Starting phenix.real_space_refine
on Fri Jun 13 23:35:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dn3_27553/06_2025/8dn3_27553_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dn3_27553/06_2025/8dn3_27553.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dn3_27553/06_2025/8dn3_27553.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dn3_27553/06_2025/8dn3_27553.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dn3_27553/06_2025/8dn3_27553_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dn3_27553/06_2025/8dn3_27553_trim.cif"
  }
  resolution = 3.55
  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=   0.008 sd=   0.086
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S     102      5.16       5
     Cl      2      4.86       5
     C    9467      2.51       5
     N    2270      2.21       5
     O    2474      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: 14315
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "D"
      Number of atoms: 2762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2762
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 15, 'TRANS': 323}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2796
          Classifications: {'peptide': 343}
          Link IDs: {'PTRANS': 15, 'TRANS': 327}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2768
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 15, 'TRANS': 324}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2785
          Classifications: {'peptide': 343}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 15, 'TRANS': 327}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "E"
      Number of atoms: 2707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2707
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 316}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 107
          Unusual residues: {'DD9': 1, 'HEX': 3, 'HP6': 2, 'NAG': 1, 'NBU': 2, 'UND': 4}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 103
          Unusual residues: {'DD9': 2, 'HEX': 4, 'HP6': 2, 'NAG': 1, 'UND': 3}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 81
          Unusual residues: {'DD9': 5, 'HEX': 3, 'NAG': 1, 'NBU': 1}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 116
          Unusual residues: {'D10': 1, 'DD9': 3, 'HEX': 3, 'HP6': 2, 'NAG': 1, 'UND': 3}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 90
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 90
          Unusual residues: {' CL': 2, 'DD9': 2, 'HEX': 2, 'HP6': 2, 'NAG': 1, 'NBU': 2, 'UND': 2}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 9.36, per 1000 atoms: 0.65
  Number of scatterers: 14315
  At special positions: 0
  Unit cell: (103.75, 127.82, 132.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S     102     16.00
     O    2474      8.00
     N    2270      7.00
     C    9467      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 138 " - pdb=" SG  CYS D 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 198 " - pdb=" SG  CYS D 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 138 " - pdb=" SG  CYS A 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 198 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 138 " - pdb=" SG  CYS B 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 198 " - pdb=" SG  CYS B 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 138 " - pdb=" SG  CYS C 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 198 " - pdb=" SG  CYS C 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 161 " - pdb=" SG  CYS E 175 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=5, symmetry=0
  Links applied
    NAG-ASN
      " NAG C 503 " - " ASN C  38 "
      " NAG D 501 " - " ASN D  38 "
      " NAG E 504 " - " ASN E 220 "
  Number of additional bonds: simple=5, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 4.24
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3252

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 13 sheets defined
      38.9% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.40
  Creating SS restraints...
    Processing helix  chain 'D' and resid 9 through 18
      removed outlier: 3.536A  pdb=" N   LEU D  14 " --> pdb=" O   PRO D  10 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ASP D  15 " --> pdb=" O   SER D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 86 through 91
    Processing helix  chain 'D' and resid 220 through 243
      Proline residue:  D 230  - end of helix
    Processing helix  chain 'D' and resid 248 through 274
      removed outlier: 4.049A  pdb=" N   ALA D 272 " --> pdb=" O   SER D 268 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   SER D 273 " --> pdb=" O   GLY D 269 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 281 through 311
      removed outlier: 3.962A  pdb=" N   TRP D 286 " --> pdb=" O   ALA D 282 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   HIS D 311 " --> pdb=" O   VAL D 307 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 385 through 419
      removed outlier: 4.280A  pdb=" N   ILE D 400 " --> pdb=" O   LYS D 396 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY D 401 " --> pdb=" O   ILE D 397 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   PHE D 402 " --> pdb=" O   SER D 398 " (cutoff:3.500A)
      Proline residue:  D 403  - end of helix
    Processing helix  chain 'A' and resid 9 through 18
    Processing helix  chain 'A' and resid 71 through 74
    Processing helix  chain 'A' and resid 86 through 93
      removed outlier: 3.617A  pdb=" N   LEU A  90 " --> pdb=" O   PRO A  87 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   ASP A  91 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ILE A  93 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 227
    Processing helix  chain 'A' and resid 228 through 243
    Processing helix  chain 'A' and resid 248 through 271
      removed outlier: 3.620A  pdb=" N   ARG A 271 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 311
      removed outlier: 3.798A  pdb=" N   HIS A 311 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 419
      removed outlier: 3.961A  pdb=" N   ILE A 400 " --> pdb=" O   LYS A 396 " (cutoff:3.500A)
      Proline residue:  A 403  - end of helix
    Processing helix  chain 'B' and resid 9 through 18
    Processing helix  chain 'B' and resid 71 through 74
    Processing helix  chain 'B' and resid 86 through 91
    Processing helix  chain 'B' and resid 221 through 243
      Proline residue:  B 230  - end of helix
    Processing helix  chain 'B' and resid 248 through 274
      removed outlier: 3.602A  pdb=" N   ARG B 271 " --> pdb=" O   SER B 267 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   ALA B 272 " --> pdb=" O   SER B 268 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   SER B 273 " --> pdb=" O   GLY B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 310
    Processing helix  chain 'B' and resid 385 through 419
      removed outlier: 3.789A  pdb=" N   ILE B 400 " --> pdb=" O   LYS B 396 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE B 402 " --> pdb=" O   SER B 398 " (cutoff:3.500A)
      Proline residue:  B 403  - end of helix
      removed outlier: 3.625A  pdb=" N   TRP B 414 " --> pdb=" O   ASN B 410 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE B 415 " --> pdb=" O   MET B 411 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 18
    Processing helix  chain 'C' and resid 86 through 91
    Processing helix  chain 'C' and resid 220 through 241
      Proline residue:  C 230  - end of helix
    Processing helix  chain 'C' and resid 248 through 274
    Processing helix  chain 'C' and resid 283 through 313
      removed outlier: 3.919A  pdb=" N   HIS C 311 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LYS C 312 " --> pdb=" O   SER C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 417
      removed outlier: 3.748A  pdb=" N   ILE C 400 " --> pdb=" O   LYS C 396 " (cutoff:3.500A)
      Proline residue:  C 403  - end of helix
    Processing helix  chain 'E' and resid 34 through 43
      removed outlier: 3.614A  pdb=" N   LEU E  38 " --> pdb=" O   THR E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 95
    Processing helix  chain 'E' and resid 112 through 116
      removed outlier: 3.520A  pdb=" N   LEU E 116 " --> pdb=" O   TYR E 113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 167 through 170
    Processing helix  chain 'E' and resid 244 through 251
    Processing helix  chain 'E' and resid 251 through 265
      removed outlier: 3.820A  pdb=" N   SER E 265 " --> pdb=" O   LEU E 261 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 266 through 268
      No H-bonds generated for 'chain 'E' and resid 266 through 268'
    Processing helix  chain 'E' and resid 272 through 295
      Proline residue:  E 278  - end of helix
    Processing helix  chain 'E' and resid 305 through 333
    Processing helix  chain 'E' and resid 448 through 475
      removed outlier: 3.805A  pdb=" N   ALA E 457 " --> pdb=" O   LEU E 453 " (cutoff:3.500A)
      Proline residue:  E 460  - end of helix
    Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 45
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 37 through 45
    current: chain 'D' and resid 57 through 68
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 57 through 68
    current: chain 'D' and resid 126 through 134
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'D' and resid 98 through 100
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 149 through 158
    current: chain 'D' and resid 205 through 217
    Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 44
      removed outlier: 6.533A  pdb=" N   ASN A  38 " --> pdb=" O   ASN A  69 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ASN A  69 " --> pdb=" O   ASN A  38 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 65 through 69
    current: chain 'A' and resid 116 through 121
      removed outlier: 4.523A  pdb=" N   ASN A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 49 through 52
      removed outlier: 5.181A  pdb=" N   SER A  50 " --> pdb=" O   ARG A  59 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   ARG A  59 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ASP A  57 " --> pdb=" O   ALA A  52 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   HIS A 107 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 100
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 151 through 158
    current: chain 'A' and resid 205 through 217
    Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 44
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 37 through 44
    current: chain 'B' and resid 57 through 69
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 57 through 69
    current: chain 'B' and resid 125 through 137
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 100
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 149 through 157
    current: chain 'B' and resid 205 through 217
    Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 52
      removed outlier: 7.071A  pdb=" N   ASN C  38 " --> pdb=" O   ASN C  69 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   ASN C  69 " --> pdb=" O   ASN C  38 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   PHE C  44 " --> pdb=" O   PHE C  63 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ASN C  61 " --> pdb=" O   ASN C  46 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   PHE C  48 " --> pdb=" O   ARG C  59 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   ARG C  59 " --> pdb=" O   PHE C  48 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   SER C  50 " --> pdb=" O   ASP C  57 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ASP C  57 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 57 through 69
    current: chain 'C' and resid 125 through 134
    Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 100
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 149 through 158
    current: chain 'C' and resid 206 through 217
    Processing sheet with id=AB1, first strand: chain 'E' and resid 105 through 106
      removed outlier: 4.464A  pdb=" N   ASP E 148 " --> pdb=" O   PHE E 144 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ASP E  78 " --> pdb=" O   SER E  71 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   SER E  71 " --> pdb=" O   ASP E  78 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   ARG E  80 " --> pdb=" O   PHE E  69 " (cutoff:3.500A)
      removed outlier: 5.291A  pdb=" N   PHE E  69 " --> pdb=" O   ARG E  80 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   ASN E  82 " --> pdb=" O   ASN E  67 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   ASN E  90 " --> pdb=" O   ASP E  59 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ASP E  59 " --> pdb=" O   ASN E  90 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   VAL E  58 " --> pdb=" O   ARG E 190 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   ILE E 192 " --> pdb=" O   VAL E  58 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   VAL E  60 " --> pdb=" O   ILE E 192 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 121 through 123
    Processing sheet with id=AB3, first strand: chain 'E' and resid 172 through 176
    Processing sheet with id=AB4, first strand: chain 'E' and resid 223 through 225
      removed outlier: 3.540A  pdb=" N   LYS E 223 " --> pdb=" O   TYR E 231 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR E 225 " --> pdb=" O   GLY E 229 " (cutoff:3.500A)

    529 hydrogen bonds defined for protein.
    1551 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: 5.24

  Time building geometry restraints manager: 4.74 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: 4181
        1.34 -     1.46: 2289
        1.46 -     1.57: 7965
        1.57 -     1.69: 0
        1.69 -     1.81: 172
  Bond restraints: 14607
  Sorted by residual:
  bond pdb=" N   GLN D 310 "
       pdb=" CA  GLN D 310 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.038 1.29e-02 6.01e+03 8.87e+00
  bond pdb=" N   VAL C  37 "
       pdb=" CA  VAL C  37 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.19e-02 7.06e+03 8.18e+00
  bond pdb=" N   VAL D  37 "
       pdb=" CA  VAL D  37 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.033 1.23e-02 6.61e+03 7.41e+00
  bond pdb=" N   ILE A 257 "
       pdb=" CA  ILE A 257 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.19e-02 7.06e+03 7.35e+00
  bond pdb=" N   LYS A 312 "
       pdb=" CA  LYS A 312 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.29e-02 6.01e+03 6.45e+00
  ... (remaining 14602 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 19189
        1.66 -     3.32: 352
        3.32 -     4.97: 58
        4.97 -     6.63: 10
        6.63 -     8.29: 3
  Bond angle restraints: 19612
  Sorted by residual:
  angle pdb=" N   ARG B 309 "
        pdb=" CA  ARG B 309 "
        pdb=" C   ARG B 309 "
      ideal   model   delta    sigma   weight residual
     112.89  107.11    5.78 1.24e+00 6.50e-01 2.17e+01
  angle pdb=" CA  HIS A 311 "
        pdb=" C   HIS A 311 "
        pdb=" O   HIS A 311 "
      ideal   model   delta    sigma   weight residual
     121.19  117.38    3.81 1.10e+00 8.26e-01 1.20e+01
  angle pdb=" CA  THR A 258 "
        pdb=" C   THR A 258 "
        pdb=" O   THR A 258 "
      ideal   model   delta    sigma   weight residual
     120.82  117.49    3.33 1.05e+00 9.07e-01 1.01e+01
  angle pdb=" N   GLN A 310 "
        pdb=" CA  GLN A 310 "
        pdb=" C   GLN A 310 "
      ideal   model   delta    sigma   weight residual
     111.71  108.07    3.64 1.15e+00 7.56e-01 1.00e+01
  angle pdb=" N   PHE D 412 "
        pdb=" CA  PHE D 412 "
        pdb=" C   PHE D 412 "
      ideal   model   delta    sigma   weight residual
     112.89  109.00    3.89 1.24e+00 6.50e-01 9.85e+00
  ... (remaining 19607 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.23: 8530
       24.23 -    48.47: 273
       48.47 -    72.70: 18
       72.70 -    96.93: 11
       96.93 -   121.16: 6
  Dihedral angle restraints: 8838
    sinusoidal: 3821
      harmonic: 5017
  Sorted by residual:
  dihedral pdb=" C3  DD9 A 508 "
           pdb=" C4  DD9 A 508 "
           pdb=" C5  DD9 A 508 "
           pdb=" C6  DD9 A 508 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.92   58.76  121.16     1      3.00e+01 1.11e-03 1.62e+01
  dihedral pdb=" C1  DD9 A 508 "
           pdb=" C2  DD9 A 508 "
           pdb=" C3  DD9 A 508 "
           pdb=" C4  DD9 A 508 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.94  -67.82 -112.24     1      3.00e+01 1.11e-03 1.47e+01
  dihedral pdb=" C2  NAG E 504 "
           pdb=" C3  NAG E 504 "
           pdb=" C4  NAG E 504 "
           pdb=" C5  NAG E 504 "
      ideal   model   delta sinusoidal    sigma   weight residual
      53.78  -48.09  101.87     1      3.00e+01 1.11e-03 1.29e+01
  ... (remaining 8835 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.173: 2154
       0.173 -    0.346: 1
       0.346 -    0.519: 0
       0.519 -    0.692: 0
       0.692 -    0.865: 1
  Chirality restraints: 2156
  Sorted by residual:
  chirality pdb=" C1  NAG D 501 "
            pdb=" ND2 ASN D  38 "
            pdb=" C2  NAG D 501 "
            pdb=" O5  NAG D 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.54   -0.86 2.00e-01 2.50e+01 1.87e+01
  chirality pdb=" C1  NAG E 504 "
            pdb=" ND2 ASN E 220 "
            pdb=" C2  NAG E 504 "
            pdb=" O5  NAG E 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  VAL C  37 "
            pdb=" N   VAL C  37 "
            pdb=" C   VAL C  37 "
            pdb=" CB  VAL C  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.15 2.00e-01 2.50e+01 5.97e-01
  ... (remaining 2153 not shown)

  Planarity restraints: 2415
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 501 "    0.321 2.00e-02 2.50e+03   2.74e-01 9.37e+02
        pdb=" C7  NAG A 501 "   -0.073 2.00e-02 2.50e+03
        pdb=" C8  NAG A 501 "   -0.003 2.00e-02 2.50e+03
        pdb=" N2  NAG A 501 "   -0.466 2.00e-02 2.50e+03
        pdb=" O7  NAG A 501 "    0.221 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D 501 "   -0.292 2.00e-02 2.50e+03   2.48e-01 7.68e+02
        pdb=" C7  NAG D 501 "    0.072 2.00e-02 2.50e+03
        pdb=" C8  NAG D 501 "   -0.178 2.00e-02 2.50e+03
        pdb=" N2  NAG D 501 "    0.429 2.00e-02 2.50e+03
        pdb=" O7  NAG D 501 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 503 "   -0.281 2.00e-02 2.50e+03   2.35e-01 6.90e+02
        pdb=" C7  NAG C 503 "    0.077 2.00e-02 2.50e+03
        pdb=" C8  NAG C 503 "   -0.185 2.00e-02 2.50e+03
        pdb=" N2  NAG C 503 "    0.396 2.00e-02 2.50e+03
        pdb=" O7  NAG C 503 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2412 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 661
        2.73 -     3.27: 14154
        3.27 -     3.81: 22580
        3.81 -     4.36: 26996
        4.36 -     4.90: 46970
  Nonbonded interactions: 111361
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  98 "
            pdb=" OG1 THR B 112 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   ALA D 282 "
            pdb=" OH  TYR D 413 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OG1 THR A 112 "
            pdb=" O   LEU E 121 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   LEU B  98 "
            pdb=" OG1 THR C 112 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG1 THR B 162 "
            pdb=" OD1 ASN B 164 "
     model   vdw
     2.238 3.040
  ... (remaining 111356 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 9 through 310 or resid 384 through 386 or (resid 387 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 388 through 419))
  selection = (chain 'B' and (resid 9 through 310 or resid 384 through 386 or (resid 387 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 388 through 419))
  selection = (chain 'C' and (resid 9 through 310 or resid 384 through 419))
  selection = (chain 'D' and (resid 9 through 310 or resid 384 through 386 or (resid 387 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 388 through 419))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.100
  Set scattering table:                    0.150
  Process input model:                     36.030
  Find NCS groups from input model:        1.030
  Set up NCS constraints:                  0.080
  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:3.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
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      :  0.006   0.423  14624  Z= 0.494
  Angle     :  0.570   8.288  19639  Z= 0.288
  Chirality :  0.046   0.865   2156
  Planarity :  0.009   0.274   2412
  Dihedral  : 11.886 121.162   5559
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.87 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  5.51 %
    Favored  : 92.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.22), residues: 1679
  helix:  2.25 (0.22), residues: 583
  sheet: -0.40 (0.30), residues: 359
  loop : -0.75 (0.23), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 243 
 HIS   0.002   0.000   HIS A 311 
 PHE   0.010   0.001   PHE D 242 
 TYR   0.017   0.001   TYR E 325 
 ARG   0.002   0.000   ARG A 271 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00574 (    3)
  link_NAG-ASN         : angle       3.72745 (    9)
  hydrogen bonds       : bond        0.13217 (  529)
  hydrogen bonds       : angle       5.77662 ( 1551)
  SS BOND              : bond        0.00105 (    9)
  SS BOND              : angle       0.63481 (   18)
  covalent geometry    : bond        0.00343 (14607)
  covalent geometry    : angle       0.56471 (19612)
  Misc. bond           : bond        0.24770 (    5)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 332
  time to evaluate  : 3.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  141 ASP cc_start: 0.8081 (t70) cc_final: 0.7671 (p0)
REVERT: D  246 MET cc_start: 0.7313 (mtm) cc_final: 0.7076 (mtt)
REVERT: A   91 ASP cc_start: 0.8812 (t0) cc_final: 0.8612 (t0)
REVERT: A  169 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7849 (mt-10)
REVERT: A  173 GLN cc_start: 0.8343 (pp30) cc_final: 0.8086 (pp30)
REVERT: A  203 ASN cc_start: 0.8690 (m-40) cc_final: 0.8006 (p0)
REVERT: A  396 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7571 (mtmm)
REVERT: A  400 ILE cc_start: 0.8271 (tp) cc_final: 0.7582 (pt)
REVERT: B   18 MET cc_start: 0.8467 (ppp) cc_final: 0.8112 (ptt)
REVERT: B   83 LEU cc_start: 0.7978 (tt) cc_final: 0.7710 (tt)
REVERT: B  397 ILE cc_start: 0.8516 (mm) cc_final: 0.8249 (mt)
REVERT: B  411 MET cc_start: 0.7501 (mmp) cc_final: 0.6547 (ttp)
REVERT: C  191 GLU cc_start: 0.8209 (tp30) cc_final: 0.7933 (tp30)
REVERT: E  176 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8196 (mmtt)
REVERT: E  187 ASP cc_start: 0.8308 (t0) cc_final: 0.7799 (t0)
REVERT: E  329 GLN cc_start: 0.8469 (tp40) cc_final: 0.8204 (tp40)
  outliers start: 30
  outliers final: 12
  residues processed: 357
  average time/residue: 0.2796
  time to fit residues: 147.4359
Evaluate side-chains
  261 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 249
  time to evaluate  : 1.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   38 ASN
Chi-restraints excluded: chain D residue  135 THR
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  240 ILE
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  312 LYS
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue  135 THR
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain E residue  167 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    5.9990
   chunk 127 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   chunk 131 optimal weight:    9.9990
   chunk 50 optimal weight:    7.9990
   chunk 80 optimal weight:    0.7980
   chunk 98 optimal weight:    0.6980
   chunk 152 optimal weight:    0.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
D 109 HIS
D 125 ASN
D 201 HIS
** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 243 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.132345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.105368 restraints weight = 21263.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.109270 restraints weight = 10498.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.111946 restraints weight = 6691.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14624  Z= 0.161
  Angle     :  0.606   9.599  19639  Z= 0.299
  Chirality :  0.044   0.350   2156
  Planarity :  0.004   0.038   2412
  Dihedral  :  6.965  68.166   2242
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.41 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 10.89 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.21), residues: 1679
  helix:  2.08 (0.21), residues: 593
  sheet: -0.57 (0.29), residues: 379
  loop : -0.78 (0.23), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 243 
 HIS   0.004   0.001   HIS A 311 
 PHE   0.012   0.001   PHE E  84 
 TYR   0.020   0.002   TYR A 301 
 ARG   0.007   0.000   ARG C 399 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00239 (    3)
  link_NAG-ASN         : angle       3.34727 (    9)
  hydrogen bonds       : bond        0.04684 (  529)
  hydrogen bonds       : angle       5.15326 ( 1551)
  SS BOND              : bond        0.00121 (    9)
  SS BOND              : angle       0.80790 (   18)
  covalent geometry    : bond        0.00382 (14607)
  covalent geometry    : angle       0.60216 (19612)
  Misc. bond           : bond        0.00042 (    5)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 263
  time to evaluate  : 1.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  141 ASP cc_start: 0.8130 (t70) cc_final: 0.7754 (p0)
REVERT: D  246 MET cc_start: 0.7433 (mtm) cc_final: 0.7168 (mtt)
REVERT: D  263 MET cc_start: 0.8558 (mmm) cc_final: 0.8119 (tmm)
REVERT: D  298 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7819 (tt)
REVERT: A  169 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7785 (mt-10)
REVERT: A  173 GLN cc_start: 0.8459 (pp30) cc_final: 0.8146 (pp30)
REVERT: A  203 ASN cc_start: 0.8675 (m-40) cc_final: 0.8032 (p0)
REVERT: A  396 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7545 (mtmm)
REVERT: A  400 ILE cc_start: 0.8443 (tp) cc_final: 0.7771 (pt)
REVERT: A  411 MET cc_start: 0.6896 (mmp) cc_final: 0.6434 (mmp)
REVERT: B   18 MET cc_start: 0.8463 (ppp) cc_final: 0.8229 (ptt)
REVERT: B   83 LEU cc_start: 0.8123 (tt) cc_final: 0.7819 (tt)
REVERT: B  397 ILE cc_start: 0.8510 (mm) cc_final: 0.8253 (mt)
REVERT: B  411 MET cc_start: 0.7639 (mmp) cc_final: 0.6563 (ttp)
REVERT: C  206 LYS cc_start: 0.7364 (mptt) cc_final: 0.6794 (ttpt)
REVERT: E   88 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7685 (tttp)
REVERT: E  176 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8184 (mmtt)
REVERT: E  187 ASP cc_start: 0.8337 (t0) cc_final: 0.7791 (t0)
REVERT: E  329 GLN cc_start: 0.8832 (tp40) cc_final: 0.8627 (tp40)
REVERT: E  331 MET cc_start: 0.8135 (mmp) cc_final: 0.7894 (mmm)
  outliers start: 41
  outliers final: 31
  residues processed: 289
  average time/residue: 0.2536
  time to fit residues: 111.1243
Evaluate side-chains
  270 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 238
  time to evaluate  : 1.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  123 ASN
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  273 SER
Chi-restraints excluded: chain D residue  278 SER
Chi-restraints excluded: chain D residue  298 LEU
Chi-restraints excluded: chain D residue  398 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  141 ASP
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  265 SER
Chi-restraints excluded: chain E residue  290 GLU
Chi-restraints excluded: chain E residue  328 VAL
Chi-restraints excluded: chain E residue  454 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 167 optimal weight:    4.9990
   chunk 85 optimal weight:    0.0980
   chunk 39 optimal weight:    7.9990
   chunk 89 optimal weight:    0.7980
   chunk 134 optimal weight:    0.9980
   chunk 147 optimal weight:    5.9990
   chunk 137 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 120 optimal weight:    0.0670
   chunk 123 optimal weight:    0.9980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
D 201 HIS
C  46 ASN
** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 243 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.135629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.108630 restraints weight = 21171.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.112664 restraints weight = 10383.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.115435 restraints weight = 6572.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  14624  Z= 0.101
  Angle     :  0.546   9.325  19639  Z= 0.269
  Chirality :  0.042   0.295   2156
  Planarity :  0.003   0.038   2412
  Dihedral  :  5.707  56.524   2229
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.57 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 11.87 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.22), residues: 1679
  helix:  2.27 (0.21), residues: 594
  sheet: -0.46 (0.29), residues: 385
  loop : -0.75 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C 243 
 HIS   0.002   0.000   HIS A 311 
 PHE   0.012   0.001   PHE C  13 
 TYR   0.018   0.001   TYR D 301 
 ARG   0.007   0.000   ARG B 271 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00539 (    3)
  link_NAG-ASN         : angle       2.79796 (    9)
  hydrogen bonds       : bond        0.03976 (  529)
  hydrogen bonds       : angle       4.88397 ( 1551)
  SS BOND              : bond        0.00141 (    9)
  SS BOND              : angle       0.67000 (   18)
  covalent geometry    : bond        0.00217 (14607)
  covalent geometry    : angle       0.54258 (19612)
  Misc. bond           : bond        0.00019 (    5)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 260
  time to evaluate  : 1.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  141 ASP cc_start: 0.8156 (t70) cc_final: 0.7700 (p0)
REVERT: D  246 MET cc_start: 0.7386 (mtm) cc_final: 0.7126 (mtt)
REVERT: D  298 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7863 (tt)
REVERT: A  169 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7761 (mt-10)
REVERT: A  173 GLN cc_start: 0.8461 (pp30) cc_final: 0.8132 (pp30)
REVERT: A  220 MET cc_start: 0.7583 (mmm) cc_final: 0.7180 (mmm)
REVERT: A  396 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7422 (mtmm)
REVERT: A  400 ILE cc_start: 0.8361 (tp) cc_final: 0.7694 (pt)
REVERT: A  411 MET cc_start: 0.6885 (mmp) cc_final: 0.6437 (mmp)
REVERT: B   18 MET cc_start: 0.8467 (ppp) cc_final: 0.8198 (ptt)
REVERT: B   83 LEU cc_start: 0.8077 (tt) cc_final: 0.7743 (tt)
REVERT: B  266 GLN cc_start: 0.8147 (tp40) cc_final: 0.7934 (tt0)
REVERT: B  397 ILE cc_start: 0.8412 (mm) cc_final: 0.8089 (mt)
REVERT: B  411 MET cc_start: 0.7537 (mmp) cc_final: 0.6514 (ttp)
REVERT: C  206 LYS cc_start: 0.7348 (mptt) cc_final: 0.6808 (ttpt)
REVERT: C  243 TRP cc_start: 0.8724 (m100) cc_final: 0.8484 (m100)
REVERT: E   77 MET cc_start: 0.8593 (mmt) cc_final: 0.8261 (mmt)
REVERT: E  176 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8104 (mmtt)
REVERT: E  187 ASP cc_start: 0.8355 (t0) cc_final: 0.7833 (t0)
REVERT: E  248 MET cc_start: 0.8717 (tpp) cc_final: 0.8327 (tpp)
REVERT: E  329 GLN cc_start: 0.8777 (tp40) cc_final: 0.8311 (tp40)
  outliers start: 41
  outliers final: 29
  residues processed: 289
  average time/residue: 0.2777
  time to fit residues: 121.5078
Evaluate side-chains
  276 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 246
  time to evaluate  : 1.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  123 ASN
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  240 ILE
Chi-restraints excluded: chain D residue  273 SER
Chi-restraints excluded: chain D residue  298 LEU
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  240 ILE
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue  240 ILE
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  265 SER
Chi-restraints excluded: chain E residue  290 GLU
Chi-restraints excluded: chain E residue  454 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 126 optimal weight:    4.9990
   chunk 150 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 120 optimal weight:   10.0000
   chunk 100 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 107 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0870
   overall best weight:    1.9562

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

Flipped N/Q/H residues before XYZ refinement:
D 186 GLN
C  42 ASN
E 243 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.130828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.103875 restraints weight = 21134.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.107729 restraints weight = 10462.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.110215 restraints weight = 6661.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.1633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14624  Z= 0.166
  Angle     :  0.582  10.348  19639  Z= 0.290
  Chirality :  0.044   0.253   2156
  Planarity :  0.004   0.040   2412
  Dihedral  :  5.844  55.941   2229
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.47 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 13.18 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.21), residues: 1679
  helix:  2.21 (0.21), residues: 594
  sheet: -0.62 (0.29), residues: 385
  loop : -0.81 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP D 243 
 HIS   0.003   0.001   HIS A 311 
 PHE   0.013   0.001   PHE A 295 
 TYR   0.024   0.002   TYR A 301 
 ARG   0.009   0.000   ARG B 271 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00565 (    3)
  link_NAG-ASN         : angle       2.51990 (    9)
  hydrogen bonds       : bond        0.04569 (  529)
  hydrogen bonds       : angle       4.95620 ( 1551)
  SS BOND              : bond        0.00114 (    9)
  SS BOND              : angle       0.76702 (   18)
  covalent geometry    : bond        0.00399 (14607)
  covalent geometry    : angle       0.57905 (19612)
  Misc. bond           : bond        0.00018 (    5)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 243
  time to evaluate  : 1.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  141 ASP cc_start: 0.8154 (t70) cc_final: 0.7653 (p0)
REVERT: D  246 MET cc_start: 0.7515 (mtm) cc_final: 0.7237 (mtt)
REVERT: D  263 MET cc_start: 0.8565 (mmm) cc_final: 0.8120 (mmm)
REVERT: D  298 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7812 (tt)
REVERT: A  169 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7769 (mt-10)
REVERT: A  173 GLN cc_start: 0.8486 (pp30) cc_final: 0.8140 (pp30)
REVERT: A  203 ASN cc_start: 0.8729 (m-40) cc_final: 0.8098 (p0)
REVERT: A  220 MET cc_start: 0.7686 (mmm) cc_final: 0.7385 (mmm)
REVERT: A  227 MET cc_start: 0.8647 (mmt) cc_final: 0.8068 (mmt)
REVERT: A  243 TRP cc_start: 0.7231 (m100) cc_final: 0.6947 (m100)
REVERT: A  396 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7489 (mtmm)
REVERT: A  400 ILE cc_start: 0.8416 (tp) cc_final: 0.7755 (pt)
REVERT: A  411 MET cc_start: 0.6819 (mmt) cc_final: 0.6384 (mmp)
REVERT: B   83 LEU cc_start: 0.8135 (tt) cc_final: 0.7738 (tt)
REVERT: B  397 ILE cc_start: 0.8410 (mm) cc_final: 0.8087 (mt)
REVERT: B  411 MET cc_start: 0.7627 (mmp) cc_final: 0.6541 (ttp)
REVERT: E   77 MET cc_start: 0.8605 (mmt) cc_final: 0.8258 (mmt)
REVERT: E  141 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8124 (tt)
REVERT: E  176 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8195 (mmtt)
REVERT: E  187 ASP cc_start: 0.8392 (t0) cc_final: 0.7855 (t0)
REVERT: E  248 MET cc_start: 0.8762 (tpp) cc_final: 0.8371 (tpp)
  outliers start: 52
  outliers final: 38
  residues processed: 277
  average time/residue: 0.2302
  time to fit residues: 97.3749
Evaluate side-chains
  266 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 226
  time to evaluate  : 1.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  123 ASN
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  240 ILE
Chi-restraints excluded: chain D residue  273 SER
Chi-restraints excluded: chain D residue  298 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  226 GLN
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  243 TRP
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue   42 ASN
Chi-restraints excluded: chain C residue   56 MET
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain C residue  240 ILE
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain C residue  304 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  265 SER
Chi-restraints excluded: chain E residue  290 GLU
Chi-restraints excluded: chain E residue  328 VAL
Chi-restraints excluded: chain E residue  332 LEU
Chi-restraints excluded: chain E residue  454 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 161 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 110 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 146 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 83 optimal weight:    0.8980
   chunk 160 optimal weight:    1.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
D 201 HIS
A  46 ASN
C  42 ASN
** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 243 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.132263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.104847 restraints weight = 21349.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.108802 restraints weight = 10607.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.111501 restraints weight = 6783.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14624  Z= 0.128
  Angle     :  0.561   9.787  19639  Z= 0.277
  Chirality :  0.043   0.228   2156
  Planarity :  0.004   0.040   2412
  Dihedral  :  5.801  58.096   2229
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 13.97 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.21), residues: 1679
  helix:  2.31 (0.21), residues: 594
  sheet: -0.58 (0.29), residues: 385
  loop : -0.79 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP C 243 
 HIS   0.007   0.001   HIS D 311 
 PHE   0.019   0.001   PHE C  13 
 TYR   0.026   0.001   TYR E 224 
 ARG   0.008   0.000   ARG B 271 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00547 (    3)
  link_NAG-ASN         : angle       2.34355 (    9)
  hydrogen bonds       : bond        0.04259 (  529)
  hydrogen bonds       : angle       4.84744 ( 1551)
  SS BOND              : bond        0.00140 (    9)
  SS BOND              : angle       0.70855 (   18)
  covalent geometry    : bond        0.00300 (14607)
  covalent geometry    : angle       0.55906 (19612)
  Misc. bond           : bond        0.00018 (    5)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 241
  time to evaluate  : 1.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  141 ASP cc_start: 0.8141 (t70) cc_final: 0.7626 (p0)
REVERT: D  246 MET cc_start: 0.7498 (mtm) cc_final: 0.7228 (mtt)
REVERT: D  263 MET cc_start: 0.8526 (mmm) cc_final: 0.8080 (mmm)
REVERT: D  298 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7812 (tt)
REVERT: A  169 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7721 (mt-10)
REVERT: A  173 GLN cc_start: 0.8507 (pp30) cc_final: 0.8150 (pp30)
REVERT: A  203 ASN cc_start: 0.8717 (m-40) cc_final: 0.8096 (p0)
REVERT: A  227 MET cc_start: 0.8629 (mmt) cc_final: 0.8071 (mmt)
REVERT: A  243 TRP cc_start: 0.7014 (m100) cc_final: 0.6783 (m100)
REVERT: A  271 ARG cc_start: 0.8160 (tpt90) cc_final: 0.7739 (tpp80)
REVERT: A  396 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7446 (mtmm)
REVERT: A  400 ILE cc_start: 0.8411 (tp) cc_final: 0.7765 (pt)
REVERT: A  411 MET cc_start: 0.6903 (mmt) cc_final: 0.6522 (mmp)
REVERT: B   83 LEU cc_start: 0.8107 (tt) cc_final: 0.7697 (tt)
REVERT: B  411 MET cc_start: 0.7602 (mmp) cc_final: 0.6494 (ttp)
REVERT: C   42 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8431 (p0)
REVERT: E   77 MET cc_start: 0.8619 (mmt) cc_final: 0.8302 (mmt)
REVERT: E  141 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8145 (tt)
REVERT: E  176 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8145 (mmtt)
REVERT: E  187 ASP cc_start: 0.8364 (t0) cc_final: 0.7848 (t0)
REVERT: E  248 MET cc_start: 0.8720 (tpp) cc_final: 0.8401 (tpp)
REVERT: E  261 LEU cc_start: 0.8399 (mt) cc_final: 0.8182 (mt)
  outliers start: 57
  outliers final: 39
  residues processed: 279
  average time/residue: 0.2367
  time to fit residues: 100.6053
Evaluate side-chains
  267 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 225
  time to evaluate  : 1.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  123 ASN
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  240 ILE
Chi-restraints excluded: chain D residue  273 SER
Chi-restraints excluded: chain D residue  298 LEU
Chi-restraints excluded: chain D residue  398 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   46 ASN
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  226 GLN
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  240 ILE
Chi-restraints excluded: chain B residue  243 TRP
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue   42 ASN
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain C residue  240 ILE
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  265 SER
Chi-restraints excluded: chain E residue  290 GLU
Chi-restraints excluded: chain E residue  454 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 159 optimal weight:    0.9980
   chunk 129 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 75 optimal weight:    9.9990
   chunk 120 optimal weight:   10.0000
   chunk 155 optimal weight:    7.9990
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
D  31 ASN
D 201 HIS
A  46 ASN
** C  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 243 GLN
E 333 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.128903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.101397 restraints weight = 21636.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.105215 restraints weight = 10852.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.107841 restraints weight = 6993.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  14624  Z= 0.216
  Angle     :  0.612  10.454  19639  Z= 0.306
  Chirality :  0.044   0.210   2156
  Planarity :  0.004   0.080   2412
  Dihedral  :  6.246  56.046   2229
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 15.02 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.21), residues: 1679
  helix:  2.17 (0.21), residues: 591
  sheet: -0.82 (0.28), residues: 392
  loop : -0.83 (0.23), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP D 243 
 HIS   0.006   0.001   HIS D 311 
 PHE   0.014   0.001   PHE B  48 
 TYR   0.024   0.002   TYR A 301 
 ARG   0.003   0.000   ARG C 399 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00546 (    3)
  link_NAG-ASN         : angle       2.23462 (    9)
  hydrogen bonds       : bond        0.04939 (  529)
  hydrogen bonds       : angle       5.01200 ( 1551)
  SS BOND              : bond        0.00130 (    9)
  SS BOND              : angle       0.84996 (   18)
  covalent geometry    : bond        0.00526 (14607)
  covalent geometry    : angle       0.61032 (19612)
  Misc. bond           : bond        0.00035 (    5)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 229
  time to evaluate  : 1.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  141 ASP cc_start: 0.8189 (t70) cc_final: 0.7688 (p0)
REVERT: D  263 MET cc_start: 0.8574 (mmm) cc_final: 0.8369 (mmm)
REVERT: D  298 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7866 (tt)
REVERT: A  169 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7742 (mt-10)
REVERT: A  173 GLN cc_start: 0.8532 (pp30) cc_final: 0.8150 (pp30)
REVERT: A  203 ASN cc_start: 0.8737 (m-40) cc_final: 0.8112 (p0)
REVERT: A  396 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7534 (mtmm)
REVERT: A  411 MET cc_start: 0.6838 (mmt) cc_final: 0.6484 (mmp)
REVERT: B   83 LEU cc_start: 0.8193 (tt) cc_final: 0.7965 (tt)
REVERT: C   42 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8442 (p0)
REVERT: C   56 MET cc_start: 0.8351 (mmm) cc_final: 0.8133 (mtp)
REVERT: E   77 MET cc_start: 0.8637 (mmt) cc_final: 0.8328 (mmt)
REVERT: E  141 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8225 (tt)
REVERT: E  176 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8193 (mmtt)
REVERT: E  187 ASP cc_start: 0.8432 (t0) cc_final: 0.7895 (t0)
REVERT: E  248 MET cc_start: 0.8759 (tpp) cc_final: 0.8416 (tpp)
REVERT: E  249 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7573 (ttm)
REVERT: E  317 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8400 (m-10)
REVERT: E  329 GLN cc_start: 0.8688 (tp40) cc_final: 0.8296 (tp40)
  outliers start: 66
  outliers final: 51
  residues processed: 270
  average time/residue: 0.2742
  time to fit residues: 114.0283
Evaluate side-chains
  275 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 219
  time to evaluate  : 1.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  123 ASN
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  240 ILE
Chi-restraints excluded: chain D residue  273 SER
Chi-restraints excluded: chain D residue  298 LEU
Chi-restraints excluded: chain D residue  398 SER
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   46 ASN
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  226 GLN
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  141 ASP
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  240 ILE
Chi-restraints excluded: chain B residue  243 TRP
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue   42 ASN
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  240 ILE
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   74 GLU
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  170 MET
Chi-restraints excluded: chain E residue  213 LYS
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  265 SER
Chi-restraints excluded: chain E residue  290 GLU
Chi-restraints excluded: chain E residue  317 PHE
Chi-restraints excluded: chain E residue  328 VAL
Chi-restraints excluded: chain E residue  332 LEU
Chi-restraints excluded: chain E residue  454 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 130 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 11 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   chunk 110 optimal weight:    5.9990
   chunk 97 optimal weight:    9.9990
   chunk 94 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 159 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
D  31 ASN
** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 243 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.133096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.105643 restraints weight = 21344.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.109618 restraints weight = 10589.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.112339 restraints weight = 6770.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14624  Z= 0.112
  Angle     :  0.557   9.414  19639  Z= 0.274
  Chirality :  0.042   0.182   2156
  Planarity :  0.004   0.045   2412
  Dihedral  :  5.969  59.649   2229
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 16.33 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.21), residues: 1679
  helix:  2.32 (0.21), residues: 594
  sheet: -0.69 (0.28), residues: 398
  loop : -0.73 (0.24), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 243 
 HIS   0.003   0.001   HIS D 311 
 PHE   0.021   0.001   PHE C  13 
 TYR   0.030   0.001   TYR E 224 
 ARG   0.002   0.000   ARG A 399 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00517 (    3)
  link_NAG-ASN         : angle       2.07194 (    9)
  hydrogen bonds       : bond        0.04078 (  529)
  hydrogen bonds       : angle       4.74478 ( 1551)
  SS BOND              : bond        0.00156 (    9)
  SS BOND              : angle       0.67985 (   18)
  covalent geometry    : bond        0.00254 (14607)
  covalent geometry    : angle       0.55474 (19612)
  Misc. bond           : bond        0.00026 (    5)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 247
  time to evaluate  : 1.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  141 ASP cc_start: 0.8171 (t70) cc_final: 0.7615 (p0)
REVERT: D  263 MET cc_start: 0.8456 (mmm) cc_final: 0.7998 (mmm)
REVERT: D  298 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7653 (tt)
REVERT: A  169 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7709 (mt-10)
REVERT: A  173 GLN cc_start: 0.8557 (pp30) cc_final: 0.8160 (pp30)
REVERT: A  203 ASN cc_start: 0.8747 (m-40) cc_final: 0.8107 (p0)
REVERT: A  227 MET cc_start: 0.8608 (mmt) cc_final: 0.8036 (mmt)
REVERT: A  396 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7638 (mtmm)
REVERT: A  411 MET cc_start: 0.6791 (mmt) cc_final: 0.6455 (mmp)
REVERT: B   83 LEU cc_start: 0.8019 (tt) cc_final: 0.7563 (tt)
REVERT: E   77 MET cc_start: 0.8657 (mmt) cc_final: 0.8395 (mmt)
REVERT: E  141 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8106 (tt)
REVERT: E  187 ASP cc_start: 0.8406 (t0) cc_final: 0.7867 (t0)
REVERT: E  248 MET cc_start: 0.8682 (tpp) cc_final: 0.8431 (tpp)
REVERT: E  316 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8261 (mp)
REVERT: E  329 GLN cc_start: 0.8601 (tp40) cc_final: 0.8220 (tp40)
  outliers start: 53
  outliers final: 40
  residues processed: 282
  average time/residue: 0.2476
  time to fit residues: 106.3640
Evaluate side-chains
  276 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 233
  time to evaluate  : 1.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  123 ASN
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  240 ILE
Chi-restraints excluded: chain D residue  298 LEU
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  226 GLN
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  240 ILE
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  240 ILE
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain C residue  300 GLU
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  170 MET
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  265 SER
Chi-restraints excluded: chain E residue  316 LEU
Chi-restraints excluded: chain E residue  454 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 166 optimal weight:    3.9990
   chunk 152 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 165 optimal weight:    8.9990
   chunk 138 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0040
   chunk 61 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 34 optimal weight:    0.1980
   overall best weight:    0.8396

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

Flipped N/Q/H residues before XYZ refinement:
C  42 ASN
** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 243 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.133713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.106270 restraints weight = 21324.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.110257 restraints weight = 10578.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.112975 restraints weight = 6766.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  14624  Z= 0.110
  Angle     :  0.558   9.516  19639  Z= 0.272
  Chirality :  0.042   0.167   2156
  Planarity :  0.004   0.044   2412
  Dihedral  :  5.790  59.565   2229
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 16.66 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.21), residues: 1679
  helix:  2.25 (0.21), residues: 596
  sheet: -0.76 (0.28), residues: 406
  loop : -0.63 (0.24), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP A 243 
 HIS   0.003   0.000   HIS D 311 
 PHE   0.012   0.001   PHE A 295 
 TYR   0.028   0.001   TYR E 224 
 ARG   0.008   0.000   ARG D 271 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00492 (    3)
  link_NAG-ASN         : angle       1.97524 (    9)
  hydrogen bonds       : bond        0.03978 (  529)
  hydrogen bonds       : angle       4.70632 ( 1551)
  SS BOND              : bond        0.00171 (    9)
  SS BOND              : angle       0.67861 (   18)
  covalent geometry    : bond        0.00251 (14607)
  covalent geometry    : angle       0.55662 (19612)
  Misc. bond           : bond        0.00022 (    5)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 239
  time to evaluate  : 1.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  141 ASP cc_start: 0.8137 (t70) cc_final: 0.7618 (p0)
REVERT: D  263 MET cc_start: 0.8465 (mmm) cc_final: 0.8034 (mmm)
REVERT: D  386 LEU cc_start: 0.8192 (pt) cc_final: 0.7584 (tt)
REVERT: A  169 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7718 (mt-10)
REVERT: A  173 GLN cc_start: 0.8534 (pp30) cc_final: 0.8153 (pp30)
REVERT: A  203 ASN cc_start: 0.8705 (m-40) cc_final: 0.8089 (p0)
REVERT: A  227 MET cc_start: 0.8599 (mmt) cc_final: 0.8014 (mmt)
REVERT: A  271 ARG cc_start: 0.8032 (tpt90) cc_final: 0.7729 (tpp80)
REVERT: A  396 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7527 (mtmm)
REVERT: A  411 MET cc_start: 0.6838 (mmt) cc_final: 0.6490 (mmp)
REVERT: B   83 LEU cc_start: 0.8158 (tt) cc_final: 0.7736 (tt)
REVERT: B  271 ARG cc_start: 0.7117 (mmt90) cc_final: 0.6643 (mpt-90)
REVERT: C  150 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7416 (tp40)
REVERT: E   77 MET cc_start: 0.8691 (mmt) cc_final: 0.8427 (mmt)
REVERT: E  141 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8149 (tt)
REVERT: E  187 ASP cc_start: 0.8395 (t0) cc_final: 0.7882 (t0)
REVERT: E  329 GLN cc_start: 0.8672 (tp40) cc_final: 0.8275 (tp40)
  outliers start: 51
  outliers final: 45
  residues processed: 273
  average time/residue: 0.2516
  time to fit residues: 105.3839
Evaluate side-chains
  277 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 231
  time to evaluate  : 1.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  123 ASN
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  240 ILE
Chi-restraints excluded: chain D residue  273 SER
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   67 GLN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  226 GLN
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  240 ILE
Chi-restraints excluded: chain B residue  243 TRP
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue   42 ASN
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  240 ILE
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  300 GLU
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  170 MET
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  265 SER
Chi-restraints excluded: chain E residue  454 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 119 optimal weight:    4.9990
   chunk 139 optimal weight:    0.9990
   chunk 156 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 74 optimal weight:    8.9990
   chunk 51 optimal weight:    4.9990
   chunk 143 optimal weight:    2.9990
   chunk 90 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 152 optimal weight:    2.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
C  42 ASN
** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 243 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.133280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.105814 restraints weight = 21196.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.109790 restraints weight = 10563.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.112499 restraints weight = 6763.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14624  Z= 0.115
  Angle     :  0.567   9.573  19639  Z= 0.275
  Chirality :  0.042   0.168   2156
  Planarity :  0.004   0.084   2412
  Dihedral  :  5.725  59.874   2229
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 17.18 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.21), residues: 1679
  helix:  2.24 (0.21), residues: 597
  sheet: -0.78 (0.28), residues: 406
  loop : -0.61 (0.24), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 243 
 HIS   0.003   0.000   HIS D 311 
 PHE   0.013   0.001   PHE E  84 
 TYR   0.028   0.001   TYR E 224 
 ARG   0.008   0.000   ARG D 271 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00474 (    3)
  link_NAG-ASN         : angle       1.93559 (    9)
  hydrogen bonds       : bond        0.03939 (  529)
  hydrogen bonds       : angle       4.68900 ( 1551)
  SS BOND              : bond        0.00159 (    9)
  SS BOND              : angle       0.67295 (   18)
  covalent geometry    : bond        0.00266 (14607)
  covalent geometry    : angle       0.56527 (19612)
  Misc. bond           : bond        0.00019 (    5)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 241
  time to evaluate  : 1.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  141 ASP cc_start: 0.8142 (t70) cc_final: 0.7614 (p0)
REVERT: D  263 MET cc_start: 0.8463 (mmm) cc_final: 0.8031 (mmm)
REVERT: D  386 LEU cc_start: 0.8157 (pt) cc_final: 0.7558 (tt)
REVERT: A  169 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7716 (mt-10)
REVERT: A  173 GLN cc_start: 0.8570 (pp30) cc_final: 0.8178 (pp30)
REVERT: A  203 ASN cc_start: 0.8704 (m-40) cc_final: 0.8086 (p0)
REVERT: A  227 MET cc_start: 0.8606 (mmt) cc_final: 0.8008 (mmt)
REVERT: A  271 ARG cc_start: 0.8006 (tpt90) cc_final: 0.7722 (tpp80)
REVERT: A  396 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7507 (mtmm)
REVERT: A  411 MET cc_start: 0.6822 (mmt) cc_final: 0.6475 (mmp)
REVERT: B   83 LEU cc_start: 0.8122 (tt) cc_final: 0.7717 (tt)
REVERT: B  271 ARG cc_start: 0.7121 (mmt90) cc_final: 0.6688 (mpt-90)
REVERT: B  411 MET cc_start: 0.7420 (mmp) cc_final: 0.6316 (ttp)
REVERT: C  150 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7501 (tp40)
REVERT: E   77 MET cc_start: 0.8693 (mmt) cc_final: 0.8404 (mmt)
REVERT: E  141 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8127 (tt)
REVERT: E  176 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8078 (mmtt)
REVERT: E  187 ASP cc_start: 0.8393 (t0) cc_final: 0.7873 (t0)
REVERT: E  316 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8246 (mp)
REVERT: E  329 GLN cc_start: 0.8666 (tp40) cc_final: 0.8246 (tp40)
  outliers start: 49
  outliers final: 42
  residues processed: 274
  average time/residue: 0.2261
  time to fit residues: 95.2754
Evaluate side-chains
  277 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 233
  time to evaluate  : 1.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  123 ASN
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  240 ILE
Chi-restraints excluded: chain D residue  273 SER
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  226 GLN
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  240 ILE
Chi-restraints excluded: chain B residue  243 TRP
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue   42 ASN
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  240 ILE
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  300 GLU
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  170 MET
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  265 SER
Chi-restraints excluded: chain E residue  316 LEU
Chi-restraints excluded: chain E residue  454 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 151 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 149 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 129 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 104 optimal weight:    0.5980
   chunk 82 optimal weight:    7.9990
   chunk 167 optimal weight:    3.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
C  42 ASN
** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 243 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.131487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.103799 restraints weight = 21303.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.107725 restraints weight = 10716.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.110386 restraints weight = 6898.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14624  Z= 0.152
  Angle     :  0.591  11.078  19639  Z= 0.289
  Chirality :  0.043   0.164   2156
  Planarity :  0.004   0.053   2412
  Dihedral  :  5.918  59.731   2229
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 17.51 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.21), residues: 1679
  helix:  2.18 (0.21), residues: 598
  sheet: -0.80 (0.28), residues: 402
  loop : -0.62 (0.24), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 243 
 HIS   0.003   0.001   HIS D 311 
 PHE   0.013   0.001   PHE A 295 
 TYR   0.029   0.002   TYR E 224 
 ARG   0.008   0.000   ARG D 271 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00470 (    3)
  link_NAG-ASN         : angle       1.89061 (    9)
  hydrogen bonds       : bond        0.04275 (  529)
  hydrogen bonds       : angle       4.77638 ( 1551)
  SS BOND              : bond        0.00152 (    9)
  SS BOND              : angle       0.73219 (   18)
  covalent geometry    : bond        0.00366 (14607)
  covalent geometry    : angle       0.58980 (19612)
  Misc. bond           : bond        0.00029 (    5)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 233
  time to evaluate  : 1.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  141 ASP cc_start: 0.8153 (t70) cc_final: 0.7625 (p0)
REVERT: D  386 LEU cc_start: 0.8169 (pt) cc_final: 0.7582 (tt)
REVERT: A  169 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7725 (mt-10)
REVERT: A  173 GLN cc_start: 0.8590 (pp30) cc_final: 0.8188 (pp30)
REVERT: A  203 ASN cc_start: 0.8710 (m-40) cc_final: 0.8085 (p0)
REVERT: A  396 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7675 (mtmm)
REVERT: A  411 MET cc_start: 0.6835 (mmt) cc_final: 0.6476 (mmp)
REVERT: B   83 LEU cc_start: 0.8133 (tt) cc_final: 0.7703 (tt)
REVERT: B  271 ARG cc_start: 0.7140 (mmt90) cc_final: 0.6747 (mpt-90)
REVERT: E   77 MET cc_start: 0.8717 (mmt) cc_final: 0.8406 (mmt)
REVERT: E  141 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8190 (tt)
REVERT: E  176 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8048 (mmtt)
REVERT: E  187 ASP cc_start: 0.8426 (t0) cc_final: 0.7912 (t0)
REVERT: E  316 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8307 (mp)
REVERT: E  329 GLN cc_start: 0.8685 (tp40) cc_final: 0.8227 (tp40)
  outliers start: 46
  outliers final: 44
  residues processed: 263
  average time/residue: 0.2594
  time to fit residues: 103.7098
Evaluate side-chains
  272 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 226
  time to evaluate  : 1.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  123 ASN
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  240 ILE
Chi-restraints excluded: chain D residue  273 SER
Chi-restraints excluded: chain D residue  388 ILE
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  226 GLN
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  240 ILE
Chi-restraints excluded: chain B residue  243 TRP
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue   42 ASN
Chi-restraints excluded: chain C residue  113 THR
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  240 ILE
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  300 GLU
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  170 MET
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  265 SER
Chi-restraints excluded: chain E residue  290 GLU
Chi-restraints excluded: chain E residue  316 LEU
Chi-restraints excluded: chain E residue  454 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 17 optimal weight:    0.1980
   chunk 12 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 128 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0270
   chunk 61 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 243 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.135053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.107524 restraints weight = 21394.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.111571 restraints weight = 10551.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.114337 restraints weight = 6715.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  14624  Z= 0.105
  Angle     :  0.575  11.032  19639  Z= 0.278
  Chirality :  0.042   0.165   2156
  Planarity :  0.004   0.058   2412
  Dihedral  :  5.642  59.500   2227
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.84 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.21), residues: 1679
  helix:  2.23 (0.21), residues: 598
  sheet: -0.75 (0.28), residues: 406
  loop : -0.55 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 243 
 HIS   0.002   0.000   HIS D 311 
 PHE   0.012   0.001   PHE E  84 
 TYR   0.029   0.001   TYR E 224 
 ARG   0.008   0.000   ARG D 271 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00471 (    3)
  link_NAG-ASN         : angle       1.85520 (    9)
  hydrogen bonds       : bond        0.03842 (  529)
  hydrogen bonds       : angle       4.65931 ( 1551)
  SS BOND              : bond        0.00158 (    9)
  SS BOND              : angle       0.64091 (   18)
  covalent geometry    : bond        0.00234 (14607)
  covalent geometry    : angle       0.57412 (19612)
  Misc. bond           : bond        0.00018 (    5)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 4588.74 seconds
wall clock time: 81 minutes 44.06 seconds (4904.06 seconds total)