Starting phenix.real_space_refine
on Sun Jun  8 22:05:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u1u_41829/06_2025/8u1u_41829.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u1u_41829/06_2025/8u1u_41829.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u1u_41829/06_2025/8u1u_41829.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u1u_41829/06_2025/8u1u_41829.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u1u_41829/06_2025/8u1u_41829.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u1u_41829/06_2025/8u1u_41829.cif"
  }
  resolution = 3.1
  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=   0.007 sd=   1.145
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 543 atoms to isotropic.
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      75      5.16       5
     C    6065      2.51       5
     N    1603      2.21       5
     O    1764      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9507
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2952
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 9, 'TRANS': 356}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1726
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 211}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "D"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "E"
      Number of atoms: 1785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1785
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "A"
      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: 6.10, per 1000 atoms: 0.64
  Number of scatterers: 9507
  At special positions: 0
  Unit cell: (91.377, 120.821, 144.173, 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      75     16.00
     O    1764      8.00
     N    1603      7.00
     C    6065      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  33 " - pdb=" SG  CYS A  57 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  38 " - pdb=" SG  CYS A 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A  91 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 121 " - pdb=" SG  CYS A 368 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 202 " - pdb=" SG  CYS A 279 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  25 " - pdb=" SG  CYS E  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 150 " - pdb=" SG  CYS E 220 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 900 " - " ASN A  52 "
  Time building additional restraints: 2.62
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2264

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 15 sheets defined
      38.1% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 79 through 88
    Processing helix  chain 'A' and resid 127 through 159
    Processing helix  chain 'A' and resid 164 through 182
    Processing helix  chain 'A' and resid 183 through 193
    Processing helix  chain 'A' and resid 197 through 233
      removed outlier: 4.102A  pdb=" N   MET A 201 " --> pdb=" O   PHE A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 242 through 267
      Proline residue:  A 263  - end of helix
    Processing helix  chain 'A' and resid 283 through 285
      No H-bonds generated for 'chain 'A' and resid 283 through 285'
    Processing helix  chain 'A' and resid 286 through 303
    Processing helix  chain 'A' and resid 303 through 324
    Processing helix  chain 'A' and resid 329 through 362
      removed outlier: 3.599A  pdb=" N   ILE A 333 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
      Proline residue:  A 349  - end of helix
    Processing helix  chain 'A' and resid 367 through 397
      removed outlier: 3.874A  pdb=" N   HIS A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   CYS A 389 " --> pdb=" O   SER A 385 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   CYS A 390 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
      Proline residue:  A 393  - end of helix
    Processing helix  chain 'A' and resid 400 through 410
      removed outlier: 3.898A  pdb=" N   LYS A 405 " --> pdb=" O   GLU A 401 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   HIS A 406 " --> pdb=" O   LYS A 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 33
      removed outlier: 3.761A  pdb=" N   GLU B  33 " --> pdb=" O   LYS B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 53
      removed outlier: 3.845A  pdb=" N   ILE B  49 " --> pdb=" O   GLY B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 216
      removed outlier: 4.442A  pdb=" N   ILE B 212 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 5.336A  pdb=" N   HIS B 213 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 230
      No H-bonds generated for 'chain 'B' and resid 228 through 230'
    Processing helix  chain 'B' and resid 242 through 255
    Processing helix  chain 'B' and resid 270 through 281
    Processing helix  chain 'B' and resid 282 through 286
      removed outlier: 3.690A  pdb=" N   ILE B 285 " --> pdb=" O   PRO B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 309
    Processing helix  chain 'B' and resid 329 through 351
    Processing helix  chain 'C' and resid 4 through 26
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'D' and resid 8 through 24
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'E' and resid 56 through 59
      removed outlier: 4.195A  pdb=" N   GLY E  59 " --> pdb=" O   SER E  56 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 56 through 59'
    Processing helix  chain 'E' and resid 77 through 79
      No H-bonds generated for 'chain 'E' and resid 77 through 79'
    Processing helix  chain 'E' and resid 90 through 94
    Processing helix  chain 'E' and resid 211 through 215
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33
    Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 52
    Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 273
    Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 191
      removed outlier: 3.618A  pdb=" N   MET B 198 " --> pdb=" O   THR B 187 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   PHE B 189 " --> pdb=" O   PHE B 196 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   LYS B  35 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   ILE B 222 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   CYS B 224 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   LEU B  39 " --> pdb=" O   CYS B 224 " (cutoff:3.500A)
      removed outlier: 8.580A  pdb=" N   ALA B 226 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ILE B 221 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   PHE B 267 " --> pdb=" O   ILE B 221 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   PHE B 223 " --> pdb=" O   PHE B 267 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ASN B 269 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL B 225 " --> pdb=" O   ASN B 269 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 51
    Processing sheet with id=AA6, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.560A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.076A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.302A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.903A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 229 through 234
      removed outlier: 3.618A  pdb=" N   SER C 245 " --> pdb=" O   THR C 249 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   THR C 249 " --> pdb=" O   SER C 245 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.648A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 6 through 10
    Processing sheet with id=AB4, first strand: chain 'E' and resid 14 through 15
      removed outlier: 6.825A  pdb=" N   MET E  37 " --> pdb=" O   TYR E  53 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   TYR E  53 " --> pdb=" O   MET E  37 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   TRP E  39 " --> pdb=" O   VAL E  51 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 131 through 132
    Processing sheet with id=AB6, first strand: chain 'E' and resid 138 through 139
      removed outlier: 6.717A  pdb=" N   LEU E 165 " --> pdb=" O   TYR E 181 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   TYR E 181 " --> pdb=" O   LEU E 165 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   TRP E 167 " --> pdb=" O   LEU E 179 " (cutoff:3.500A)

    498 hydrogen bonds defined for protein.
    1383 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.09

  Time building geometry restraints manager: 3.10 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: 3029
        1.34 -     1.46: 2225
        1.46 -     1.58: 4346
        1.58 -     1.70: 0
        1.70 -     1.82: 105
  Bond restraints: 9705
  Sorted by residual:
  bond pdb=" C   ARG E 209 "
       pdb=" N   LEU E 210 "
    ideal  model  delta    sigma   weight residual
    1.333  1.384 -0.050 1.33e-02 5.65e+03 1.44e+01
  bond pdb=" C   SER E 208 "
       pdb=" N   ARG E 209 "
    ideal  model  delta    sigma   weight residual
    1.331  1.285  0.045 1.34e-02 5.57e+03 1.14e+01
  bond pdb=" N   THR B   4 "
       pdb=" CA  THR B   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.24e+00
  bond pdb=" CA  SER A  58 "
       pdb=" CB  SER A  58 "
    ideal  model  delta    sigma   weight residual
    1.529  1.500  0.029 1.63e-02 3.76e+03 3.21e+00
  bond pdb=" N   ALA D   7 "
       pdb=" CA  ALA D   7 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.00e+00
  ... (remaining 9700 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 12320
        1.31 -     2.62: 652
        2.62 -     3.93: 111
        3.93 -     5.24: 34
        5.24 -     6.55: 13
  Bond angle restraints: 13130
  Sorted by residual:
  angle pdb=" C   ARG E 182 "
        pdb=" N   MET E 183 "
        pdb=" CA  MET E 183 "
      ideal   model   delta    sigma   weight residual
     121.54  128.09   -6.55 1.91e+00 2.74e-01 1.18e+01
  angle pdb=" C   GLN C   9 "
        pdb=" N   GLU C  10 "
        pdb=" CA  GLU C  10 "
      ideal   model   delta    sigma   weight residual
     121.14  115.58    5.56 1.75e+00 3.27e-01 1.01e+01
  angle pdb=" CG  ARG C 214 "
        pdb=" CD  ARG C 214 "
        pdb=" NE  ARG C 214 "
      ideal   model   delta    sigma   weight residual
     112.00  118.51   -6.51 2.20e+00 2.07e-01 8.75e+00
  angle pdb=" CA  SER A  58 "
        pdb=" C   SER A  58 "
        pdb=" O   SER A  58 "
      ideal   model   delta    sigma   weight residual
     119.79  116.46    3.33 1.18e+00 7.18e-01 7.94e+00
  angle pdb=" CA  GLU C  10 "
        pdb=" CB  GLU C  10 "
        pdb=" CG  GLU C  10 "
      ideal   model   delta    sigma   weight residual
     114.10  119.62   -5.52 2.00e+00 2.50e-01 7.62e+00
  ... (remaining 13125 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 5289
       17.67 -    35.33: 416
       35.33 -    53.00: 59
       53.00 -    70.66: 16
       70.66 -    88.32: 8
  Dihedral angle restraints: 5788
    sinusoidal: 2282
      harmonic: 3506
  Sorted by residual:
  dihedral pdb=" CB  CYS A 121 "
           pdb=" SG  CYS A 121 "
           pdb=" SG  CYS A 368 "
           pdb=" CB  CYS A 368 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.68  -88.32     1      1.00e+01 1.00e-02 9.32e+01
  dihedral pdb=" CA  ASP C 291 "
           pdb=" C   ASP C 291 "
           pdb=" N   PHE C 292 "
           pdb=" CA  PHE C 292 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.91  -28.09     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" CA  ILE A  47 "
           pdb=" C   ILE A  47 "
           pdb=" N   LEU A  48 "
           pdb=" CA  LEU A  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.01   26.99     0      5.00e+00 4.00e-02 2.91e+01
  ... (remaining 5785 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1141
       0.049 -    0.099: 280
       0.099 -    0.148: 68
       0.148 -    0.197: 6
       0.197 -    0.247: 1
  Chirality restraints: 1496
  Sorted by residual:
  chirality pdb=" C1  NAG A 900 "
            pdb=" ND2 ASN A  52 "
            pdb=" C2  NAG A 900 "
            pdb=" O5  NAG A 900 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CA  ILE E  61 "
            pdb=" N   ILE E  61 "
            pdb=" C   ILE E  61 "
            pdb=" CB  ILE E  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.01e-01
  chirality pdb=" CA  ILE C  81 "
            pdb=" N   ILE C  81 "
            pdb=" C   ILE C  81 "
            pdb=" CB  ILE C  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.34e-01
  ... (remaining 1493 not shown)

  Planarity restraints: 1650
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  85 "    0.214 9.50e-02 1.11e+02   9.59e-02 5.75e+00
        pdb=" NE  ARG A  85 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  85 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  85 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  85 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 346 "    0.018 2.00e-02 2.50e+03   1.60e-02 4.51e+00
        pdb=" CG  PHE A 346 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 346 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 346 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 346 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 346 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 346 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 203 "    0.011 2.00e-02 2.50e+03   1.41e-02 3.47e+00
        pdb=" CG  PHE E 203 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 203 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 203 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 203 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 203 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 203 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1647 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 103
        2.58 -     3.16: 8320
        3.16 -     3.74: 14938
        3.74 -     4.32: 21612
        4.32 -     4.90: 36045
  Nonbonded interactions: 81018
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 304 "
            pdb=" OG1 THR A 308 "
     model   vdw
     2.003 3.040
  nonbonded pdb=" OG1 THR C  29 "
            pdb=" OE1 GLN C  32 "
     model   vdw
     2.036 3.040
  nonbonded pdb=" OE2 GLU B   8 "
            pdb=" OH  TYR E 166 "
     model   vdw
     2.038 3.040
  nonbonded pdb=" O   VAL A 158 "
            pdb=" NZ  LYS A 161 "
     model   vdw
     2.071 3.120
  nonbonded pdb=" OG  SER A 176 "
            pdb=" OG  SER A 215 "
     model   vdw
     2.119 3.040
  ... (remaining 81013 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:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.090
  Find NCS groups from input model:        0.140
  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:             0.010
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
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   0.053   9713  Z= 0.201
  Angle     :  0.719   6.954  13147  Z= 0.388
  Chirality :  0.046   0.247   1496
  Planarity :  0.005   0.096   1649
  Dihedral  : 13.153  84.395   3503
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.24), residues: 1188
  helix:  1.58 (0.26), residues: 402
  sheet: -0.52 (0.29), residues: 301
  loop : -0.47 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  82 
 HIS   0.008   0.002   HIS A 327 
 PHE   0.037   0.002   PHE A 346 
 TYR   0.019   0.002   TYR D  40 
 ARG   0.021   0.001   ARG C 214 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00008 (    1)
  link_NAG-ASN         : angle       3.39863 (    3)
  hydrogen bonds       : bond        0.14184 (  498)
  hydrogen bonds       : angle       6.48780 ( 1383)
  SS BOND              : bond        0.00450 (    7)
  SS BOND              : angle       3.10498 (   14)
  covalent geometry    : bond        0.00446 ( 9705)
  covalent geometry    : angle       0.71072 (13130)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 ASP cc_start: 0.8244 (m-30) cc_final: 0.7916 (m-30)
REVERT: A  201 MET cc_start: 0.8427 (mmm) cc_final: 0.8195 (tpp)
REVERT: A  284 ASN cc_start: 0.7560 (t0) cc_final: 0.6988 (t0)
REVERT: B   21 ARG cc_start: 0.8101 (ptp90) cc_final: 0.7843 (mtm-85)
REVERT: B  252 SER cc_start: 0.9135 (t) cc_final: 0.8933 (t)
REVERT: D   21 MET cc_start: 0.8337 (tmm) cc_final: 0.7880 (tmm)
REVERT: D   46 LYS cc_start: 0.9153 (mmmm) cc_final: 0.8913 (mmpt)
REVERT: E  177 GLN cc_start: 0.8936 (pt0) cc_final: 0.8567 (pt0)
REVERT: E  193 ARG cc_start: 0.8651 (ptt90) cc_final: 0.8451 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.3289
  time to fit residues: 83.6521
Evaluate side-chains
  158 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 92 optimal weight:    0.3980
   chunk 35 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 172 ASN
A 299 ASN
B  52 GLN
B 195 HIS
B 255 ASN
B 306 GLN
C 176 GLN
C 220 GLN
C 259 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.115989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.090095 restraints weight = 15601.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.67
r_work: 0.3012 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.1388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9713  Z= 0.165
  Angle     :  0.609   7.395  13147  Z= 0.328
  Chirality :  0.043   0.172   1496
  Planarity :  0.004   0.034   1649
  Dihedral  :  5.400  50.148   1322
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  5.91 %
    Favored  : 93.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.24), residues: 1188
  helix:  1.60 (0.26), residues: 406
  sheet: -0.48 (0.29), residues: 300
  loop : -0.40 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  82 
 HIS   0.004   0.001   HIS A 388 
 PHE   0.033   0.002   PHE A 346 
 TYR   0.020   0.001   TYR B 230 
 ARG   0.006   0.001   ARG C 214 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00216 (    1)
  link_NAG-ASN         : angle       3.34934 (    3)
  hydrogen bonds       : bond        0.04546 (  498)
  hydrogen bonds       : angle       5.45335 ( 1383)
  SS BOND              : bond        0.00502 (    7)
  SS BOND              : angle       2.13467 (   14)
  covalent geometry    : bond        0.00372 ( 9705)
  covalent geometry    : angle       0.60301 (13130)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 167
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 ASP cc_start: 0.8620 (m-30) cc_final: 0.8196 (m-30)
REVERT: A  284 ASN cc_start: 0.7643 (t0) cc_final: 0.7427 (t0)
REVERT: A  401 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8030 (mm-30)
REVERT: A  405 LYS cc_start: 0.8093 (mmpt) cc_final: 0.7866 (mmpt)
REVERT: B   24 ARG cc_start: 0.7950 (ttt180) cc_final: 0.7217 (ttp80)
REVERT: B  279 LYS cc_start: 0.8827 (pttm) cc_final: 0.8611 (pttm)
REVERT: C  124 TYR cc_start: 0.9022 (m-80) cc_final: 0.8808 (m-80)
REVERT: C  172 GLU cc_start: 0.8893 (tp30) cc_final: 0.8569 (tm-30)
REVERT: C  175 GLN cc_start: 0.8061 (mp10) cc_final: 0.7814 (mp10)
REVERT: D   21 MET cc_start: 0.8494 (tmm) cc_final: 0.7896 (tmm)
REVERT: E  210 LEU cc_start: 0.9008 (mm) cc_final: 0.8415 (mm)
  outliers start: 5
  outliers final: 1
  residues processed: 169
  average time/residue: 0.3685
  time to fit residues: 82.3517
Evaluate side-chains
  149 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  153 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 21 optimal weight:    0.3980
   chunk 57 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  84 HIS
A 187 GLN
** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 GLN
E  80 ASN
E  85 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.115224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.089202 restraints weight = 15847.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 2.69
r_work: 0.3006 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9713  Z= 0.151
  Angle     :  0.564   7.545  13147  Z= 0.303
  Chirality :  0.042   0.167   1496
  Planarity :  0.003   0.035   1649
  Dihedral  :  5.203  49.910   1322
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  9.15 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.24), residues: 1188
  helix:  1.71 (0.26), residues: 407
  sheet: -0.52 (0.30), residues: 286
  loop : -0.47 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  80 
 HIS   0.004   0.001   HIS A 388 
 PHE   0.027   0.001   PHE A 346 
 TYR   0.016   0.001   TYR E 181 
 ARG   0.003   0.000   ARG E  90 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00017 (    1)
  link_NAG-ASN         : angle       2.81638 (    3)
  hydrogen bonds       : bond        0.04063 (  498)
  hydrogen bonds       : angle       5.24555 ( 1383)
  SS BOND              : bond        0.00357 (    7)
  SS BOND              : angle       1.77436 (   14)
  covalent geometry    : bond        0.00346 ( 9705)
  covalent geometry    : angle       0.55939 (13130)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 150
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 ASP cc_start: 0.8613 (m-30) cc_final: 0.8165 (m-30)
REVERT: A  284 ASN cc_start: 0.7684 (t0) cc_final: 0.7279 (t0)
REVERT: A  401 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8029 (mm-30)
REVERT: A  405 LYS cc_start: 0.8085 (mmpt) cc_final: 0.7821 (mmpt)
REVERT: B   24 ARG cc_start: 0.7975 (ttt180) cc_final: 0.7270 (ttp80)
REVERT: C   23 LYS cc_start: 0.9060 (ttpp) cc_final: 0.8818 (tptt)
REVERT: C   32 GLN cc_start: 0.8300 (mp10) cc_final: 0.7983 (mp10)
REVERT: C  172 GLU cc_start: 0.8912 (tp30) cc_final: 0.8586 (tm-30)
REVERT: C  175 GLN cc_start: 0.8133 (mp10) cc_final: 0.7884 (mp10)
REVERT: C  217 MET cc_start: 0.7929 (tpt) cc_final: 0.7020 (mtp)
REVERT: C  226 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8595 (mm-30)
REVERT: D   21 MET cc_start: 0.8581 (tmm) cc_final: 0.8355 (tmm)
REVERT: E   46 LYS cc_start: 0.8982 (mmtp) cc_final: 0.8769 (mmmm)
REVERT: E  210 LEU cc_start: 0.8966 (mm) cc_final: 0.8439 (mm)
  outliers start: 14
  outliers final: 10
  residues processed: 160
  average time/residue: 0.2821
  time to fit residues: 59.3670
Evaluate side-chains
  153 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 143
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain C residue   10 GLU
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  153 ASP
Chi-restraints excluded: chain C residue  322 ASP
Chi-restraints excluded: chain E residue   61 ILE
Chi-restraints excluded: chain E residue  123 SER
Chi-restraints excluded: chain E residue  193 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0980
   chunk 78 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9980
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
B 306 GLN
E 177 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.112352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.086540 restraints weight = 15642.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 2.63
r_work: 0.2965 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9713  Z= 0.195
  Angle     :  0.583   8.008  13147  Z= 0.313
  Chirality :  0.043   0.176   1496
  Planarity :  0.004   0.039   1649
  Dihedral  :  5.241  50.171   1322
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.44 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.24), residues: 1188
  helix:  1.71 (0.26), residues: 408
  sheet: -0.56 (0.29), residues: 301
  loop : -0.55 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  80 
 HIS   0.004   0.001   HIS C  62 
 PHE   0.026   0.001   PHE A 346 
 TYR   0.016   0.001   TYR E 181 
 ARG   0.004   0.000   ARG B  32 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00105 (    1)
  link_NAG-ASN         : angle       2.31038 (    3)
  hydrogen bonds       : bond        0.04088 (  498)
  hydrogen bonds       : angle       5.25591 ( 1383)
  SS BOND              : bond        0.00398 (    7)
  SS BOND              : angle       2.11714 (   14)
  covalent geometry    : bond        0.00454 ( 9705)
  covalent geometry    : angle       0.57795 (13130)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 ASP cc_start: 0.8680 (m-30) cc_final: 0.8320 (m-30)
REVERT: A  193 ASP cc_start: 0.8247 (t0) cc_final: 0.8021 (t0)
REVERT: A  401 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8185 (mm-30)
REVERT: A  405 LYS cc_start: 0.8119 (mmpt) cc_final: 0.7813 (mmpt)
REVERT: B   24 ARG cc_start: 0.8088 (ttt180) cc_final: 0.7332 (ttp80)
REVERT: B  279 LYS cc_start: 0.8856 (pttm) cc_final: 0.8514 (pttp)
REVERT: B  302 TYR cc_start: 0.8517 (t80) cc_final: 0.7763 (t80)
REVERT: C   23 LYS cc_start: 0.9025 (ttpp) cc_final: 0.8762 (tptt)
REVERT: C  172 GLU cc_start: 0.9077 (tp30) cc_final: 0.8593 (tm-30)
REVERT: C  175 GLN cc_start: 0.8263 (mp10) cc_final: 0.7929 (mp10)
REVERT: D   21 MET cc_start: 0.8620 (tmm) cc_final: 0.8279 (tmm)
REVERT: E   46 LYS cc_start: 0.8976 (mmtp) cc_final: 0.8712 (mmmm)
REVERT: E  210 LEU cc_start: 0.8977 (mm) cc_final: 0.8467 (mm)
  outliers start: 17
  outliers final: 14
  residues processed: 169
  average time/residue: 0.2647
  time to fit residues: 58.9988
Evaluate side-chains
  157 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain B residue  246 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   10 GLU
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  153 ASP
Chi-restraints excluded: chain C residue  322 ASP
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain E residue   80 ASN
Chi-restraints excluded: chain E residue  123 SER
Chi-restraints excluded: chain E residue  193 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 31 optimal weight:    0.4980
   chunk 6 optimal weight:   10.0000
   chunk 113 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
B 269 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.110789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.084933 restraints weight = 15707.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 2.62
r_work: 0.2936 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2801 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   9713  Z= 0.242
  Angle     :  0.619   8.547  13147  Z= 0.330
  Chirality :  0.044   0.193   1496
  Planarity :  0.004   0.040   1649
  Dihedral  :  5.356  49.854   1322
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.20 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.24), residues: 1188
  helix:  1.60 (0.26), residues: 409
  sheet: -0.67 (0.29), residues: 303
  loop : -0.59 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  99 
 HIS   0.003   0.001   HIS C 183 
 PHE   0.025   0.002   PHE A 346 
 TYR   0.015   0.001   TYR E 181 
 ARG   0.004   0.000   ARG E 193 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    1)
  link_NAG-ASN         : angle       1.97422 (    3)
  hydrogen bonds       : bond        0.04268 (  498)
  hydrogen bonds       : angle       5.30734 ( 1383)
  SS BOND              : bond        0.00400 (    7)
  SS BOND              : angle       2.21673 (   14)
  covalent geometry    : bond        0.00566 ( 9705)
  covalent geometry    : angle       0.61458 (13130)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 MET cc_start: 0.9260 (mmm) cc_final: 0.8721 (tpp)
REVERT: A  167 ASP cc_start: 0.8710 (m-30) cc_final: 0.8350 (m-30)
REVERT: A  276 VAL cc_start: 0.8169 (t) cc_final: 0.7952 (p)
REVERT: A  401 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8297 (mm-30)
REVERT: A  405 LYS cc_start: 0.8180 (mmpt) cc_final: 0.7824 (mmpt)
REVERT: B   24 ARG cc_start: 0.8156 (ttt180) cc_final: 0.7375 (ttp80)
REVERT: B  279 LYS cc_start: 0.8862 (pttm) cc_final: 0.8553 (pttp)
REVERT: B  302 TYR cc_start: 0.8467 (t80) cc_final: 0.7849 (t80)
REVERT: C   23 LYS cc_start: 0.9042 (ttpp) cc_final: 0.8787 (tptt)
REVERT: C  172 GLU cc_start: 0.9113 (tp30) cc_final: 0.8565 (tm-30)
REVERT: C  175 GLN cc_start: 0.8290 (mp10) cc_final: 0.7970 (mp10)
REVERT: D   21 MET cc_start: 0.8627 (tmm) cc_final: 0.8276 (tmm)
REVERT: D   42 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8158 (tm-30)
REVERT: E  210 LEU cc_start: 0.9006 (mm) cc_final: 0.8431 (mm)
  outliers start: 21
  outliers final: 18
  residues processed: 168
  average time/residue: 0.3175
  time to fit residues: 71.0747
Evaluate side-chains
  162 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 1.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  246 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   10 GLU
Chi-restraints excluded: chain C residue   33 ILE
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  153 ASP
Chi-restraints excluded: chain C residue  322 ASP
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain E residue   80 ASN
Chi-restraints excluded: chain E residue  123 SER
Chi-restraints excluded: chain E residue  193 ARG
Chi-restraints excluded: chain E residue  201 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 60 optimal weight:    0.4980
   chunk 111 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0020
   chunk 47 optimal weight:    0.1980
   chunk 52 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 93 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
C 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.115099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.089026 restraints weight = 15810.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 2.65
r_work: 0.3010 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9713  Z= 0.122
  Angle     :  0.547   7.739  13147  Z= 0.293
  Chirality :  0.041   0.163   1496
  Planarity :  0.003   0.034   1649
  Dihedral  :  5.081  50.145   1322
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.96 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.25), residues: 1188
  helix:  1.87 (0.26), residues: 408
  sheet: -0.66 (0.30), residues: 291
  loop : -0.53 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  80 
 HIS   0.003   0.001   HIS A 388 
 PHE   0.023   0.001   PHE A 310 
 TYR   0.016   0.001   TYR E 181 
 ARG   0.005   0.000   ARG A  89 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00017 (    1)
  link_NAG-ASN         : angle       2.07021 (    3)
  hydrogen bonds       : bond        0.03690 (  498)
  hydrogen bonds       : angle       5.06998 ( 1383)
  SS BOND              : bond        0.00222 (    7)
  SS BOND              : angle       1.79855 (   14)
  covalent geometry    : bond        0.00275 ( 9705)
  covalent geometry    : angle       0.54311 (13130)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 ASP cc_start: 0.8664 (m-30) cc_final: 0.8298 (m-30)
REVERT: A  401 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8269 (mm-30)
REVERT: A  405 LYS cc_start: 0.8062 (mmpt) cc_final: 0.7706 (mmpt)
REVERT: B   24 ARG cc_start: 0.8065 (ttt180) cc_final: 0.7297 (ttp80)
REVERT: B  279 LYS cc_start: 0.8882 (pttm) cc_final: 0.8565 (pttp)
REVERT: C   23 LYS cc_start: 0.9025 (ttpp) cc_final: 0.8752 (tptt)
REVERT: C   32 GLN cc_start: 0.8234 (mp10) cc_final: 0.7868 (mp10)
REVERT: C  172 GLU cc_start: 0.9111 (tp30) cc_final: 0.8582 (tm-30)
REVERT: C  175 GLN cc_start: 0.8369 (mp10) cc_final: 0.8089 (mp10)
REVERT: C  217 MET cc_start: 0.8159 (tpt) cc_final: 0.7823 (mmm)
REVERT: D   21 MET cc_start: 0.8663 (tmm) cc_final: 0.8308 (tmm)
REVERT: E  210 LEU cc_start: 0.8914 (mm) cc_final: 0.8401 (mm)
  outliers start: 20
  outliers final: 16
  residues processed: 172
  average time/residue: 0.2910
  time to fit residues: 66.1878
Evaluate side-chains
  163 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   10 GLU
Chi-restraints excluded: chain C residue   33 ILE
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  322 ASP
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   80 ASN
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  123 SER
Chi-restraints excluded: chain E residue  193 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 114 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 117 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    1.2986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.112483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.086478 restraints weight = 15961.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 2.66
r_work: 0.2956 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2822 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9713  Z= 0.202
  Angle     :  0.594   8.074  13147  Z= 0.318
  Chirality :  0.043   0.180   1496
  Planarity :  0.003   0.034   1649
  Dihedral  :  5.179  50.359   1322
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.16 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.25), residues: 1188
  helix:  1.78 (0.26), residues: 408
  sheet: -0.66 (0.30), residues: 304
  loop : -0.60 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  80 
 HIS   0.003   0.001   HIS C 183 
 PHE   0.022   0.001   PHE A 346 
 TYR   0.015   0.001   TYR E 181 
 ARG   0.005   0.000   ARG A  89 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00096 (    1)
  link_NAG-ASN         : angle       1.90794 (    3)
  hydrogen bonds       : bond        0.03989 (  498)
  hydrogen bonds       : angle       5.15737 ( 1383)
  SS BOND              : bond        0.00272 (    7)
  SS BOND              : angle       2.11649 (   14)
  covalent geometry    : bond        0.00476 ( 9705)
  covalent geometry    : angle       0.58956 (13130)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 149
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 ASP cc_start: 0.8676 (m-30) cc_final: 0.8335 (m-30)
REVERT: A  276 VAL cc_start: 0.8170 (t) cc_final: 0.7958 (p)
REVERT: A  401 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8332 (mm-30)
REVERT: A  405 LYS cc_start: 0.8082 (mmpt) cc_final: 0.7715 (mmpt)
REVERT: B   24 ARG cc_start: 0.8105 (ttt180) cc_final: 0.7338 (ttp80)
REVERT: B  279 LYS cc_start: 0.8899 (pttm) cc_final: 0.8588 (pttp)
REVERT: C   23 LYS cc_start: 0.9026 (ttpp) cc_final: 0.8783 (tptt)
REVERT: C   32 GLN cc_start: 0.8316 (mp10) cc_final: 0.7858 (mp10)
REVERT: C  172 GLU cc_start: 0.9112 (tp30) cc_final: 0.8533 (tm-30)
REVERT: C  175 GLN cc_start: 0.8308 (mp10) cc_final: 0.7964 (mp10)
REVERT: D   21 MET cc_start: 0.8673 (tmm) cc_final: 0.8253 (tmm)
REVERT: D   42 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8139 (tm-30)
REVERT: D   58 GLU cc_start: 0.8367 (pm20) cc_final: 0.8066 (pm20)
REVERT: E   46 LYS cc_start: 0.8935 (mmtm) cc_final: 0.8511 (mmmm)
REVERT: E  210 LEU cc_start: 0.8955 (mm) cc_final: 0.8384 (mm)
  outliers start: 25
  outliers final: 21
  residues processed: 168
  average time/residue: 0.2701
  time to fit residues: 60.3181
Evaluate side-chains
  165 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  246 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   10 GLU
Chi-restraints excluded: chain C residue   33 ILE
Chi-restraints excluded: chain C residue  153 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  322 ASP
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  123 SER
Chi-restraints excluded: chain E residue  193 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 35 optimal weight:    0.0050
   chunk 64 optimal weight:    0.9980
   chunk 112 optimal weight:    0.5980
   chunk 49 optimal weight:    6.9990
   chunk 85 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 92 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
B 195 HIS
B 269 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.114030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.087939 restraints weight = 15961.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.69
r_work: 0.2993 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9713  Z= 0.140
  Angle     :  0.560   7.886  13147  Z= 0.299
  Chirality :  0.042   0.165   1496
  Planarity :  0.003   0.034   1649
  Dihedral  :  5.056  50.258   1322
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.20 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.25), residues: 1188
  helix:  1.91 (0.26), residues: 408
  sheet: -0.66 (0.30), residues: 288
  loop : -0.60 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  80 
 HIS   0.004   0.001   HIS A 388 
 PHE   0.022   0.001   PHE A 310 
 TYR   0.016   0.001   TYR E 181 
 ARG   0.005   0.000   ARG A  89 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00014 (    1)
  link_NAG-ASN         : angle       1.95410 (    3)
  hydrogen bonds       : bond        0.03690 (  498)
  hydrogen bonds       : angle       5.02385 ( 1383)
  SS BOND              : bond        0.00243 (    7)
  SS BOND              : angle       1.80683 (   14)
  covalent geometry    : bond        0.00324 ( 9705)
  covalent geometry    : angle       0.55599 (13130)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 1.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 ASP cc_start: 0.8490 (m-30) cc_final: 0.8143 (m-30)
REVERT: A  401 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8154 (mm-30)
REVERT: A  405 LYS cc_start: 0.7915 (mmpt) cc_final: 0.7600 (mmpt)
REVERT: B   24 ARG cc_start: 0.7992 (ttt180) cc_final: 0.7283 (ttp80)
REVERT: B  279 LYS cc_start: 0.8911 (pttm) cc_final: 0.8581 (pttp)
REVERT: C   23 LYS cc_start: 0.9019 (ttpp) cc_final: 0.8749 (tptt)
REVERT: C   32 GLN cc_start: 0.8259 (mp10) cc_final: 0.7947 (mp10)
REVERT: C  172 GLU cc_start: 0.8969 (tp30) cc_final: 0.8422 (tm-30)
REVERT: C  175 GLN cc_start: 0.8246 (mp10) cc_final: 0.7945 (mp10)
REVERT: D   21 MET cc_start: 0.8628 (tmm) cc_final: 0.8220 (tmm)
REVERT: D   42 GLU cc_start: 0.8238 (tm-30) cc_final: 0.8032 (tm-30)
REVERT: D   58 GLU cc_start: 0.8298 (pm20) cc_final: 0.8080 (pm20)
REVERT: E   46 LYS cc_start: 0.8998 (mmtm) cc_final: 0.8622 (mmmm)
REVERT: E  210 LEU cc_start: 0.8872 (mm) cc_final: 0.8334 (mm)
  outliers start: 21
  outliers final: 18
  residues processed: 161
  average time/residue: 0.3622
  time to fit residues: 76.6573
Evaluate side-chains
  159 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 2.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain B residue  246 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   10 GLU
Chi-restraints excluded: chain C residue   33 ILE
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   61 ILE
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  123 SER
Chi-restraints excluded: chain E residue  193 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 78 optimal weight:    0.0970
   chunk 21 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 27 optimal weight:    0.8980
   chunk 6 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 91 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 255 ASN
C 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.115176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.089577 restraints weight = 15773.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 2.64
r_work: 0.2995 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9713  Z= 0.144
  Angle     :  0.564   7.351  13147  Z= 0.302
  Chirality :  0.042   0.163   1496
  Planarity :  0.003   0.034   1649
  Dihedral  :  5.018  50.542   1322
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.68 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.25), residues: 1188
  helix:  1.92 (0.26), residues: 408
  sheet: -0.61 (0.31), residues: 286
  loop : -0.62 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A  80 
 HIS   0.003   0.001   HIS A 388 
 PHE   0.021   0.001   PHE A 310 
 TYR   0.015   0.001   TYR E 181 
 ARG   0.005   0.000   ARG A  89 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00050 (    1)
  link_NAG-ASN         : angle       1.91700 (    3)
  hydrogen bonds       : bond        0.03692 (  498)
  hydrogen bonds       : angle       5.00536 ( 1383)
  SS BOND              : bond        0.00208 (    7)
  SS BOND              : angle       2.14641 (   14)
  covalent geometry    : bond        0.00337 ( 9705)
  covalent geometry    : angle       0.55967 (13130)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 ASP cc_start: 0.8633 (m-30) cc_final: 0.8278 (m-30)
REVERT: A  276 VAL cc_start: 0.8197 (t) cc_final: 0.7980 (p)
REVERT: A  401 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8231 (mm-30)
REVERT: A  405 LYS cc_start: 0.8044 (mmpt) cc_final: 0.7677 (mmpt)
REVERT: B   24 ARG cc_start: 0.8049 (ttt180) cc_final: 0.7298 (ttp80)
REVERT: B  279 LYS cc_start: 0.8921 (pttm) cc_final: 0.8604 (pttm)
REVERT: C   23 LYS cc_start: 0.9004 (ttpp) cc_final: 0.8734 (tptt)
REVERT: C  172 GLU cc_start: 0.9113 (tp30) cc_final: 0.8500 (tm-30)
REVERT: C  175 GLN cc_start: 0.8380 (mp10) cc_final: 0.8056 (mp10)
REVERT: D   21 MET cc_start: 0.8603 (tmm) cc_final: 0.8196 (tmm)
REVERT: D   42 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8152 (tm-30)
REVERT: E   46 LYS cc_start: 0.8980 (mmtm) cc_final: 0.8578 (mmmm)
REVERT: E  210 LEU cc_start: 0.8912 (mm) cc_final: 0.8368 (mm)
  outliers start: 22
  outliers final: 20
  residues processed: 156
  average time/residue: 0.2940
  time to fit residues: 61.3882
Evaluate side-chains
  157 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 1.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain B residue  246 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   33 ILE
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  153 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   61 ILE
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  123 SER
Chi-restraints excluded: chain E residue  193 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 94 optimal weight:    0.6980
   chunk 66 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.114521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.088494 restraints weight = 15897.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 2.66
r_work: 0.2998 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9713  Z= 0.147
  Angle     :  0.585   8.990  13147  Z= 0.312
  Chirality :  0.042   0.158   1496
  Planarity :  0.003   0.034   1649
  Dihedral  :  5.012  50.832   1322
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.25 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.25), residues: 1188
  helix:  1.92 (0.26), residues: 408
  sheet: -0.60 (0.31), residues: 288
  loop : -0.61 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A  80 
 HIS   0.003   0.001   HIS A 388 
 PHE   0.020   0.001   PHE A 310 
 TYR   0.016   0.001   TYR E 181 
 ARG   0.005   0.000   ARG A  89 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00035 (    1)
  link_NAG-ASN         : angle       1.82137 (    3)
  hydrogen bonds       : bond        0.03700 (  498)
  hydrogen bonds       : angle       5.01484 ( 1383)
  SS BOND              : bond        0.00246 (    7)
  SS BOND              : angle       2.01663 (   14)
  covalent geometry    : bond        0.00342 ( 9705)
  covalent geometry    : angle       0.58115 (13130)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 ASP cc_start: 0.8507 (m-30) cc_final: 0.8169 (m-30)
REVERT: A  401 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8088 (mm-30)
REVERT: A  405 LYS cc_start: 0.7955 (mmpt) cc_final: 0.7606 (mmpt)
REVERT: B   24 ARG cc_start: 0.7986 (ttt180) cc_final: 0.7277 (ttp80)
REVERT: C   23 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8782 (tptt)
REVERT: C   32 GLN cc_start: 0.8060 (mp10) cc_final: 0.7777 (mp10)
REVERT: C  172 GLU cc_start: 0.8974 (tp30) cc_final: 0.8408 (tm-30)
REVERT: C  175 GLN cc_start: 0.8221 (mp10) cc_final: 0.7927 (mp10)
REVERT: D   21 MET cc_start: 0.8575 (tmm) cc_final: 0.8169 (tmm)
REVERT: D   42 GLU cc_start: 0.8263 (tm-30) cc_final: 0.8045 (tm-30)
REVERT: E   46 LYS cc_start: 0.8997 (mmtm) cc_final: 0.8638 (mmmm)
REVERT: E  210 LEU cc_start: 0.8878 (mm) cc_final: 0.8348 (mm)
  outliers start: 21
  outliers final: 21
  residues processed: 156
  average time/residue: 0.2736
  time to fit residues: 56.5791
Evaluate side-chains
  157 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  246 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   33 ILE
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  153 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   61 ILE
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  123 SER
Chi-restraints excluded: chain E residue  193 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.114802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.088109 restraints weight = 15820.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 2.73
r_work: 0.2983 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9713  Z= 0.158
  Angle     :  0.587  11.434  13147  Z= 0.312
  Chirality :  0.042   0.161   1496
  Planarity :  0.003   0.034   1649
  Dihedral  :  5.031  51.100   1322
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.97 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.25), residues: 1188
  helix:  1.90 (0.26), residues: 408
  sheet: -0.59 (0.31), residues: 288
  loop : -0.61 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A  80 
 HIS   0.003   0.001   HIS A 388 
 PHE   0.021   0.001   PHE A 310 
 TYR   0.017   0.001   TYR E 181 
 ARG   0.006   0.000   ARG A  89 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00036 (    1)
  link_NAG-ASN         : angle       1.70893 (    3)
  hydrogen bonds       : bond        0.03756 (  498)
  hydrogen bonds       : angle       5.04185 ( 1383)
  SS BOND              : bond        0.00249 (    7)
  SS BOND              : angle       1.99589 (   14)
  covalent geometry    : bond        0.00369 ( 9705)
  covalent geometry    : angle       0.58307 (13130)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5809.03 seconds
wall clock time: 104 minutes 36.07 seconds (6276.07 seconds total)