Starting phenix.real_space_refine
on Sun Apr 27 22:32:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z0t_39033/04_2025/8z0t_39033.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z0t_39033/04_2025/8z0t_39033.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z0t_39033/04_2025/8z0t_39033.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z0t_39033/04_2025/8z0t_39033.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z0t_39033/04_2025/8z0t_39033.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z0t_39033/04_2025/8z0t_39033.cif"
  }
  resolution = 3.58
  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=   0.026
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      27      5.16       5
     C    4096      2.51       5
     N    1121      2.21       5
     O    1312      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6556
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 170, 1393
          Classifications: {'peptide': 170}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 162}
    Chain: "D"
      Number of atoms: 2467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2467
          Classifications: {'peptide': 316}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 293}
    Chain: "E"
      Number of atoms: 2467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2467
          Classifications: {'peptide': 316}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 292}
    Chain: "B"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 53
          Unusual residues: {'BMA': 1, 'NAG': 3}
          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: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 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: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          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: "E"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.42, per 1000 atoms: 0.67
  Number of scatterers: 6556
  At special positions: 0
  Unit cell: (101.65, 87.74, 116.63, 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      27     16.00
     O    1312      8.00
     N    1121      7.00
     C    4096      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  51 " - pdb=" SG  CYS A  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 132 " - pdb=" SG  CYS A 176 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 121 " - pdb=" SG  CYS E 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 135 " - pdb=" SG  CYS D 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 209 " - pdb=" SG  CYS E 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 239 " - pdb=" SG  CYS D 299 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 345 " - pdb=" SG  CYS D 405 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 135 " - pdb=" SG  CYS E 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 239 " - pdb=" SG  CYS E 299 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 345 " - pdb=" SG  CYS E 405 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " BMA B   3 " - " NAG B   4 "
      " NAG C   1 " - " NAG C   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
    NAG-ASN
      " NAG A 301 " - " ASN A  46 "
      " NAG A 302 " - " ASN A 191 "
      " NAG A 303 " - " ASN A  99 "
      " NAG A 304 " - " ASN A 165 "
      " NAG B   1 " - " ASN A  67 "
      " NAG C   1 " - " ASN A 160 "
      " NAG E 501 " - " ASN E 252 "
      " NAG F   1 " - " ASN D 275 "
      " NAG G   1 " - " ASN E 275 "
  Time building additional restraints: 1.57
  Conformation dependent library (CDL) restraints added in 846.4 milliseconds
  

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1514

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 20 sheets defined
      6.7% alpha, 41.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.601A  pdb=" N   ASP A  87 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 138
      No H-bonds generated for 'chain 'A' and resid 136 through 138'
    Processing helix  chain 'D' and resid 181 through 187
      removed outlier: 3.523A  pdb=" N   TRP D 185 " --> pdb=" O   SER D 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 225 through 231
    Processing helix  chain 'D' and resid 287 through 293
    Processing helix  chain 'D' and resid 394 through 398
    Processing helix  chain 'E' and resid 184 through 188
      removed outlier: 3.742A  pdb=" N   ASP E 188 " --> pdb=" O   TRP E 185 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 287 through 294
    Processing helix  chain 'E' and resid 393 through 399
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35
      removed outlier: 3.641A  pdb=" N   VAL A  47 " --> pdb=" O   ILE A  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 42
      removed outlier: 6.256A  pdb=" N   ILE A  41 " --> pdb=" O   PHE A 109 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   TRP A  64 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 117
    Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 122
      removed outlier: 4.841A  pdb=" N   LYS A 179 " --> pdb=" O   LYS A 142 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   LYS A 142 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   VAL A 143 " --> pdb=" O   TYR A 154 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   TYR A 154 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   TYR A 145 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLU A 150 " --> pdb=" O   LYS A 147 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122
    Processing sheet with id=AA6, first strand: chain 'D' and resid 113 through 117
      removed outlier: 6.023A  pdb=" N   ALA D 172 " --> pdb=" O   GLY D 139 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 146 through 151
      removed outlier: 3.880A  pdb=" N   ASN D 146 " --> pdb=" O   THR D 196 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 218 through 222
      removed outlier: 3.786A  pdb=" N   THR D 238 " --> pdb=" O   SER D 222 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASP D 243 " --> pdb=" O   LEU D 278 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   LEU D 278 " --> pdb=" O   ASP D 243 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 252 through 257
    Processing sheet with id=AB1, first strand: chain 'D' and resid 325 through 329
      removed outlier: 5.865A  pdb=" N   PHE D 384 " --> pdb=" O   ASN D 349 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 356 through 360
    Processing sheet with id=AB3, first strand: chain 'E' and resid 113 through 118
      removed outlier: 5.842A  pdb=" N   ALA E 172 " --> pdb=" O   GLY E 139 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 113 through 118
    Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 151
      removed outlier: 3.580A  pdb=" N   ASP E 204 " --> pdb=" O   CYS E 193 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 219 through 222
      removed outlier: 3.908A  pdb=" N   THR E 238 " --> pdb=" O   SER E 222 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 219 through 222
      removed outlier: 3.908A  pdb=" N   THR E 238 " --> pdb=" O   SER E 222 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 252 through 256
    Processing sheet with id=AB9, first strand: chain 'E' and resid 327 through 329
    Processing sheet with id=AC1, first strand: chain 'E' and resid 327 through 329
    Processing sheet with id=AC2, first strand: chain 'E' and resid 364 through 365
      removed outlier: 3.612A  pdb=" N   CYS E 405 " --> pdb=" O   ARG E 420 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL E 418 " --> pdb=" O   ALA E 407 " (cutoff:3.500A)

    252 hydrogen bonds defined for protein.
    624 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.17

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2019
        1.34 -     1.46: 1572
        1.46 -     1.58: 3091
        1.58 -     1.70: 1
        1.70 -     1.82: 34
  Bond restraints: 6717
  Sorted by residual:
  bond pdb=" C1  NAG A 304 "
       pdb=" O5  NAG A 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.463 -0.057 2.00e-02 2.50e+03 8.21e+00
  bond pdb=" C4  BMA B   3 "
       pdb=" C5  BMA B   3 "
    ideal  model  delta    sigma   weight residual
    1.528  1.575 -0.047 2.00e-02 2.50e+03 5.44e+00
  bond pdb=" C1  NAG E 501 "
       pdb=" O5  NAG E 501 "
    ideal  model  delta    sigma   weight residual
    1.406  1.452 -0.046 2.00e-02 2.50e+03 5.39e+00
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.451 -0.045 2.00e-02 2.50e+03 4.96e+00
  bond pdb=" C3  BMA B   3 "
       pdb=" C4  BMA B   3 "
    ideal  model  delta    sigma   weight residual
    1.541  1.585 -0.044 2.00e-02 2.50e+03 4.88e+00
  ... (remaining 6712 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 8946
        2.78 -     5.55: 169
        5.55 -     8.33: 31
        8.33 -    11.10: 7
       11.10 -    13.88: 2
  Bond angle restraints: 9155
  Sorted by residual:
  angle pdb=" C   ASP E 122 "
        pdb=" N   GLY E 123 "
        pdb=" CA  GLY E 123 "
      ideal   model   delta    sigma   weight residual
     121.70  135.58  -13.88 1.80e+00 3.09e-01 5.94e+01
  angle pdb=" C   HIS E 361 "
        pdb=" N   ASN E 362 "
        pdb=" CA  ASN E 362 "
      ideal   model   delta    sigma   weight residual
     121.54  130.68   -9.14 1.91e+00 2.74e-01 2.29e+01
  angle pdb=" C   PHE E 227 "
        pdb=" N   ASP E 228 "
        pdb=" CA  ASP E 228 "
      ideal   model   delta    sigma   weight residual
     121.54  130.54   -9.00 1.91e+00 2.74e-01 2.22e+01
  angle pdb=" CA  VAL E 242 "
        pdb=" CB  VAL E 242 "
        pdb=" CG1 VAL E 242 "
      ideal   model   delta    sigma   weight residual
     110.40  118.15   -7.75 1.70e+00 3.46e-01 2.08e+01
  angle pdb=" CB  MET E 351 "
        pdb=" CG  MET E 351 "
        pdb=" SD  MET E 351 "
      ideal   model   delta    sigma   weight residual
     112.70  125.96  -13.26 3.00e+00 1.11e-01 1.95e+01
  ... (remaining 9150 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.71: 3744
       21.71 -    43.41: 414
       43.41 -    65.12: 67
       65.12 -    86.83: 31
       86.83 -   108.54: 10
  Dihedral angle restraints: 4266
    sinusoidal: 1931
      harmonic: 2335
  Sorted by residual:
  dihedral pdb=" CB  CYS E 135 "
           pdb=" SG  CYS E 135 "
           pdb=" SG  CYS E 193 "
           pdb=" CB  CYS E 193 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   28.70   64.30     1      1.00e+01 1.00e-02 5.44e+01
  dihedral pdb=" CA  VAL E 242 "
           pdb=" C   VAL E 242 "
           pdb=" N   ASP E 243 "
           pdb=" CA  ASP E 243 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.82   36.18     0      5.00e+00 4.00e-02 5.24e+01
  dihedral pdb=" CB  CYS D 121 "
           pdb=" SG  CYS D 121 "
           pdb=" SG  CYS E 209 "
           pdb=" CB  CYS E 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.37  -53.37     1      1.00e+01 1.00e-02 3.87e+01
  ... (remaining 4263 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.133: 1037
       0.133 -    0.266: 30
       0.266 -    0.398: 4
       0.398 -    0.531: 1
       0.531 -    0.664: 1
  Chirality restraints: 1073
  Sorted by residual:
  chirality pdb=" C1  NAG A 304 "
            pdb=" ND2 ASN A 165 "
            pdb=" C2  NAG A 304 "
            pdb=" O5  NAG A 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.74   -0.66 2.00e-01 2.50e+01 1.10e+01
  chirality pdb=" C1  NAG A 303 "
            pdb=" ND2 ASN A  99 "
            pdb=" C2  NAG A 303 "
            pdb=" O5  NAG A 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.92   -0.48 2.00e-01 2.50e+01 5.65e+00
  chirality pdb=" CB  ILE E 116 "
            pdb=" CA  ILE E 116 "
            pdb=" CG1 ILE E 116 "
            pdb=" CG2 ILE E 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.39 2.00e-01 2.50e+01 3.75e+00
  ... (remaining 1070 not shown)

  Planarity restraints: 1166
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 242 "    0.017 2.00e-02 2.50e+03   3.44e-02 1.18e+01
        pdb=" C   VAL E 242 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   VAL E 242 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ASP E 243 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 149 "    0.021 2.00e-02 2.50e+03   1.95e-02 9.53e+00
        pdb=" CG  TRP D 149 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 149 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 149 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 149 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 149 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 149 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 149 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 149 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 149 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 185 "   -0.012 2.00e-02 2.50e+03   1.92e-02 7.38e+00
        pdb=" CG  TYR A 185 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 185 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 185 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 185 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 185 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 185 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 185 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1163 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1395
        2.79 -     3.32: 5429
        3.32 -     3.84: 11037
        3.84 -     4.37: 11823
        4.37 -     4.90: 21302
  Nonbonded interactions: 50986
  Sorted by model distance:
  nonbonded pdb=" O   LYS D 183 "
            pdb=" OG  SER D 187 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OD1 ASP A 170 "
            pdb=" OH  TYR A 174 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OG1 THR E 393 "
            pdb=" OE1 GLU E 396 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   THR D 196 "
            pdb=" OG1 THR D 196 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" OG  SER A  33 "
            pdb=" OG1 THR A  50 "
     model   vdw
     2.348 3.040
  ... (remaining 50981 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = (chain 'E' and resid 110 through 425)
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     19.120
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   6744  Z= 0.259
  Angle     :  1.022  13.878   9226  Z= 0.509
  Chirality :  0.062   0.664   1073
  Planarity :  0.007   0.057   1157
  Dihedral  : 19.033 108.536   2722
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 31.47 %
    Favored  : 67.55 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.28), residues: 796
  helix: -3.15 (0.51), residues: 35
  sheet: -0.04 (0.29), residues: 318
  loop : -1.25 (0.27), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP D 149 
 HIS   0.011   0.001   HIS D 361 
 PHE   0.040   0.003   PHE A  56 
 TYR   0.044   0.002   TYR A 185 
 ARG   0.007   0.000   ARG E 289 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01383 (    9)
  link_NAG-ASN         : angle       4.79273 (   27)
  link_BETA1-4         : bond        0.00619 (    8)
  link_BETA1-4         : angle       2.65920 (   24)
  hydrogen bonds       : bond        0.14536 (  222)
  hydrogen bonds       : angle       6.67878 (  624)
  SS BOND              : bond        0.00188 (   10)
  SS BOND              : angle       1.22473 (   20)
  covalent geometry    : bond        0.00540 ( 6717)
  covalent geometry    : angle       0.98102 ( 9155)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.7847 (tppt) cc_final: 0.7600 (mmtt)
  outliers start: 7
  outliers final: 3
  residues processed: 102
  average time/residue: 0.1903
  time to fit residues: 26.9204
Evaluate side-chains
  93 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASN
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  209 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 182 GLN
D 154 GLN
E 399 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.140187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.107344 restraints weight = 10808.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.109510 restraints weight = 6239.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.110731 restraints weight = 4952.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   6744  Z= 0.190
  Angle     :  0.680   7.685   9226  Z= 0.331
  Chirality :  0.047   0.367   1073
  Planarity :  0.004   0.039   1157
  Dihedral  : 10.604  61.492   1220
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 28.81 %
    Favored  : 66.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.29), residues: 796
  helix: -1.59 (0.74), residues: 35
  sheet: -0.02 (0.29), residues: 323
  loop : -0.88 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 149 
 HIS   0.004   0.001   HIS D 361 
 PHE   0.008   0.001   PHE E 350 
 TYR   0.014   0.001   TYR A 185 
 ARG   0.003   0.000   ARG D 341 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00846 (    9)
  link_NAG-ASN         : angle       3.08303 (   27)
  link_BETA1-4         : bond        0.00478 (    8)
  link_BETA1-4         : angle       2.42865 (   24)
  hydrogen bonds       : bond        0.03423 (  222)
  hydrogen bonds       : angle       5.28005 (  624)
  SS BOND              : bond        0.00513 (   10)
  SS BOND              : angle       1.08246 (   20)
  covalent geometry    : bond        0.00443 ( 6717)
  covalent geometry    : angle       0.64781 ( 9155)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  132 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7369 (mp10)
  outliers start: 30
  outliers final: 17
  residues processed: 121
  average time/residue: 0.1489
  time to fit residues: 25.2505
Evaluate side-chains
  105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASN
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  209 CYS
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  418 VAL
Chi-restraints excluded: chain E residue  120 SER
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  152 ASP
Chi-restraints excluded: chain E residue  179 THR
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  256 SER
Chi-restraints excluded: chain E residue  353 GLU
Chi-restraints excluded: chain E residue  374 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 39 optimal weight:    0.2980
   chunk 73 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 182 GLN
D 371 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.141269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.108095 restraints weight = 10981.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.110450 restraints weight = 6241.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.112500 restraints weight = 4907.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.1244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6744  Z= 0.137
  Angle     :  0.627   7.004   9226  Z= 0.303
  Chirality :  0.046   0.356   1073
  Planarity :  0.004   0.035   1157
  Dihedral  :  9.044  54.985   1220
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 28.67 %
    Favored  : 66.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.29), residues: 796
  helix: -1.14 (0.80), residues: 35
  sheet: -0.11 (0.29), residues: 337
  loop : -0.78 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP D 149 
 HIS   0.004   0.001   HIS D 371 
 PHE   0.006   0.001   PHE D 385 
 TYR   0.008   0.001   TYR A 185 
 ARG   0.002   0.000   ARG D 341 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00775 (    9)
  link_NAG-ASN         : angle       2.98256 (   27)
  link_BETA1-4         : bond        0.00489 (    8)
  link_BETA1-4         : angle       2.24029 (   24)
  hydrogen bonds       : bond        0.03077 (  222)
  hydrogen bonds       : angle       5.05005 (  624)
  SS BOND              : bond        0.00236 (   10)
  SS BOND              : angle       0.88787 (   20)
  covalent geometry    : bond        0.00316 ( 6717)
  covalent geometry    : angle       0.59540 ( 9155)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 100
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.7799 (tppt) cc_final: 0.7545 (tppt)
REVERT: D  132 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7424 (mp10)
REVERT: E  184 HIS cc_start: 0.7946 (m90) cc_final: 0.7658 (m90)
REVERT: E  221 LEU cc_start: 0.8505 (tp) cc_final: 0.8210 (tp)
  outliers start: 38
  outliers final: 24
  residues processed: 134
  average time/residue: 0.1406
  time to fit residues: 26.9473
Evaluate side-chains
  117 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASN
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  209 CYS
Chi-restraints excluded: chain D residue  317 THR
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  386 VAL
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  152 ASP
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  179 THR
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  237 ILE
Chi-restraints excluded: chain E residue  243 ASP
Chi-restraints excluded: chain E residue  283 THR
Chi-restraints excluded: chain E residue  353 GLU
Chi-restraints excluded: chain E residue  374 THR
Chi-restraints excluded: chain E residue  392 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 15 optimal weight:    0.4980
   chunk 19 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 371 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.139667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.106286 restraints weight = 10967.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.107265 restraints weight = 8265.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.108847 restraints weight = 6352.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   6744  Z= 0.171
  Angle     :  0.643   7.616   9226  Z= 0.310
  Chirality :  0.047   0.367   1073
  Planarity :  0.004   0.034   1157
  Dihedral  :  7.989  46.383   1218
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 28.11 %
    Favored  : 66.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.30), residues: 796
  helix: -0.83 (0.82), residues: 36
  sheet: -0.11 (0.29), residues: 334
  loop : -0.72 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 149 
 HIS   0.004   0.001   HIS D 361 
 PHE   0.007   0.001   PHE E 387 
 TYR   0.009   0.001   TYR A 185 
 ARG   0.003   0.000   ARG D 341 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00752 (    9)
  link_NAG-ASN         : angle       3.01592 (   27)
  link_BETA1-4         : bond        0.00405 (    8)
  link_BETA1-4         : angle       2.33062 (   24)
  hydrogen bonds       : bond        0.02968 (  222)
  hydrogen bonds       : angle       4.91268 (  624)
  SS BOND              : bond        0.00278 (   10)
  SS BOND              : angle       0.84622 (   20)
  covalent geometry    : bond        0.00403 ( 6717)
  covalent geometry    : angle       0.61106 ( 9155)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 99
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.7847 (tppt) cc_final: 0.7613 (tppt)
REVERT: D  132 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7436 (mp10)
REVERT: D  306 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8322 (mp)
REVERT: D  390 LEU cc_start: 0.8250 (tt) cc_final: 0.7915 (tt)
REVERT: E  221 LEU cc_start: 0.8543 (tp) cc_final: 0.8176 (tp)
  outliers start: 41
  outliers final: 34
  residues processed: 132
  average time/residue: 0.1394
  time to fit residues: 26.1187
Evaluate side-chains
  130 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 94
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ASN
Chi-restraints excluded: chain A residue   99 ASN
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  209 CYS
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  306 LEU
Chi-restraints excluded: chain D residue  317 THR
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  331 THR
Chi-restraints excluded: chain D residue  386 VAL
Chi-restraints excluded: chain D residue  418 VAL
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  152 ASP
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  179 THR
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  213 ASN
Chi-restraints excluded: chain E residue  237 ILE
Chi-restraints excluded: chain E residue  241 VAL
Chi-restraints excluded: chain E residue  243 ASP
Chi-restraints excluded: chain E residue  256 SER
Chi-restraints excluded: chain E residue  283 THR
Chi-restraints excluded: chain E residue  305 HIS
Chi-restraints excluded: chain E residue  353 GLU
Chi-restraints excluded: chain E residue  374 THR
Chi-restraints excluded: chain E residue  392 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   chunk 72 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 3 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 182 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.138248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.104079 restraints weight = 10696.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.105038 restraints weight = 8616.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.106468 restraints weight = 6175.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   6744  Z= 0.178
  Angle     :  0.632   7.704   9226  Z= 0.307
  Chirality :  0.046   0.356   1073
  Planarity :  0.004   0.034   1157
  Dihedral  :  7.565  46.419   1218
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  6.85 %
    Allowed  : 26.71 %
    Favored  : 66.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.29), residues: 796
  helix: -0.02 (0.85), residues: 35
  sheet: -0.06 (0.29), residues: 331
  loop : -0.79 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP D 149 
 HIS   0.003   0.001   HIS D 361 
 PHE   0.007   0.001   PHE E 385 
 TYR   0.010   0.001   TYR A 185 
 ARG   0.003   0.000   ARG D 341 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00726 (    9)
  link_NAG-ASN         : angle       2.99143 (   27)
  link_BETA1-4         : bond        0.00412 (    8)
  link_BETA1-4         : angle       2.25360 (   24)
  hydrogen bonds       : bond        0.02902 (  222)
  hydrogen bonds       : angle       4.87231 (  624)
  SS BOND              : bond        0.00252 (   10)
  SS BOND              : angle       0.86175 (   20)
  covalent geometry    : bond        0.00421 ( 6717)
  covalent geometry    : angle       0.60115 ( 9155)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 93
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.7889 (tppt) cc_final: 0.7657 (tppt)
REVERT: D  132 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7433 (mp10)
REVERT: E  184 HIS cc_start: 0.8143 (m90) cc_final: 0.7852 (m90)
REVERT: E  289 ARG cc_start: 0.7721 (tpm170) cc_final: 0.7090 (tpm170)
  outliers start: 49
  outliers final: 37
  residues processed: 132
  average time/residue: 0.1436
  time to fit residues: 26.7372
Evaluate side-chains
  125 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 87
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ASN
Chi-restraints excluded: chain A residue   99 ASN
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  205 SER
Chi-restraints excluded: chain D residue  209 CYS
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  317 THR
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  331 THR
Chi-restraints excluded: chain D residue  386 VAL
Chi-restraints excluded: chain D residue  418 VAL
Chi-restraints excluded: chain E residue  120 SER
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  152 ASP
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  179 THR
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  237 ILE
Chi-restraints excluded: chain E residue  241 VAL
Chi-restraints excluded: chain E residue  243 ASP
Chi-restraints excluded: chain E residue  256 SER
Chi-restraints excluded: chain E residue  283 THR
Chi-restraints excluded: chain E residue  299 CYS
Chi-restraints excluded: chain E residue  305 HIS
Chi-restraints excluded: chain E residue  353 GLU
Chi-restraints excluded: chain E residue  374 THR
Chi-restraints excluded: chain E residue  392 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0870
   chunk 17 optimal weight:    0.5980
   chunk 57 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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 = 0.3728 r_free = 0.3728 target = 0.139168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.105283 restraints weight = 10576.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.105858 restraints weight = 8627.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.107039 restraints weight = 6325.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6744  Z= 0.147
  Angle     :  0.625   7.233   9226  Z= 0.303
  Chirality :  0.046   0.349   1073
  Planarity :  0.004   0.033   1157
  Dihedral  :  7.207  43.907   1218
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 26.29 %
    Favored  : 67.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.29), residues: 796
  helix:  0.13 (0.89), residues: 34
  sheet: -0.05 (0.28), residues: 333
  loop : -0.74 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 149 
 HIS   0.002   0.001   HIS D 409 
 PHE   0.008   0.001   PHE D 385 
 TYR   0.011   0.001   TYR A 185 
 ARG   0.002   0.000   ARG D 341 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00709 (    9)
  link_NAG-ASN         : angle       2.94910 (   27)
  link_BETA1-4         : bond        0.00408 (    8)
  link_BETA1-4         : angle       2.16677 (   24)
  hydrogen bonds       : bond        0.02796 (  222)
  hydrogen bonds       : angle       4.82619 (  624)
  SS BOND              : bond        0.00207 (   10)
  SS BOND              : angle       0.75864 (   20)
  covalent geometry    : bond        0.00345 ( 6717)
  covalent geometry    : angle       0.59502 ( 9155)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 103
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.7905 (tppt) cc_final: 0.7690 (tppt)
REVERT: D  132 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7443 (mp10)
REVERT: E  221 LEU cc_start: 0.8486 (tp) cc_final: 0.8189 (tp)
  outliers start: 43
  outliers final: 33
  residues processed: 139
  average time/residue: 0.1417
  time to fit residues: 27.8854
Evaluate side-chains
  129 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 95
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASN
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  209 CYS
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  317 THR
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  331 THR
Chi-restraints excluded: chain D residue  386 VAL
Chi-restraints excluded: chain D residue  418 VAL
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  152 ASP
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  179 THR
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  213 ASN
Chi-restraints excluded: chain E residue  237 ILE
Chi-restraints excluded: chain E residue  243 ASP
Chi-restraints excluded: chain E residue  283 THR
Chi-restraints excluded: chain E residue  299 CYS
Chi-restraints excluded: chain E residue  305 HIS
Chi-restraints excluded: chain E residue  353 GLU
Chi-restraints excluded: chain E residue  374 THR
Chi-restraints excluded: chain E residue  392 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 74 optimal weight:    0.4980
   chunk 24 optimal weight:    0.2980
   chunk 51 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 182 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.135531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.099491 restraints weight = 10820.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.102544 restraints weight = 6492.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.104540 restraints weight = 4781.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.105   6744  Z= 0.268
  Angle     :  0.708   9.290   9226  Z= 0.345
  Chirality :  0.048   0.354   1073
  Planarity :  0.004   0.035   1157
  Dihedral  :  7.858  46.851   1218
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  6.57 %
    Allowed  : 26.15 %
    Favored  : 67.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.30), residues: 796
  helix: -0.18 (0.95), residues: 35
  sheet: -0.03 (0.29), residues: 320
  loop : -0.70 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D 149 
 HIS   0.006   0.001   HIS D 361 
 PHE   0.010   0.002   PHE A  42 
 TYR   0.013   0.002   TYR D 297 
 ARG   0.003   0.000   ARG E 289 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00710 (    9)
  link_NAG-ASN         : angle       3.21744 (   27)
  link_BETA1-4         : bond        0.00320 (    8)
  link_BETA1-4         : angle       2.48232 (   24)
  hydrogen bonds       : bond        0.03174 (  222)
  hydrogen bonds       : angle       5.13873 (  624)
  SS BOND              : bond        0.00456 (   10)
  SS BOND              : angle       0.97030 (   20)
  covalent geometry    : bond        0.00642 ( 6717)
  covalent geometry    : angle       0.67598 ( 9155)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 91
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  132 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7520 (mp10)
REVERT: E  184 HIS cc_start: 0.8217 (m90) cc_final: 0.7966 (m90)
  outliers start: 47
  outliers final: 36
  residues processed: 129
  average time/residue: 0.1948
  time to fit residues: 35.0200
Evaluate side-chains
  121 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 84
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 ASN
Chi-restraints excluded: chain A residue   99 ASN
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  205 SER
Chi-restraints excluded: chain D residue  209 CYS
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  317 THR
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  331 THR
Chi-restraints excluded: chain D residue  386 VAL
Chi-restraints excluded: chain D residue  418 VAL
Chi-restraints excluded: chain E residue  120 SER
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  152 ASP
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  213 ASN
Chi-restraints excluded: chain E residue  237 ILE
Chi-restraints excluded: chain E residue  241 VAL
Chi-restraints excluded: chain E residue  243 ASP
Chi-restraints excluded: chain E residue  256 SER
Chi-restraints excluded: chain E residue  283 THR
Chi-restraints excluded: chain E residue  299 CYS
Chi-restraints excluded: chain E residue  305 HIS
Chi-restraints excluded: chain E residue  353 GLU
Chi-restraints excluded: chain E residue  374 THR
Chi-restraints excluded: chain E residue  392 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0980
   chunk 68 optimal weight:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 58 optimal weight:    0.0470
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 273 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.138805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.103714 restraints weight = 10754.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.106881 restraints weight = 6365.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.108905 restraints weight = 4607.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6744  Z= 0.128
  Angle     :  0.639   7.000   9226  Z= 0.310
  Chirality :  0.046   0.322   1073
  Planarity :  0.004   0.033   1157
  Dihedral  :  7.012  41.385   1218
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 28.39 %
    Favored  : 66.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.30), residues: 796
  helix:  0.35 (0.92), residues: 34
  sheet: -0.06 (0.29), residues: 333
  loop : -0.67 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP D 149 
 HIS   0.003   0.001   HIS E 361 
 PHE   0.010   0.001   PHE D 385 
 TYR   0.016   0.001   TYR A 185 
 ARG   0.002   0.000   ARG E 232 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00663 (    9)
  link_NAG-ASN         : angle       2.88812 (   27)
  link_BETA1-4         : bond        0.00455 (    8)
  link_BETA1-4         : angle       2.07898 (   24)
  hydrogen bonds       : bond        0.02771 (  222)
  hydrogen bonds       : angle       4.90323 (  624)
  SS BOND              : bond        0.00196 (   10)
  SS BOND              : angle       0.88270 (   20)
  covalent geometry    : bond        0.00298 ( 6717)
  covalent geometry    : angle       0.61095 ( 9155)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 99
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  132 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7483 (mp10)
REVERT: E  184 HIS cc_start: 0.8058 (m90) cc_final: 0.7773 (m90)
  outliers start: 34
  outliers final: 29
  residues processed: 127
  average time/residue: 0.2170
  time to fit residues: 39.0807
Evaluate side-chains
  125 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASN
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  205 SER
Chi-restraints excluded: chain D residue  209 CYS
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  317 THR
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  331 THR
Chi-restraints excluded: chain D residue  418 VAL
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  152 ASP
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  213 ASN
Chi-restraints excluded: chain E residue  243 ASP
Chi-restraints excluded: chain E residue  283 THR
Chi-restraints excluded: chain E residue  299 CYS
Chi-restraints excluded: chain E residue  305 HIS
Chi-restraints excluded: chain E residue  353 GLU
Chi-restraints excluded: chain E residue  374 THR
Chi-restraints excluded: chain E residue  392 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:   10.0000
   chunk 67 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0970
   chunk 11 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 182 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.138476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.103204 restraints weight = 10845.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.106410 restraints weight = 6386.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.108480 restraints weight = 4613.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   6744  Z= 0.148
  Angle     :  0.638   7.419   9226  Z= 0.308
  Chirality :  0.046   0.332   1073
  Planarity :  0.004   0.033   1157
  Dihedral  :  6.852  39.950   1218
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 28.25 %
    Favored  : 66.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.30), residues: 796
  helix:  0.42 (0.93), residues: 34
  sheet: -0.03 (0.29), residues: 333
  loop : -0.63 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 149 
 HIS   0.002   0.001   HIS E 361 
 PHE   0.009   0.001   PHE D 385 
 TYR   0.017   0.001   TYR A 185 
 ARG   0.002   0.000   ARG E 232 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00656 (    9)
  link_NAG-ASN         : angle       2.90281 (   27)
  link_BETA1-4         : bond        0.00385 (    8)
  link_BETA1-4         : angle       2.15434 (   24)
  hydrogen bonds       : bond        0.02748 (  222)
  hydrogen bonds       : angle       4.85797 (  624)
  SS BOND              : bond        0.00180 (   10)
  SS BOND              : angle       0.80009 (   20)
  covalent geometry    : bond        0.00353 ( 6717)
  covalent geometry    : angle       0.60928 ( 9155)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 101
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8126 (tt0) cc_final: 0.7732 (tm-30)
REVERT: D  132 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7475 (mp10)
REVERT: E  184 HIS cc_start: 0.8055 (m90) cc_final: 0.7761 (m90)
REVERT: E  391 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7011 (mt-10)
  outliers start: 35
  outliers final: 31
  residues processed: 131
  average time/residue: 0.2106
  time to fit residues: 37.8818
Evaluate side-chains
  130 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 97
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 GLN
Chi-restraints excluded: chain A residue   99 ASN
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  205 SER
Chi-restraints excluded: chain D residue  209 CYS
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  317 THR
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  331 THR
Chi-restraints excluded: chain D residue  418 VAL
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  152 ASP
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  213 ASN
Chi-restraints excluded: chain E residue  243 ASP
Chi-restraints excluded: chain E residue  283 THR
Chi-restraints excluded: chain E residue  299 CYS
Chi-restraints excluded: chain E residue  305 HIS
Chi-restraints excluded: chain E residue  353 GLU
Chi-restraints excluded: chain E residue  374 THR
Chi-restraints excluded: chain E residue  391 GLU
Chi-restraints excluded: chain E residue  392 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 126 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.137628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.101964 restraints weight = 10916.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.105107 restraints weight = 6465.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.107229 restraints weight = 4712.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   6744  Z= 0.174
  Angle     :  0.660   7.729   9226  Z= 0.320
  Chirality :  0.046   0.331   1073
  Planarity :  0.004   0.033   1157
  Dihedral  :  6.913  41.305   1218
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 28.11 %
    Favored  : 66.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.30), residues: 796
  helix:  0.46 (0.95), residues: 34
  sheet:  0.01 (0.29), residues: 338
  loop : -0.66 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  64 
 HIS   0.002   0.001   HIS E 361 
 PHE   0.008   0.001   PHE E 385 
 TYR   0.030   0.002   TYR A 185 
 ARG   0.003   0.000   ARG E 232 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00644 (    9)
  link_NAG-ASN         : angle       2.95153 (   27)
  link_BETA1-4         : bond        0.00359 (    8)
  link_BETA1-4         : angle       2.22057 (   24)
  hydrogen bonds       : bond        0.02800 (  222)
  hydrogen bonds       : angle       4.90070 (  624)
  SS BOND              : bond        0.00222 (   10)
  SS BOND              : angle       0.83571 (   20)
  covalent geometry    : bond        0.00416 ( 6717)
  covalent geometry    : angle       0.63174 ( 9155)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 98
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  132 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7483 (mp10)
REVERT: E  391 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.7000 (mt-10)
  outliers start: 37
  outliers final: 33
  residues processed: 129
  average time/residue: 0.1781
  time to fit residues: 32.3495
Evaluate side-chains
  131 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 96
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASN
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  205 SER
Chi-restraints excluded: chain D residue  209 CYS
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  292 ILE
Chi-restraints excluded: chain D residue  317 THR
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  331 THR
Chi-restraints excluded: chain D residue  386 VAL
Chi-restraints excluded: chain D residue  418 VAL
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  152 ASP
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  213 ASN
Chi-restraints excluded: chain E residue  241 VAL
Chi-restraints excluded: chain E residue  243 ASP
Chi-restraints excluded: chain E residue  283 THR
Chi-restraints excluded: chain E residue  299 CYS
Chi-restraints excluded: chain E residue  305 HIS
Chi-restraints excluded: chain E residue  353 GLU
Chi-restraints excluded: chain E residue  374 THR
Chi-restraints excluded: chain E residue  391 GLU
Chi-restraints excluded: chain E residue  392 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    0.0370
   chunk 60 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   chunk 35 optimal weight:    0.0570
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.5976

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

Flipped N/Q/H residues before XYZ refinement:
A 126 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.138741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.103311 restraints weight = 11070.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.106538 restraints weight = 6464.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.108412 restraints weight = 4669.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6744  Z= 0.142
  Angle     :  0.648   7.633   9226  Z= 0.314
  Chirality :  0.046   0.323   1073
  Planarity :  0.004   0.033   1157
  Dihedral  :  6.669  39.999   1218
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 27.69 %
    Favored  : 66.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.30), residues: 796
  helix:  0.34 (0.93), residues: 34
  sheet: -0.04 (0.29), residues: 335
  loop : -0.54 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 149 
 HIS   0.003   0.001   HIS E 184 
 PHE   0.009   0.001   PHE D 385 
 TYR   0.025   0.001   TYR A 185 
 ARG   0.004   0.000   ARG E 232 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00618 (    9)
  link_NAG-ASN         : angle       2.83042 (   27)
  link_BETA1-4         : bond        0.00394 (    8)
  link_BETA1-4         : angle       2.09849 (   24)
  hydrogen bonds       : bond        0.02713 (  222)
  hydrogen bonds       : angle       4.85589 (  624)
  SS BOND              : bond        0.00157 (   10)
  SS BOND              : angle       0.91510 (   20)
  covalent geometry    : bond        0.00338 ( 6717)
  covalent geometry    : angle       0.62187 ( 9155)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2942.44 seconds
wall clock time: 53 minutes 46.82 seconds (3226.82 seconds total)