57), residues: 100
  sheet: -1.15 (0.39), residues: 180
  loop : -2.38 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 263 
 HIS   0.002   0.001   HIS A  23 
 PHE   0.016   0.001   PHE B 151 
 TYR   0.016   0.001   TYR A 295 
 ARG   0.002   0.000   ARG A 340 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00640 (   14)
  link_NAG-ASN         : angle       3.18966 (   42)
  link_ALPHA1-6        : bond        0.00778 (    2)
  link_ALPHA1-6        : angle       1.29521 (    6)
  link_BETA1-4         : bond        0.00528 (   14)
  link_BETA1-4         : angle       1.43375 (   42)
  link_ALPHA1-3        : bond        0.01085 (    4)
  link_ALPHA1-3        : angle       1.32316 (   12)
  hydrogen bonds       : bond        0.02832 (  120)
  hydrogen bonds       : angle       5.06007 (  312)
  SS BOND              : bond        0.00175 (   12)
  SS BOND              : angle       0.32857 (   24)
  covalent geometry    : bond        0.00242 ( 6028)
  covalent geometry    : angle       0.60237 ( 8198)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 SER cc_start: 0.8968 (m) cc_final: 0.8619 (p)
REVERT: B   95 GLU cc_start: 0.8057 (pp20) cc_final: 0.7746 (pp20)
REVERT: B  197 TYR cc_start: 0.8729 (m-80) cc_final: 0.8363 (m-80)
REVERT: B  316 SER cc_start: 0.8957 (m) cc_final: 0.8605 (p)
  outliers start: 18
  outliers final: 15
  residues processed: 89
  average time/residue: 0.1539
  time to fit residues: 18.8078
Evaluate side-chains
  83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  273 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.123624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.097103 restraints weight = 9088.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 3.01
r_work: 0.3184 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6074  Z= 0.143
  Angle     :  0.660   9.907   8324  Z= 0.307
  Chirality :  0.048   0.386    964
  Planarity :  0.004   0.040    992
  Dihedral  :  7.649  54.951   1434
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 13.03 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.32), residues: 660
  helix:  0.29 (0.58), residues: 100
  sheet: -1.10 (0.39), residues: 180
  loop : -2.35 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 116 
 HIS   0.002   0.001   HIS B  23 
 PHE   0.016   0.002   PHE B 151 
 TYR   0.015   0.001   TYR A 295 
 ARG   0.002   0.000   ARG B 285 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00618 (   14)
  link_NAG-ASN         : angle       3.09828 (   42)
  link_ALPHA1-6        : bond        0.00794 (    2)
  link_ALPHA1-6        : angle       1.33038 (    6)
  link_BETA1-4         : bond        0.00480 (   14)
  link_BETA1-4         : angle       1.39515 (   42)
  link_ALPHA1-3        : bond        0.01065 (    4)
  link_ALPHA1-3        : angle       1.23039 (   12)
  hydrogen bonds       : bond        0.02949 (  120)
  hydrogen bonds       : angle       5.06793 (  312)
  SS BOND              : bond        0.00246 (   12)
  SS BOND              : angle       0.45387 (   24)
  covalent geometry    : bond        0.00331 ( 6028)
  covalent geometry    : angle       0.61542 ( 8198)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 1.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  224 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9155 (mt)
REVERT: A  316 SER cc_start: 0.8976 (m) cc_final: 0.8623 (p)
REVERT: B   95 GLU cc_start: 0.8094 (pp20) cc_final: 0.7718 (pp20)
REVERT: B  316 SER cc_start: 0.8999 (m) cc_final: 0.8630 (p)
  outliers start: 18
  outliers final: 15
  residues processed: 88
  average time/residue: 0.2938
  time to fit residues: 36.0980
Evaluate side-chains
  83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  341 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0870
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0470
   chunk 56 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.4856

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.124819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.098685 restraints weight = 9123.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 3.01
r_work: 0.3206 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3215
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.3518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6074  Z= 0.122
  Angle     :  0.644   9.846   8324  Z= 0.301
  Chirality :  0.048   0.379    964
  Planarity :  0.004   0.040    992
  Dihedral  :  7.498  55.218   1434
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 13.03 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.32), residues: 660
  helix:  0.33 (0.57), residues: 100
  sheet: -1.06 (0.39), residues: 180
  loop : -2.36 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 116 
 HIS   0.003   0.001   HIS B 103 
 PHE   0.017   0.002   PHE B 151 
 TYR   0.016   0.001   TYR B 197 
 ARG   0.005   0.000   ARG B 267 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00609 (   14)
  link_NAG-ASN         : angle       3.04767 (   42)
  link_ALPHA1-6        : bond        0.00785 (    2)
  link_ALPHA1-6        : angle       1.29799 (    6)
  link_BETA1-4         : bond        0.00506 (   14)
  link_BETA1-4         : angle       1.38787 (   42)
  link_ALPHA1-3        : bond        0.00976 (    4)
  link_ALPHA1-3        : angle       1.21354 (   12)
  hydrogen bonds       : bond        0.02853 (  120)
  hydrogen bonds       : angle       4.97664 (  312)
  SS BOND              : bond        0.00205 (   12)
  SS BOND              : angle       0.37857 (   24)
  covalent geometry    : bond        0.00276 ( 6028)
  covalent geometry    : angle       0.60019 ( 8198)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.8117 (pp20) cc_final: 0.7719 (pp20)
REVERT: A  224 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9124 (mt)
REVERT: A  262 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.6472 (pmt100)
REVERT: A  316 SER cc_start: 0.8990 (m) cc_final: 0.8643 (p)
REVERT: B   95 GLU cc_start: 0.8117 (pp20) cc_final: 0.7720 (pp20)
REVERT: B  316 SER cc_start: 0.8991 (m) cc_final: 0.8625 (p)
  outliers start: 19
  outliers final: 16
  residues processed: 88
  average time/residue: 0.1638
  time to fit residues: 19.6206
Evaluate side-chains
  85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  262 ARG
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  341 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0970
   chunk 63 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.6378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.123569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.097515 restraints weight = 9182.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 3.01
r_work: 0.3212 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3204
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6074  Z= 0.137
  Angle     :  0.652   9.644   8324  Z= 0.305
  Chirality :  0.048   0.374    964
  Planarity :  0.004   0.038    992
  Dihedral  :  7.441  55.819   1434
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 13.84 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.32), residues: 660
  helix:  0.36 (0.57), residues: 100
  sheet: -1.04 (0.39), residues: 180
  loop : -2.38 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 116 
 HIS   0.003   0.001   HIS B 299 
 PHE   0.018   0.002   PHE B 151 
 TYR   0.017   0.001   TYR A 295 
 ARG   0.002   0.000   ARG A 340 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00596 (   14)
  link_NAG-ASN         : angle       2.98611 (   42)
  link_ALPHA1-6        : bond        0.00764 (    2)
  link_ALPHA1-6        : angle       1.30499 (    6)
  link_BETA1-4         : bond        0.00487 (   14)
  link_BETA1-4         : angle       1.36716 (   42)
  link_ALPHA1-3        : bond        0.00960 (    4)
  link_ALPHA1-3        : angle       1.21054 (   12)
  hydrogen bonds       : bond        0.02868 (  120)
  hydrogen bonds       : angle       4.96279 (  312)
  SS BOND              : bond        0.00243 (   12)
  SS BOND              : angle       0.42817 (   24)
  covalent geometry    : bond        0.00314 ( 6028)
  covalent geometry    : angle       0.61048 ( 8198)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  224 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9109 (mt)
REVERT: A  262 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.6459 (pmt100)
REVERT: A  316 SER cc_start: 0.9001 (m) cc_final: 0.8635 (p)
REVERT: B   95 GLU cc_start: 0.8143 (pp20) cc_final: 0.7712 (pp20)
REVERT: B  262 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.6668 (pmt100)
REVERT: B  316 SER cc_start: 0.9014 (m) cc_final: 0.8629 (p)
  outliers start: 19
  outliers final: 16
  residues processed: 88
  average time/residue: 0.1776
  time to fit residues: 20.9708
Evaluate side-chains
  85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  262 ARG
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  262 ARG
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  341 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    1.0184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.121202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.094532 restraints weight = 9367.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 3.05
r_work: 0.3137 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   6074  Z= 0.187
  Angle     :  0.686   9.362   8324  Z= 0.323
  Chirality :  0.048   0.365    964
  Planarity :  0.004   0.040    992
  Dihedral  :  7.510  56.831   1434
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 14.01 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.32), residues: 660
  helix:  0.39 (0.58), residues: 100
  sheet: -1.12 (0.38), residues: 180
  loop : -2.38 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 116 
 HIS   0.003   0.001   HIS B  23 
 PHE   0.018   0.002   PHE B 151 
 TYR   0.021   0.002   TYR A 295 
 ARG   0.002   0.000   ARG A 285 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00599 (   14)
  link_NAG-ASN         : angle       2.92270 (   42)
  link_ALPHA1-6        : bond        0.00741 (    2)
  link_ALPHA1-6        : angle       1.32151 (    6)
  link_BETA1-4         : bond        0.00449 (   14)
  link_BETA1-4         : angle       1.34616 (   42)
  link_ALPHA1-3        : bond        0.00916 (    4)
  link_ALPHA1-3        : angle       1.23640 (   12)
  hydrogen bonds       : bond        0.03154 (  120)
  hydrogen bonds       : angle       5.05257 (  312)
  SS BOND              : bond        0.00329 (   12)
  SS BOND              : angle       0.55698 (   24)
  covalent geometry    : bond        0.00437 ( 6028)
  covalent geometry    : angle       0.64840 ( 8198)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3256.82 seconds
wall clock time: 59 minutes 14.25 seconds (3554.25 seconds total)