Starting phenix.real_space_refine
on Tue Apr 29 21:36:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zhq_60112/04_2025/8zhq_60112.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zhq_60112/04_2025/8zhq_60112.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zhq_60112/04_2025/8zhq_60112.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zhq_60112/04_2025/8zhq_60112.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zhq_60112/04_2025/8zhq_60112.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zhq_60112/04_2025/8zhq_60112.cif"
  }
  resolution = 2.37
  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=   0.010
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      48      5.16       5
     C    5577      2.51       5
     N    1505      2.21       5
     O    1774      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8904
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1580
          Classifications: {'peptide': 210}
          Link IDs: {'PTRANS': 14, 'TRANS': 195}
    Chain: "B"
      Number of atoms: 1621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1621
          Classifications: {'peptide': 212}
          Link IDs: {'PTRANS': 11, 'TRANS': 200}
    Chain: "C"
      Number of atoms: 1591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1591
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 11, 'TRANS': 202}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1567
          Classifications: {'peptide': 207}
          Link IDs: {'PTRANS': 12, 'TRANS': 194}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 2464
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 321, 2464
          Classifications: {'peptide': 321}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 302}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      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: 6.41, per 1000 atoms: 0.72
  Number of scatterers: 8904
  At special positions: 0
  Unit cell: (67.89, 100.74, 185.42, 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      48     16.00
     O    1774      8.00
     N    1505      7.00
     C    5577      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  26 " - pdb=" SG  CYS E  49 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 143 " - pdb=" SG  CYS E 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 180 " - pdb=" SG  CYS E 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 206 " - pdb=" SG  CYS E 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 258 " - pdb=" SG  CYS E 305 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 266 " - pdb=" SG  CYS E 303 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 274 " - pdb=" SG  CYS E 280 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 287 " - pdb=" SG  CYS E 292 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-4
      " NAG G   2 " - " MAN G   3 "
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG D 301 " - " ASN D  28 "
      " NAG F   1 " - " ASN E  33 "
      " NAG G   1 " - " ASN E  63 "
  Time building additional restraints: 2.45
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2124

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 22 sheets defined
      12.2% alpha, 29.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 29
    Processing helix  chain 'A' and resid 78 through 82
      removed outlier: 3.635A  pdb=" N   GLU A  82 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.854A  pdb=" N   PHE B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 128
    Processing helix  chain 'B' and resid 182 through 189
    Processing helix  chain 'C' and resid 61 through 64
      removed outlier: 3.629A  pdb=" N   LYS C  64 " --> pdb=" O   ASP C  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 61 through 64'
    Processing helix  chain 'C' and resid 73 through 75
      No H-bonds generated for 'chain 'C' and resid 73 through 75'
    Processing helix  chain 'C' and resid 86 through 90
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.918A  pdb=" N   ASN D  32 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 193 through 197
    Processing helix  chain 'E' and resid 43 through 53
    Processing helix  chain 'E' and resid 54 through 65
    Processing helix  chain 'E' and resid 76 through 80
    Processing helix  chain 'E' and resid 87 through 92
      removed outlier: 4.005A  pdb=" N   ARG E  91 " --> pdb=" O   ASN E  87 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   TRP E  92 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 87 through 92'
    Processing helix  chain 'E' and resid 97 through 104
    Processing helix  chain 'E' and resid 160 through 163
    Processing helix  chain 'E' and resid 168 through 170
      No H-bonds generated for 'chain 'E' and resid 168 through 170'
    Processing helix  chain 'E' and resid 187 through 202
    Processing helix  chain 'E' and resid 252 through 254
      No H-bonds generated for 'chain 'E' and resid 252 through 254'
    Processing helix  chain 'E' and resid 267 through 278
      removed outlier: 3.797A  pdb=" N   GLY E 278 " --> pdb=" O   CYS E 274 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 283 through 291
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6
    Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 47
      removed outlier: 6.623A  pdb=" N   TRP A  34 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 148
    Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6
      removed outlier: 3.602A  pdb=" N   ASP B  70 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 14
      removed outlier: 6.338A  pdb=" N   LEU B  11 " --> pdb=" O   GLN B 105 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   LYS B 107 " --> pdb=" O   LEU B  11 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ALA B  13 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LEU B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   TYR B  49 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 114 through 118
      removed outlier: 5.387A  pdb=" N   VAL B 133 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   LEU B 179 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 5.441A  pdb=" N   LEU B 135 " --> pdb=" O   SER B 177 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   SER B 177 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 5.410A  pdb=" N   ASN B 137 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   LEU B 175 " --> pdb=" O   ASN B 137 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.996A  pdb=" N   TYR C  33 " --> pdb=" O   ALA C  98 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   MET C  34 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   VAL C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.751A  pdb=" N   LEU C 108 " --> pdb=" O   ARG C  97 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 127 through 129
      removed outlier: 5.976A  pdb=" N   TYR C 182 " --> pdb=" O   ASP C 150 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 127 through 129
      removed outlier: 5.976A  pdb=" N   TYR C 182 " --> pdb=" O   ASP C 150 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 156 through 157
      removed outlier: 3.507A  pdb=" N   ASN C 205 " --> pdb=" O   THR C 157 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 5
    Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12
      removed outlier: 3.795A  pdb=" N   THR D 119 " --> pdb=" O   GLU D  10 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   TRP D  33 " --> pdb=" O   LEU D  99 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ILE D  34 " --> pdb=" O   ILE D  50 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   ILE D  50 " --> pdb=" O   ILE D  34 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   TRP D  36 " --> pdb=" O   MET D  48 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 9 through 12
      removed outlier: 3.795A  pdb=" N   THR D 119 " --> pdb=" O   GLU D  10 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   CYS D  96 " --> pdb=" O   TRP D 112 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   TRP D 112 " --> pdb=" O   CYS D  96 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ARG D  98 " --> pdb=" O   ASP D 110 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR D 106 " --> pdb=" O   ARG D 102 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 70 through 71
      removed outlier: 6.668A  pdb=" N   TYR E  70 " --> pdb=" O   LEU E 167 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'E' and resid 81 through 83
      removed outlier: 6.631A  pdb=" N   SER E  81 " --> pdb=" O   TRP E 174 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   PHE E 129 " --> pdb=" O   LEU E 173 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   ILE E 175 " --> pdb=" O   PHE E 129 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   GLU E 131 " --> pdb=" O   ILE E 175 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   LYS E 110 " --> pdb=" O   GLY E 140 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   GLY E 142 " --> pdb=" O   LYS E 110 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 147 through 149
    Processing sheet with id=AC1, first strand: chain 'E' and resid 177 through 180
      removed outlier: 6.656A  pdb=" N   MET E 334 " --> pdb=" O   ILE E 208 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   ILE E 208 " --> pdb=" O   MET E 334 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   THR E 336 " --> pdb=" O   CYS E 206 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 177 through 180
      removed outlier: 4.007A  pdb=" N   ALA E 228 " --> pdb=" O   MET E 240 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 244 through 248
    Processing sheet with id=AC4, first strand: chain 'E' and resid 256 through 259
      removed outlier: 6.906A  pdb=" N   ARG E 281 " --> pdb=" O   CYS E 305 " (cutoff:3.500A)
      removed outlier: 8.873A  pdb=" N   LEU E 307 " --> pdb=" O   ARG E 281 " (cutoff:3.500A)

    276 hydrogen bonds defined for protein.
    663 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: 2.39

  Time building geometry restraints manager: 2.86 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2863
        1.34 -     1.46: 2187
        1.46 -     1.58: 3997
        1.58 -     1.70: 2
        1.70 -     1.82: 63
  Bond restraints: 9112
  Sorted by residual:
  bond pdb=" C1  NAG F   1 "
       pdb=" O5  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.489 -0.083 2.00e-02 2.50e+03 1.73e+01
  bond pdb=" C1  MAN G   3 "
       pdb=" C2  MAN G   3 "
    ideal  model  delta    sigma   weight residual
    1.526  1.596 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" C1  MAN G   3 "
       pdb=" O5  MAN G   3 "
    ideal  model  delta    sigma   weight residual
    1.399  1.451 -0.052 2.00e-02 2.50e+03 6.89e+00
  bond pdb=" CB  PRO D 176 "
       pdb=" CG  PRO D 176 "
    ideal  model  delta    sigma   weight residual
    1.492  1.586 -0.094 5.00e-02 4.00e+02 3.54e+00
  bond pdb=" C1  NAG D 301 "
       pdb=" O5  NAG D 301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.75e+00
  ... (remaining 9107 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 12064
        1.76 -     3.52: 248
        3.52 -     5.28: 46
        5.28 -     7.04: 11
        7.04 -     8.79: 4
  Bond angle restraints: 12373
  Sorted by residual:
  angle pdb=" C   PRO D 156 "
        pdb=" N   GLU D 157 "
        pdb=" CA  GLU D 157 "
      ideal   model   delta    sigma   weight residual
     122.28  116.79    5.49 1.02e+00 9.61e-01 2.90e+01
  angle pdb=" CB  LYS D  13 "
        pdb=" CG  LYS D  13 "
        pdb=" CD  LYS D  13 "
      ideal   model   delta    sigma   weight residual
     111.30  120.09   -8.79 2.30e+00 1.89e-01 1.46e+01
  angle pdb=" CA  PRO D 176 "
        pdb=" N   PRO D 176 "
        pdb=" CD  PRO D 176 "
      ideal   model   delta    sigma   weight residual
     112.00  106.83    5.17 1.40e+00 5.10e-01 1.36e+01
  angle pdb=" CA  ARG E  91 "
        pdb=" CB  ARG E  91 "
        pdb=" CG  ARG E  91 "
      ideal   model   delta    sigma   weight residual
     114.10  121.35   -7.25 2.00e+00 2.50e-01 1.31e+01
  angle pdb=" N   GLU D 157 "
        pdb=" CA  GLU D 157 "
        pdb=" C   GLU D 157 "
      ideal   model   delta    sigma   weight residual
     110.73  115.38   -4.65 1.55e+00 4.16e-01 9.00e+00
  ... (remaining 12368 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.38: 5059
       23.38 -    46.77: 374
       46.77 -    70.15: 69
       70.15 -    93.53: 11
       93.53 -   116.92: 25
  Dihedral angle restraints: 5538
    sinusoidal: 2208
      harmonic: 3330
  Sorted by residual:
  dihedral pdb=" CB  CYS E 266 "
           pdb=" SG  CYS E 266 "
           pdb=" SG  CYS E 303 "
           pdb=" CB  CYS E 303 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -131.28   45.28     1      1.00e+01 1.00e-02 2.85e+01
  dihedral pdb=" CB  CYS B  23 "
           pdb=" SG  CYS B  23 "
           pdb=" SG  CYS B  88 "
           pdb=" CB  CYS B  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   59.92   33.08     1      1.00e+01 1.00e-02 1.56e+01
  dihedral pdb=" C1  NAG F   1 "
           pdb=" C5  NAG F   1 "
           pdb=" O5  NAG F   1 "
           pdb=" C4  NAG F   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.11   52.81 -116.92     1      3.00e+01 1.11e-03 1.55e+01
  ... (remaining 5535 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.158: 1379
       0.158 -    0.316: 1
       0.316 -    0.474: 0
       0.474 -    0.631: 0
       0.631 -    0.789: 1
  Chirality restraints: 1381
  Sorted by residual:
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN E  33 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.61   -0.79 2.00e-01 2.50e+01 1.56e+01
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN E  63 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 9.60e-01
  chirality pdb=" C1  NAG D 301 "
            pdb=" ND2 ASN D  28 "
            pdb=" C2  NAG D 301 "
            pdb=" O5  NAG D 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-01 2.50e+01 5.08e-01
  ... (remaining 1378 not shown)

  Planarity restraints: 1588
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 207 "    0.052 5.00e-02 4.00e+02   7.82e-02 9.78e+00
        pdb=" N   PRO C 208 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO C 208 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO C 208 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  38 "    0.041 5.00e-02 4.00e+02   6.11e-02 5.97e+00
        pdb=" N   PRO A  39 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A  39 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A  39 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D  13 "   -0.036 5.00e-02 4.00e+02   5.54e-02 4.91e+00
        pdb=" N   PRO D  14 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO D  14 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D  14 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1585 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 521
        2.72 -     3.27: 8817
        3.27 -     3.81: 14970
        3.81 -     4.36: 18808
        4.36 -     4.90: 31257
  Nonbonded interactions: 74373
  Sorted by model distance:
  nonbonded pdb=" O   ILE C  27 "
            pdb=" ND2 ASN C  76 "
     model   vdw
     2.181 3.120
  nonbonded pdb=" O   ASN A 131 "
            pdb=" OG  SER A 193 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" N   GLU B 143 "
            pdb=" OE1 GLU B 143 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" N   GLN D  67 "
            pdb=" OE1 GLN D  67 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" OD2 ASP B 170 "
            pdb=" OG1 THR B 172 "
     model   vdw
     2.236 3.040
  ... (remaining 74368 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.390
  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:             0.020
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.540
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  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:12.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094   9130  Z= 0.168
  Angle     :  0.680  15.887  12415  Z= 0.339
  Chirality :  0.049   0.789   1381
  Planarity :  0.006   0.078   1585
  Dihedral  : 18.661 116.916   3378
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 19.33 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.25), residues: 1150
  helix:  0.89 (0.52), residues: 100
  sheet: -0.12 (0.30), residues: 322
  loop : -1.21 (0.23), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 141 
 HIS   0.004   0.001   HIS E  56 
 PHE   0.015   0.001   PHE E 130 
 TYR   0.012   0.001   TYR E  83 
 ARG   0.010   0.001   ARG E  74 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00836 (    3)
  link_NAG-ASN         : angle       6.59895 (    9)
  link_ALPHA1-4        : bond        0.01258 (    1)
  link_ALPHA1-4        : angle       1.24273 (    3)
  link_BETA1-4         : bond        0.01335 (    2)
  link_BETA1-4         : angle       5.80367 (    6)
  hydrogen bonds       : bond        0.13393 (  254)
  hydrogen bonds       : angle       6.76483 (  663)
  SS BOND              : bond        0.00261 (   12)
  SS BOND              : angle       0.72095 (   24)
  covalent geometry    : bond        0.00384 ( 9112)
  covalent geometry    : angle       0.64438 (12373)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 105
  time to evaluate  : 0.951 
Fit side-chains
REVERT: D   67 GLN cc_start: 0.8686 (mp10) cc_final: 0.8306 (mt0)
  outliers start: 34
  outliers final: 26
  residues processed: 134
  average time/residue: 1.3261
  time to fit residues: 189.1105
Evaluate side-chains
  130 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  202 CYS
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  161 VAL
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  207 VAL
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue  100 ASP
Chi-restraints excluded: chain E residue  323 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0980
   chunk 48 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 90 optimal weight:    0.0020
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9980
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
B 137 ASN
B 189 HIS
C 113 ASN
D  82 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.142012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.082289 restraints weight = 13234.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 2.68
r_work: 0.2967 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.0658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9130  Z= 0.131
  Angle     :  0.656  12.586  12415  Z= 0.322
  Chirality :  0.046   0.332   1381
  Planarity :  0.005   0.061   1585
  Dihedral  : 13.719 102.870   1410
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 17.31 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.25), residues: 1150
  helix:  1.23 (0.54), residues: 100
  sheet:  0.01 (0.30), residues: 320
  loop : -1.18 (0.23), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 141 
 HIS   0.004   0.001   HIS E  56 
 PHE   0.013   0.001   PHE E 130 
 TYR   0.012   0.001   TYR E  83 
 ARG   0.006   0.001   ARG E  74 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00631 (    3)
  link_NAG-ASN         : angle       5.07725 (    9)
  link_ALPHA1-4        : bond        0.00876 (    1)
  link_ALPHA1-4        : angle       1.70910 (    3)
  link_BETA1-4         : bond        0.00960 (    2)
  link_BETA1-4         : angle       4.20995 (    6)
  hydrogen bonds       : bond        0.03319 (  254)
  hydrogen bonds       : angle       5.42597 (  663)
  SS BOND              : bond        0.00192 (   12)
  SS BOND              : angle       0.67774 (   24)
  covalent geometry    : bond        0.00303 ( 9112)
  covalent geometry    : angle       0.63482 (12373)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 115
  time to evaluate  : 0.949 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8111 (tp30) cc_final: 0.7906 (tp30)
REVERT: B  190 LYS cc_start: 0.8540 (mptt) cc_final: 0.8299 (mmmt)
REVERT: C   72 ASP cc_start: 0.8332 (t0) cc_final: 0.7966 (t70)
REVERT: D   19 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7985 (tttp)
REVERT: D   65 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8699 (mmtt)
REVERT: D   67 GLN cc_start: 0.8564 (mp10) cc_final: 0.8268 (mt0)
REVERT: D  100 TYR cc_start: 0.9018 (t80) cc_final: 0.8811 (t80)
  outliers start: 49
  outliers final: 28
  residues processed: 151
  average time/residue: 1.2842
  time to fit residues: 206.5340
Evaluate side-chains
  139 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 109
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  105 LYS
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain B residue  137 ASN
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain D residue   46 GLU
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue   82 GLN
Chi-restraints excluded: chain D residue   93 ILE
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  161 VAL
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  207 VAL
Chi-restraints excluded: chain E residue  248 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 84 optimal weight:    0.0270
   chunk 106 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0030
   chunk 94 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 19 optimal weight:   30.0000
   chunk 69 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.4648

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
B 137 ASN
C 113 ASN
C 177 GLN
E  87 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.142606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.082393 restraints weight = 13544.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 2.77
r_work: 0.2968 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.0938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9130  Z= 0.122
  Angle     :  0.609   7.625  12415  Z= 0.305
  Chirality :  0.045   0.261   1381
  Planarity :  0.005   0.051   1585
  Dihedral  : 11.853  97.627   1396
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 17.91 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.25), residues: 1150
  helix:  1.31 (0.54), residues: 100
  sheet:  0.04 (0.30), residues: 320
  loop : -1.15 (0.23), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 141 
 HIS   0.003   0.001   HIS C 206 
 PHE   0.012   0.001   PHE E 130 
 TYR   0.012   0.001   TYR D 100 
 ARG   0.006   0.001   ARG E  74 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00201 (    3)
  link_NAG-ASN         : angle       2.33265 (    9)
  link_ALPHA1-4        : bond        0.00894 (    1)
  link_ALPHA1-4        : angle       1.76752 (    3)
  link_BETA1-4         : bond        0.01028 (    2)
  link_BETA1-4         : angle       4.12638 (    6)
  hydrogen bonds       : bond        0.03164 (  254)
  hydrogen bonds       : angle       5.22044 (  663)
  SS BOND              : bond        0.00186 (   12)
  SS BOND              : angle       0.68400 (   24)
  covalent geometry    : bond        0.00280 ( 9112)
  covalent geometry    : angle       0.59820 (12373)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 111
  time to evaluate  : 1.013 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8099 (tp30) cc_final: 0.7866 (tp30)
REVERT: A   82 GLU cc_start: 0.9060 (tt0) cc_final: 0.8820 (mt-10)
REVERT: B  190 LYS cc_start: 0.8513 (mptt) cc_final: 0.8281 (mmmt)
REVERT: C   72 ASP cc_start: 0.8361 (t0) cc_final: 0.7981 (t70)
REVERT: D   19 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.7935 (ttpp)
REVERT: D   65 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8582 (mmtt)
REVERT: D   67 GLN cc_start: 0.8494 (mp10) cc_final: 0.8248 (mt0)
REVERT: D   82 GLN cc_start: 0.8191 (pt0) cc_final: 0.7161 (mp10)
REVERT: D  100 TYR cc_start: 0.8936 (t80) cc_final: 0.8727 (t80)
  outliers start: 52
  outliers final: 26
  residues processed: 150
  average time/residue: 1.2970
  time to fit residues: 207.2222
Evaluate side-chains
  139 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain D residue   46 GLU
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue   93 ILE
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  161 VAL
Chi-restraints excluded: chain D residue  168 LEU
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  207 VAL
Chi-restraints excluded: chain E residue  248 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 110 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
A 170 GLN
C 113 ASN
D  39 GLN
D  82 GLN
E  87 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.141432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.081637 restraints weight = 13316.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 2.69
r_work: 0.2959 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.0998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9130  Z= 0.161
  Angle     :  0.633   8.331  12415  Z= 0.316
  Chirality :  0.046   0.289   1381
  Planarity :  0.005   0.051   1585
  Dihedral  : 11.226  92.420   1392
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 17.81 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.25), residues: 1150
  helix:  1.02 (0.55), residues: 100
  sheet:  0.09 (0.30), residues: 318
  loop : -1.13 (0.23), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 141 
 HIS   0.005   0.001   HIS E  56 
 PHE   0.015   0.001   PHE E 130 
 TYR   0.013   0.001   TYR C 104 
 ARG   0.006   0.001   ARG E  74 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00415 (    3)
  link_NAG-ASN         : angle       2.32356 (    9)
  link_ALPHA1-4        : bond        0.01174 (    1)
  link_ALPHA1-4        : angle       1.84086 (    3)
  link_BETA1-4         : bond        0.00993 (    2)
  link_BETA1-4         : angle       4.33727 (    6)
  hydrogen bonds       : bond        0.03261 (  254)
  hydrogen bonds       : angle       5.16556 (  663)
  SS BOND              : bond        0.00279 (   12)
  SS BOND              : angle       0.87891 (   24)
  covalent geometry    : bond        0.00376 ( 9112)
  covalent geometry    : angle       0.62156 (12373)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 114
  time to evaluate  : 1.043 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8177 (tp30) cc_final: 0.7962 (tp30)
REVERT: A   82 GLU cc_start: 0.9094 (tt0) cc_final: 0.8887 (mt-10)
REVERT: B  190 LYS cc_start: 0.8482 (mptt) cc_final: 0.8227 (mmmt)
REVERT: C   72 ASP cc_start: 0.8368 (t0) cc_final: 0.8009 (t0)
REVERT: D   43 LYS cc_start: 0.8967 (ttmm) cc_final: 0.8754 (mmmm)
REVERT: D   65 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8739 (mmtt)
REVERT: D   82 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7659 (pm20)
REVERT: D  100 TYR cc_start: 0.8868 (t80) cc_final: 0.8633 (t80)
  outliers start: 48
  outliers final: 24
  residues processed: 149
  average time/residue: 1.3261
  time to fit residues: 210.1157
Evaluate side-chains
  137 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   46 GLU
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue   82 GLN
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  161 VAL
Chi-restraints excluded: chain D residue  168 LEU
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  207 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  323 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 110 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0970
   chunk 48 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9980
   chunk 109 optimal weight:    0.9980
   chunk 112 optimal weight:    0.6980
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
C 113 ASN
D  39 GLN
D  82 GLN
E  87 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.142636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.083640 restraints weight = 13600.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 2.72
r_work: 0.2973 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.1093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9130  Z= 0.139
  Angle     :  0.624   8.769  12415  Z= 0.311
  Chirality :  0.046   0.289   1381
  Planarity :  0.005   0.049   1585
  Dihedral  : 10.677  89.512   1388
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 18.72 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.25), residues: 1150
  helix:  0.90 (0.53), residues: 106
  sheet:  0.06 (0.30), residues: 318
  loop : -1.13 (0.23), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 141 
 HIS   0.004   0.001   HIS E  56 
 PHE   0.013   0.001   PHE E 130 
 TYR   0.012   0.001   TYR D 100 
 ARG   0.008   0.001   ARG E 322 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00332 (    3)
  link_NAG-ASN         : angle       2.11696 (    9)
  link_ALPHA1-4        : bond        0.01096 (    1)
  link_ALPHA1-4        : angle       1.87949 (    3)
  link_BETA1-4         : bond        0.01024 (    2)
  link_BETA1-4         : angle       4.30554 (    6)
  hydrogen bonds       : bond        0.03109 (  254)
  hydrogen bonds       : angle       5.11539 (  663)
  SS BOND              : bond        0.00239 (   12)
  SS BOND              : angle       0.77770 (   24)
  covalent geometry    : bond        0.00323 ( 9112)
  covalent geometry    : angle       0.61334 (12373)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 111
  time to evaluate  : 0.936 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8175 (tp30) cc_final: 0.7966 (tp30)
REVERT: A   82 GLU cc_start: 0.9066 (tt0) cc_final: 0.8854 (mt-10)
REVERT: B  190 LYS cc_start: 0.8492 (mptt) cc_final: 0.8228 (mmmt)
REVERT: C   72 ASP cc_start: 0.8448 (t0) cc_final: 0.8094 (t0)
REVERT: D   65 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8574 (mmtt)
REVERT: D   67 GLN cc_start: 0.8494 (mp10) cc_final: 0.8208 (mt0)
REVERT: D   82 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7751 (pm20)
  outliers start: 42
  outliers final: 24
  residues processed: 141
  average time/residue: 1.3321
  time to fit residues: 199.7012
Evaluate side-chains
  136 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  216 LYS
Chi-restraints excluded: chain D residue   46 GLU
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue   82 GLN
Chi-restraints excluded: chain D residue   93 ILE
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  161 VAL
Chi-restraints excluded: chain D residue  168 LEU
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  207 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  323 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0370
   chunk 98 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    1.3864

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
C 113 ASN
C 203 ASN
D  39 GLN
D  82 GLN
E  68 GLN
E  87 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.140123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.078366 restraints weight = 13276.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 2.85
r_work: 0.2826 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2693 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9130  Z= 0.203
  Angle     :  0.674   9.805  12415  Z= 0.332
  Chirality :  0.048   0.331   1381
  Planarity :  0.005   0.050   1585
  Dihedral  : 10.503  87.071   1387
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 18.83 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.25), residues: 1150
  helix:  0.80 (0.53), residues: 106
  sheet:  0.01 (0.30), residues: 318
  loop : -1.16 (0.23), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 163 
 HIS   0.006   0.001   HIS E  56 
 PHE   0.016   0.001   PHE E 130 
 TYR   0.017   0.001   TYR D 100 
 ARG   0.005   0.001   ARG E 322 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00540 (    3)
  link_NAG-ASN         : angle       2.77357 (    9)
  link_ALPHA1-4        : bond        0.01567 (    1)
  link_ALPHA1-4        : angle       2.01340 (    3)
  link_BETA1-4         : bond        0.00916 (    2)
  link_BETA1-4         : angle       4.73713 (    6)
  hydrogen bonds       : bond        0.03426 (  254)
  hydrogen bonds       : angle       5.20006 (  663)
  SS BOND              : bond        0.00391 (   12)
  SS BOND              : angle       1.10455 (   24)
  covalent geometry    : bond        0.00474 ( 9112)
  covalent geometry    : angle       0.66061 (12373)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 111
  time to evaluate  : 0.973 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8199 (tp30) cc_final: 0.7769 (tp30)
REVERT: A   82 GLU cc_start: 0.9104 (tt0) cc_final: 0.8900 (mt-10)
REVERT: B  190 LYS cc_start: 0.8505 (mptt) cc_final: 0.8257 (mmmt)
REVERT: C   72 ASP cc_start: 0.8325 (t0) cc_final: 0.7927 (t0)
REVERT: D   65 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8601 (mmtt)
REVERT: D   67 GLN cc_start: 0.8514 (mp10) cc_final: 0.8242 (mt0)
  outliers start: 43
  outliers final: 24
  residues processed: 144
  average time/residue: 1.3305
  time to fit residues: 204.3285
Evaluate side-chains
  136 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   46 GLU
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  168 LEU
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  207 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  323 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 54 optimal weight:    5.9990
   chunk 102 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:   20.0000
   chunk 95 optimal weight:    2.9990
   chunk 76 optimal weight:   20.0000
   chunk 20 optimal weight:    2.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
A 170 GLN
C 113 ASN
** D  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.138070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.075479 restraints weight = 13426.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 2.89
r_work: 0.2773 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2640 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060   9130  Z= 0.314
  Angle     :  0.751   9.934  12415  Z= 0.368
  Chirality :  0.052   0.442   1381
  Planarity :  0.005   0.052   1585
  Dihedral  : 10.666  84.393   1386
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 18.72 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.25), residues: 1150
  helix:  0.44 (0.51), residues: 106
  sheet:  0.11 (0.30), residues: 315
  loop : -1.27 (0.23), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D 163 
 HIS   0.006   0.001   HIS E  56 
 PHE   0.020   0.002   PHE E 130 
 TYR   0.018   0.002   TYR C 104 
 ARG   0.010   0.001   ARG E 322 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00881 (    3)
  link_NAG-ASN         : angle       4.01427 (    9)
  link_ALPHA1-4        : bond        0.01729 (    1)
  link_ALPHA1-4        : angle       2.34857 (    3)
  link_BETA1-4         : bond        0.01024 (    2)
  link_BETA1-4         : angle       5.37696 (    6)
  hydrogen bonds       : bond        0.03973 (  254)
  hydrogen bonds       : angle       5.39100 (  663)
  SS BOND              : bond        0.00504 (   12)
  SS BOND              : angle       1.42658 (   24)
  covalent geometry    : bond        0.00738 ( 9112)
  covalent geometry    : angle       0.73102 (12373)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 108
  time to evaluate  : 1.113 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8274 (tp30) cc_final: 0.8003 (tp30)
REVERT: A   82 GLU cc_start: 0.9122 (tt0) cc_final: 0.8901 (mt-10)
REVERT: B  190 LYS cc_start: 0.8473 (mptt) cc_final: 0.8220 (mmmt)
REVERT: C  211 THR cc_start: 0.7937 (m) cc_final: 0.7732 (m)
REVERT: E   91 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6937 (tpt170)
  outliers start: 40
  outliers final: 25
  residues processed: 139
  average time/residue: 1.4010
  time to fit residues: 206.7072
Evaluate side-chains
  124 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  216 LYS
Chi-restraints excluded: chain D residue   46 GLU
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  168 LEU
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  207 VAL
Chi-restraints excluded: chain E residue   91 ARG
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  323 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9990
   chunk 93 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 12 optimal weight:   30.0000
   chunk 32 optimal weight:    5.9990
   chunk 77 optimal weight:    9.9990
   chunk 109 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
C 113 ASN
** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.140999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.081563 restraints weight = 13842.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 2.74
r_work: 0.2932 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2816 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.1269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9130  Z= 0.174
  Angle     :  0.678   9.226  12415  Z= 0.335
  Chirality :  0.047   0.347   1381
  Planarity :  0.005   0.053   1585
  Dihedral  : 10.307  83.462   1386
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.14 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.25), residues: 1150
  helix:  1.07 (0.53), residues: 100
  sheet: -0.05 (0.30), residues: 313
  loop : -1.19 (0.23), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 163 
 HIS   0.005   0.001   HIS E  56 
 PHE   0.015   0.001   PHE E 130 
 TYR   0.017   0.001   TYR D 154 
 ARG   0.014   0.001   ARG E 322 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00439 (    3)
  link_NAG-ASN         : angle       3.02057 (    9)
  link_ALPHA1-4        : bond        0.01409 (    1)
  link_ALPHA1-4        : angle       1.87813 (    3)
  link_BETA1-4         : bond        0.01108 (    2)
  link_BETA1-4         : angle       4.71980 (    6)
  hydrogen bonds       : bond        0.03278 (  254)
  hydrogen bonds       : angle       5.22228 (  663)
  SS BOND              : bond        0.00293 (   12)
  SS BOND              : angle       0.95463 (   24)
  covalent geometry    : bond        0.00407 ( 9112)
  covalent geometry    : angle       0.66446 (12373)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 103
  time to evaluate  : 1.391 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8275 (tp30) cc_final: 0.7891 (tp30)
REVERT: A   60 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7850 (ptt90)
REVERT: A   80 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7493 (tm-30)
REVERT: B  190 LYS cc_start: 0.8474 (mptt) cc_final: 0.8204 (mmmt)
REVERT: C   72 ASP cc_start: 0.8473 (t0) cc_final: 0.8006 (t70)
REVERT: D   67 GLN cc_start: 0.8503 (mp10) cc_final: 0.8045 (mt0)
  outliers start: 31
  outliers final: 21
  residues processed: 128
  average time/residue: 1.5980
  time to fit residues: 218.1047
Evaluate side-chains
  124 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   60 ARG
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   46 GLU
Chi-restraints excluded: chain D residue  168 LEU
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  207 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  323 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0980
   chunk 110 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 18 optimal weight:   20.0000
   chunk 50 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 105 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
C 113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.141168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.081112 restraints weight = 13530.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 2.77
r_work: 0.2944 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9130  Z= 0.139
  Angle     :  0.677  10.743  12415  Z= 0.334
  Chirality :  0.047   0.317   1381
  Planarity :  0.005   0.050   1585
  Dihedral  :  9.651  80.299   1383
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 20.14 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.25), residues: 1150
  helix:  1.39 (0.55), residues: 94
  sheet:  0.02 (0.30), residues: 311
  loop : -1.20 (0.23), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 163 
 HIS   0.003   0.001   HIS E  56 
 PHE   0.013   0.001   PHE E 130 
 TYR   0.017   0.001   TYR D 154 
 ARG   0.009   0.001   ARG E  74 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00384 (    3)
  link_NAG-ASN         : angle       2.48958 (    9)
  link_ALPHA1-4        : bond        0.01148 (    1)
  link_ALPHA1-4        : angle       2.06677 (    3)
  link_BETA1-4         : bond        0.01219 (    2)
  link_BETA1-4         : angle       4.72638 (    6)
  hydrogen bonds       : bond        0.03041 (  254)
  hydrogen bonds       : angle       5.09263 (  663)
  SS BOND              : bond        0.00229 (   12)
  SS BOND              : angle       0.84034 (   24)
  covalent geometry    : bond        0.00324 ( 9112)
  covalent geometry    : angle       0.66503 (12373)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.951 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8265 (tp30) cc_final: 0.7875 (tp30)
REVERT: A   60 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7884 (ptt90)
REVERT: B  190 LYS cc_start: 0.8453 (mptt) cc_final: 0.8240 (mmmt)
REVERT: C   72 ASP cc_start: 0.8455 (t0) cc_final: 0.7980 (t70)
REVERT: D   67 GLN cc_start: 0.8477 (mp10) cc_final: 0.8003 (mt0)
  outliers start: 29
  outliers final: 21
  residues processed: 127
  average time/residue: 1.5330
  time to fit residues: 206.8481
Evaluate side-chains
  126 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   60 ARG
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain D residue   46 GLU
Chi-restraints excluded: chain D residue  168 LEU
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  207 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  323 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 112 optimal weight:    0.4980
   chunk 72 optimal weight:    0.9980
   chunk 82 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0670
   chunk 114 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.5122

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
C 113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.139303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.078520 restraints weight = 13493.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 2.75
r_work: 0.2813 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9130  Z= 0.222
  Angle     :  0.726  10.074  12415  Z= 0.358
  Chirality :  0.049   0.380   1381
  Planarity :  0.005   0.064   1585
  Dihedral  :  9.487  77.891   1383
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 20.14 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.25), residues: 1150
  helix:  1.24 (0.54), residues: 94
  sheet:  0.05 (0.30), residues: 308
  loop : -1.22 (0.23), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 163 
 HIS   0.006   0.001   HIS E  56 
 PHE   0.017   0.002   PHE E 130 
 TYR   0.018   0.002   TYR D 154 
 ARG   0.016   0.001   ARG E 322 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00557 (    3)
  link_NAG-ASN         : angle       3.08771 (    9)
  link_ALPHA1-4        : bond        0.01380 (    1)
  link_ALPHA1-4        : angle       2.36936 (    3)
  link_BETA1-4         : bond        0.01099 (    2)
  link_BETA1-4         : angle       5.13241 (    6)
  hydrogen bonds       : bond        0.03455 (  254)
  hydrogen bonds       : angle       5.16163 (  663)
  SS BOND              : bond        0.00378 (   12)
  SS BOND              : angle       1.11372 (   24)
  covalent geometry    : bond        0.00523 ( 9112)
  covalent geometry    : angle       0.71078 (12373)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8299 (tp30) cc_final: 0.7884 (tp30)
REVERT: A   60 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7680 (ptt90)
REVERT: B  190 LYS cc_start: 0.8468 (mptt) cc_final: 0.8179 (mmtt)
REVERT: C   72 ASP cc_start: 0.8329 (t0) cc_final: 0.7832 (t70)
REVERT: C  211 THR cc_start: 0.7998 (m) cc_final: 0.7779 (m)
REVERT: D   67 GLN cc_start: 0.8530 (mp10) cc_final: 0.8075 (mt0)
  outliers start: 28
  outliers final: 21
  residues processed: 124
  average time/residue: 1.3399
  time to fit residues: 176.4464
Evaluate side-chains
  122 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   60 ARG
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   46 GLU
Chi-restraints excluded: chain D residue  168 LEU
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  207 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  323 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 60 optimal weight:    8.9990
   chunk 101 optimal weight:    0.5980
   chunk 80 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0070
   chunk 79 optimal weight:    8.9990
   chunk 107 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    1.1002

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
C 113 ASN
D  61 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.140045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.079454 restraints weight = 13461.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.78
r_work: 0.2824 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2693 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9130  Z= 0.177
  Angle     :  0.701  10.003  12415  Z= 0.347
  Chirality :  0.048   0.355   1381
  Planarity :  0.005   0.053   1585
  Dihedral  :  9.306  76.984   1383
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 20.65 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.25), residues: 1150
  helix:  1.31 (0.54), residues: 94
  sheet:  0.03 (0.30), residues: 308
  loop : -1.20 (0.23), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 163 
 HIS   0.005   0.001   HIS E  56 
 PHE   0.015   0.001   PHE E 130 
 TYR   0.017   0.001   TYR D 154 
 ARG   0.011   0.001   ARG E  74 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00470 (    3)
  link_NAG-ASN         : angle       2.87349 (    9)
  link_ALPHA1-4        : bond        0.01272 (    1)
  link_ALPHA1-4        : angle       2.25932 (    3)
  link_BETA1-4         : bond        0.01185 (    2)
  link_BETA1-4         : angle       4.98198 (    6)
  hydrogen bonds       : bond        0.03249 (  254)
  hydrogen bonds       : angle       5.13730 (  663)
  SS BOND              : bond        0.00304 (   12)
  SS BOND              : angle       0.96735 (   24)
  covalent geometry    : bond        0.00419 ( 9112)
  covalent geometry    : angle       0.68742 (12373)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11867.35 seconds
wall clock time: 205 minutes 1.45 seconds (12301.45 seconds total)