Starting phenix.real_space_refine
on Mon Jun  9 21:08:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hpu_34944/06_2025/8hpu_34944.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hpu_34944/06_2025/8hpu_34944.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hpu_34944/06_2025/8hpu_34944.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hpu_34944/06_2025/8hpu_34944.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hpu_34944/06_2025/8hpu_34944.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hpu_34944/06_2025/8hpu_34944.cif"
  }
  resolution = 2.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.075
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3142 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    5224      2.51       5
     N    1390      2.21       5
     O    1633      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8281
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1555
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 194, 1547
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 12, 'TRANS': 181}
      Conformer: "B"
        Number of residues, atoms: 194, 1547
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 12, 'TRANS': 181}
          bond proxies already assigned to first conformer: 1584
    Chain: "H"
      Number of atoms: 1756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1756
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214}
    Chain: "L"
      Number of atoms: 1658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1658
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203}
    Chain: "M"
      Number of atoms: 1656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1656
          Classifications: {'peptide': 224}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210}
    Chain: "N"
      Number of atoms: 1642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1642
          Classifications: {'peptide': 216}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 8.43, per 1000 atoms: 1.02
  Number of scatterers: 8281
  At special positions: 0
  Unit cell: (117.6, 124.32, 120.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1633      8.00
     N    1390      7.00
     C    5224      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 350 " - pdb=" SG  CYS A 375 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 393 " - pdb=" SG  CYS A 446 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 405 " - pdb=" SG  CYS A 539 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 494 " - pdb=" SG  CYS A 502 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 155 " - pdb=" SG  CYS H 211 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 231 " - pdb=" SG  CYS L 215 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  22 " - pdb=" SG  CYS M  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 149 " - pdb=" SG  CYS M 205 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M 225 " - pdb=" SG  CYS N 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N 136 " - pdb=" SG  CYS N 196 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1201 " - " ASN A 357 "
  Time building additional restraints: 2.03
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1996

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 23 sheets defined
      8.4% alpha, 43.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 351 through 358
      removed outlier: 3.583A  pdb=" N   VAL A 355 " --> pdb=" O   PRO A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 367
      removed outlier: 3.564A  pdb=" N   TRP A 367 " --> pdb=" O   VAL A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 385
    Processing helix  chain 'A' and resid 397 through 404
      removed outlier: 3.869A  pdb=" N   LEU A 401 " --> pdb=" O   PRO A 398 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   ASN A 402 " --> pdb=" O   THR A 399 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LEU A 404 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 424
    Processing helix  chain 'A' and resid 431 through 436
    Processing helix  chain 'H' and resid 88 through 92
      removed outlier: 3.644A  pdb=" N   THR H  92 " --> pdb=" O   PRO H  89 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 171 through 173
      No H-bonds generated for 'chain 'H' and resid 171 through 173'
    Processing helix  chain 'H' and resid 200 through 204
      removed outlier: 3.796A  pdb=" N   LEU H 204 " --> pdb=" O   SER H 201 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 32
      No H-bonds generated for 'chain 'L' and resid 30 through 32'
    Processing helix  chain 'L' and resid 183 through 188
    Processing helix  chain 'M' and resid 61 through 64
    Processing helix  chain 'M' and resid 86 through 90
    Processing helix  chain 'M' and resid 165 through 167
      No H-bonds generated for 'chain 'M' and resid 165 through 167'
    Processing helix  chain 'M' and resid 196 through 201
      removed outlier: 4.488A  pdb=" N   THR M 200 " --> pdb=" O   SER M 196 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 123 through 128
    Processing helix  chain 'N' and resid 185 through 190
      removed outlier: 3.867A  pdb=" N   LYS N 190 " --> pdb=" O   ALA N 186 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 372
    Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 468
    Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.194A  pdb=" N   ARG H  40 " --> pdb=" O   TRP H  49 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   TRP H  49 " --> pdb=" O   ARG H  40 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 7.350A  pdb=" N   PHE H 101 " --> pdb=" O   PHE H 115 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   PHE H 115 " --> pdb=" O   PHE H 101 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 135 through 139
      removed outlier: 6.212A  pdb=" N   TYR H 191 " --> pdb=" O   ASP H 159 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 135 through 139
      removed outlier: 6.212A  pdb=" N   TYR H 191 " --> pdb=" O   ASP H 159 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 166 through 169
      removed outlier: 4.180A  pdb=" N   TYR H 209 " --> pdb=" O   VAL H 226 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.748A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 115 through 119
      removed outlier: 5.954A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 145 through 151
    Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 7
      removed outlier: 3.825A  pdb=" N   GLN M   3 " --> pdb=" O   SER M  25 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'M' and resid 10 through 12
      removed outlier: 4.389A  pdb=" N   TYR M  33 " --> pdb=" O   GLU M  98 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   MET M  34 " --> pdb=" O   VAL M  50 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   VAL M  50 " --> pdb=" O   MET M  34 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   TRP M  36 " --> pdb=" O   VAL M  48 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'M' and resid 10 through 12
      removed outlier: 6.732A  pdb=" N   CYS M  95 " --> pdb=" O   TRP M 112 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   TRP M 112 " --> pdb=" O   CYS M  95 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   ARG M  97 " --> pdb=" O   ASP M 110 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ALA M 108 " --> pdb=" O   SER M  99 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'M' and resid 129 through 133
      removed outlier: 5.953A  pdb=" N   TYR M 185 " --> pdb=" O   ASP M 153 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'M' and resid 129 through 133
      removed outlier: 5.953A  pdb=" N   TYR M 185 " --> pdb=" O   ASP M 153 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'M' and resid 160 through 163
      removed outlier: 3.586A  pdb=" N   TYR M 203 " --> pdb=" O   VAL M 220 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'N' and resid 4 through 7
      removed outlier: 3.630A  pdb=" N   ASP N  70 " --> pdb=" O   SER N  67 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'N' and resid 10 through 13
      removed outlier: 3.618A  pdb=" N   GLU N 107 " --> pdb=" O   LEU N  11 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   LEU N  33 " --> pdb=" O   SER N  49 " (cutoff:3.500A)
      removed outlier: 5.269A  pdb=" N   SER N  49 " --> pdb=" O   LEU N  33 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   TRP N  35 " --> pdb=" O   LEU N  47 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'N' and resid 116 through 120
      removed outlier: 5.744A  pdb=" N   TYR N 175 " --> pdb=" O   ASN N 140 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   SER N 176 " --> pdb=" O   THR N 166 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'N' and resid 155 through 157
      removed outlier: 4.155A  pdb=" N   TRP N 150 " --> pdb=" O   GLN N 157 " (cutoff:3.500A)

    355 hydrogen bonds defined for protein.
    879 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.82

  Time building geometry restraints manager: 2.44 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: 2642
        1.34 -     1.46: 2053
        1.46 -     1.58: 3752
        1.58 -     1.70: 0
        1.70 -     1.82: 40
  Bond restraints: 8487
  Sorted by residual:
  bond pdb=" CA  CYS A 393 "
       pdb=" CB  CYS A 393 "
    ideal  model  delta    sigma   weight residual
    1.530  1.496  0.034 1.53e-02 4.27e+03 5.06e+00
  bond pdb=" C   PHE M 102 "
       pdb=" N   PRO M 103 "
    ideal  model  delta    sigma   weight residual
    1.334  1.345 -0.012 8.40e-03 1.42e+04 1.99e+00
  bond pdb=" C1  NAG A1201 "
       pdb=" O5  NAG A1201 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.75e+00
  bond pdb=" C   ALA A 386 "
       pdb=" N   PRO A 387 "
    ideal  model  delta    sigma   weight residual
    1.337  1.350 -0.014 1.06e-02 8.90e+03 1.66e+00
  bond pdb=" C   ASP N 187 "
       pdb=" N   TYR N 188 "
    ideal  model  delta    sigma   weight residual
    1.332  1.315  0.017 1.40e-02 5.10e+03 1.49e+00
  ... (remaining 8482 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.11: 11476
        3.11 -     6.23: 70
        6.23 -     9.34: 5
        9.34 -    12.46: 0
       12.46 -    15.57: 2
  Bond angle restraints: 11553
  Sorted by residual:
  angle pdb=" C   LEU H 139 "
        pdb=" N   ALA H 140 "
        pdb=" CA  ALA H 140 "
      ideal   model   delta    sigma   weight residual
     120.94  136.51  -15.57 1.90e+00 2.77e-01 6.72e+01
  angle pdb=" CA  CYS A 446 "
        pdb=" CB  CYS A 446 "
        pdb=" SG  CYS A 446 "
      ideal   model   delta    sigma   weight residual
     114.40  128.26  -13.86 2.30e+00 1.89e-01 3.63e+01
  angle pdb=" N   CYS A 393 "
        pdb=" CA  CYS A 393 "
        pdb=" C   CYS A 393 "
      ideal   model   delta    sigma   weight residual
     107.88  116.19   -8.31 1.41e+00 5.03e-01 3.47e+01
  angle pdb=" N   CYS A 446 "
        pdb=" CA  CYS A 446 "
        pdb=" C   CYS A 446 "
      ideal   model   delta    sigma   weight residual
     107.88  113.55   -5.67 1.41e+00 5.03e-01 1.61e+01
  angle pdb=" CA  GLY A 445 "
        pdb=" C   GLY A 445 "
        pdb=" O   GLY A 445 "
      ideal   model   delta    sigma   weight residual
     122.24  117.97    4.27 1.08e+00 8.57e-01 1.56e+01
  ... (remaining 11548 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 4625
       17.65 -    35.31: 366
       35.31 -    52.96: 68
       52.96 -    70.61: 15
       70.61 -    88.26: 13
  Dihedral angle restraints: 5087
    sinusoidal: 1963
      harmonic: 3124
  Sorted by residual:
  dihedral pdb=" CA  ASP H 116 "
           pdb=" C   ASP H 116 "
           pdb=" N   PRO H 117 "
           pdb=" CA  PRO H 117 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.45  -48.55     0      5.00e+00 4.00e-02 9.43e+01
  dihedral pdb=" CB  CYS A 393 "
           pdb=" SG  CYS A 393 "
           pdb=" SG  CYS A 446 "
           pdb=" CB  CYS A 446 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -11.06  -74.94     1      1.00e+01 1.00e-02 7.11e+01
  dihedral pdb=" CB  CYS H 155 "
           pdb=" SG  CYS H 155 "
           pdb=" SG  CYS H 211 "
           pdb=" CB  CYS H 211 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.84  -61.84     1      1.00e+01 1.00e-02 5.07e+01
  ... (remaining 5084 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1001
       0.051 -    0.101: 231
       0.101 -    0.152: 54
       0.152 -    0.203: 3
       0.203 -    0.253: 1
  Chirality restraints: 1290
  Sorted by residual:
  chirality pdb=" CA  CYS A 393 "
            pdb=" N   CYS A 393 "
            pdb=" C   CYS A 393 "
            pdb=" CB  CYS A 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  LYS M 215 "
            pdb=" N   LYS M 215 "
            pdb=" C   LYS M 215 "
            pdb=" CB  LYS M 215 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.95e-01
  chirality pdb=" CA  CYS A 446 "
            pdb=" N   CYS A 446 "
            pdb=" C   CYS A 446 "
            pdb=" CB  CYS A 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.81e-01
  ... (remaining 1287 not shown)

  Planarity restraints: 1489
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 163 "    0.038 5.00e-02 4.00e+02   5.68e-02 5.17e+00
        pdb=" N   PRO H 164 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO H 164 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO H 164 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP H 116 "   -0.036 5.00e-02 4.00e+02   5.49e-02 4.83e+00
        pdb=" N   PRO H 117 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO H 117 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO H 117 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE M 131 "   -0.031 5.00e-02 4.00e+02   4.67e-02 3.49e+00
        pdb=" N   PRO M 132 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO M 132 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO M 132 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1486 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 832
        2.75 -     3.29: 7851
        3.29 -     3.83: 13703
        3.83 -     4.36: 16707
        4.36 -     4.90: 28781
  Nonbonded interactions: 67874
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG N  61 "
            pdb=" OE2 GLU N  81 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" OD1 ASP A 456 "
            pdb=" OH  TYR A 465 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG1 THR A 514 "
            pdb=" OH  TYR L  33 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" CB  CYS A 393 "
            pdb=" CB  CYS A 446 "
     model   vdw
     2.276 3.072
  nonbonded pdb=" NE2 GLN L 148 "
            pdb=" O   GLN L 156 "
     model   vdw
     2.286 3.120
  ... (remaining 67869 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.360
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
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      :  0.003   0.044   8502  Z= 0.148
  Angle     :  0.708  15.572  11584  Z= 0.372
  Chirality :  0.046   0.253   1290
  Planarity :  0.005   0.057   1488
  Dihedral  : 13.597  88.265   3049
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.21 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    Twisted General : 0.10 %

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: -0.21 (0.26), residues: 1071
  helix: -2.94 (0.64), residues: 41
  sheet:  0.91 (0.25), residues: 427
  loop : -0.72 (0.26), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N 150 
 HIS   0.010   0.001   HIS A 519 
 PHE   0.017   0.001   PHE A 391 
 TYR   0.018   0.002   TYR L 174 
 ARG   0.003   0.000   ARG A 369 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00041 (    1)
  link_NAG-ASN         : angle       0.79650 (    3)
  hydrogen bonds       : bond        0.10302 (  313)
  hydrogen bonds       : angle       7.39353 (  879)
  SS BOND              : bond        0.00491 (   14)
  SS BOND              : angle       3.16265 (   28)
  covalent geometry    : bond        0.00326 ( 8487)
  covalent geometry    : angle       0.69191 (11553)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  160 TYR cc_start: 0.6168 (p90) cc_final: 0.5852 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 1.3149
  time to fit residues: 185.1592
Evaluate side-chains
  86 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.2980
   chunk 80 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    8.9990
   chunk 42 optimal weight:    0.0670
   chunk 83 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 61 optimal weight:    9.9990
   chunk 96 optimal weight:    9.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
H 179 HIS
H 219 ASN
** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 206 ASN
N 126 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.148711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.123828 restraints weight = 33121.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 3.15
r_work: 0.3826 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3827
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3827 r_free = 0.3827    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3827 r_free = 0.3827    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.1067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8502  Z= 0.138
  Angle     :  0.666  14.967  11584  Z= 0.343
  Chirality :  0.046   0.190   1290
  Planarity :  0.006   0.065   1488
  Dihedral  :  5.433  46.288   1189
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  9.32 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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: -0.07 (0.26), residues: 1071
  helix: -2.92 (0.63), residues: 40
  sheet:  0.97 (0.25), residues: 429
  loop : -0.59 (0.27), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L 149 
 HIS   0.008   0.001   HIS A 519 
 PHE   0.013   0.001   PHE N 141 
 TYR   0.013   0.002   TYR L 141 
 ARG   0.008   0.001   ARG N  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    1)
  link_NAG-ASN         : angle       1.45974 (    3)
  hydrogen bonds       : bond        0.03399 (  313)
  hydrogen bonds       : angle       6.14411 (  879)
  SS BOND              : bond        0.00517 (   14)
  SS BOND              : angle       2.85654 (   28)
  covalent geometry    : bond        0.00321 ( 8487)
  covalent geometry    : angle       0.65164 (11553)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
REVERT: A  391 PHE cc_start: 0.7864 (t80) cc_final: 0.7560 (t80)
REVERT: A  405 CYS cc_start: 0.4688 (t) cc_final: 0.4459 (t)
REVERT: H  160 TYR cc_start: 0.6409 (p90) cc_final: 0.5814 (p90)
REVERT: N   18 ARG cc_start: 0.7562 (mtp-110) cc_final: 0.7330 (mtp180)
  outliers start: 14
  outliers final: 3
  residues processed: 105
  average time/residue: 1.2078
  time to fit residues: 135.3742
Evaluate side-chains
  82 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain M residue  179 LEU
Chi-restraints excluded: chain N residue  138 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 100 optimal weight:    0.3980
   chunk 68 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 101 optimal weight:    4.9990
   chunk 97 optimal weight:    0.1980
   chunk 104 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
H 219 ASN
** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.148523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.124876 restraints weight = 30619.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 2.98
r_work: 0.3836 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3838 r_free = 0.3838    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3838 r_free = 0.3838    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8502  Z= 0.138
  Angle     :  0.658  16.653  11584  Z= 0.337
  Chirality :  0.045   0.185   1290
  Planarity :  0.006   0.069   1488
  Dihedral  :  5.313  45.298   1189
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 10.83 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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: -0.03 (0.26), residues: 1071
  helix: -2.94 (0.62), residues: 40
  sheet:  1.01 (0.25), residues: 429
  loop : -0.58 (0.27), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 118 
 HIS   0.007   0.001   HIS A 519 
 PHE   0.019   0.001   PHE N 141 
 TYR   0.014   0.002   TYR L 174 
 ARG   0.009   0.001   ARG A 371 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00064 (    1)
  link_NAG-ASN         : angle       1.58302 (    3)
  hydrogen bonds       : bond        0.03241 (  313)
  hydrogen bonds       : angle       5.87277 (  879)
  SS BOND              : bond        0.00567 (   14)
  SS BOND              : angle       2.93172 (   28)
  covalent geometry    : bond        0.00323 ( 8487)
  covalent geometry    : angle       0.64266 (11553)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 CYS cc_start: 0.4640 (t) cc_final: 0.4373 (t)
REVERT: H  160 TYR cc_start: 0.6459 (p90) cc_final: 0.5871 (p90)
REVERT: L  171 ASP cc_start: 0.6168 (t0) cc_final: 0.5853 (p0)
REVERT: M   64 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7515 (mmtm)
  outliers start: 22
  outliers final: 8
  residues processed: 105
  average time/residue: 1.1791
  time to fit residues: 131.9908
Evaluate side-chains
  91 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain M residue   64 LYS
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue  104 LEU
Chi-restraints excluded: chain M residue  179 LEU
Chi-restraints excluded: chain N residue   21 ILE
Chi-restraints excluded: chain N residue  126 GLN
Chi-restraints excluded: chain N residue  138 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0670
   chunk 35 optimal weight:    0.0980
   chunk 39 optimal weight:    0.1980
   chunk 56 optimal weight:    0.0570
   chunk 100 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.2036

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

Flipped N/Q/H residues before XYZ refinement:
A 408 ASN
H 214 ASN
H 219 ASN
** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.150432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.126792 restraints weight = 25888.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3990 rms_B_bonded: 2.62
r_work: 0.3880 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3883
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3883 r_free = 0.3883    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3883 r_free = 0.3883    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8502  Z= 0.103
  Angle     :  0.613  15.203  11584  Z= 0.312
  Chirality :  0.044   0.218   1290
  Planarity :  0.005   0.063   1488
  Dihedral  :  4.884  42.226   1189
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.29 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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:  0.12 (0.27), residues: 1071
  helix: -2.47 (0.75), residues: 34
  sheet:  1.18 (0.25), residues: 411
  loop : -0.53 (0.26), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 118 
 HIS   0.005   0.001   HIS A 519 
 PHE   0.020   0.001   PHE A 391 
 TYR   0.011   0.001   TYR L 141 
 ARG   0.008   0.001   ARG L  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00010 (    1)
  link_NAG-ASN         : angle       1.61654 (    3)
  hydrogen bonds       : bond        0.02860 (  313)
  hydrogen bonds       : angle       5.45204 (  879)
  SS BOND              : bond        0.00375 (   14)
  SS BOND              : angle       2.78394 (   28)
  covalent geometry    : bond        0.00233 ( 8487)
  covalent geometry    : angle       0.59767 (11553)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
REVERT: A  385 PHE cc_start: 0.5662 (OUTLIER) cc_final: 0.5392 (m-80)
REVERT: H  160 TYR cc_start: 0.6343 (p90) cc_final: 0.5736 (p90)
REVERT: L  171 ASP cc_start: 0.6044 (t0) cc_final: 0.5778 (p0)
  outliers start: 19
  outliers final: 3
  residues processed: 114
  average time/residue: 1.3448
  time to fit residues: 163.7886
Evaluate side-chains
  89 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain H residue  219 ASN
Chi-restraints excluded: chain M residue  179 LEU
Chi-restraints excluded: chain N residue  138 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 70 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 82 optimal weight:    0.6980
   chunk 96 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0370
   overall best weight:    0.5660

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

Flipped N/Q/H residues before XYZ refinement:
H 219 ASN
** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.149385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.125988 restraints weight = 25224.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3978 rms_B_bonded: 2.68
r_work: 0.3862 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3761 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3760
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3760 r_free = 0.3760    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3760 r_free = 0.3760    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3760
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8502  Z= 0.124
  Angle     :  0.629  14.267  11584  Z= 0.323
  Chirality :  0.045   0.170   1290
  Planarity :  0.005   0.064   1488
  Dihedral  :  4.925  40.548   1189
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 14.15 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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:  0.10 (0.27), residues: 1071
  helix: -2.86 (0.64), residues: 40
  sheet:  1.21 (0.25), residues: 412
  loop : -0.53 (0.26), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L 149 
 HIS   0.006   0.001   HIS A 519 
 PHE   0.023   0.001   PHE A 391 
 TYR   0.014   0.001   TYR L 141 
 ARG   0.010   0.001   ARG L  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00005 (    1)
  link_NAG-ASN         : angle       1.45784 (    3)
  hydrogen bonds       : bond        0.03023 (  313)
  hydrogen bonds       : angle       5.45729 (  879)
  SS BOND              : bond        0.00467 (   14)
  SS BOND              : angle       2.62030 (   28)
  covalent geometry    : bond        0.00291 ( 8487)
  covalent geometry    : angle       0.61638 (11553)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 CYS cc_start: 0.4828 (t) cc_final: 0.4563 (t)
REVERT: H  160 TYR cc_start: 0.6428 (p90) cc_final: 0.5798 (p90)
REVERT: L  168 ASP cc_start: 0.6996 (m-30) cc_final: 0.6711 (m-30)
REVERT: L  171 ASP cc_start: 0.6265 (t0) cc_final: 0.5870 (p0)
REVERT: N  118 PHE cc_start: 0.6169 (m-80) cc_final: 0.5907 (m-80)
  outliers start: 25
  outliers final: 7
  residues processed: 107
  average time/residue: 1.1097
  time to fit residues: 127.4174
Evaluate side-chains
  90 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 TYR
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain M residue  104 LEU
Chi-restraints excluded: chain M residue  140 THR
Chi-restraints excluded: chain M residue  191 VAL
Chi-restraints excluded: chain N residue  138 LEU
Chi-restraints excluded: chain N residue  208 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.146752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.121819 restraints weight = 22113.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3924 rms_B_bonded: 2.25
r_work: 0.3850 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3752 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3752
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3752 r_free = 0.3752    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3752 r_free = 0.3752    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3752
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   8502  Z= 0.224
  Angle     :  0.747  17.350  11584  Z= 0.387
  Chirality :  0.048   0.199   1290
  Planarity :  0.006   0.074   1488
  Dihedral  :  5.641  48.068   1189
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.65 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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: -0.11 (0.26), residues: 1071
  helix: -2.87 (0.64), residues: 40
  sheet:  1.07 (0.25), residues: 425
  loop : -0.73 (0.27), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP H 114 
 HIS   0.008   0.001   HIS A 519 
 PHE   0.030   0.002   PHE A 391 
 TYR   0.023   0.002   TYR L 141 
 ARG   0.011   0.001   ARG L  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00081 (    1)
  link_NAG-ASN         : angle       1.48873 (    3)
  hydrogen bonds       : bond        0.03710 (  313)
  hydrogen bonds       : angle       6.01697 (  879)
  SS BOND              : bond        0.00692 (   14)
  SS BOND              : angle       3.21331 (   28)
  covalent geometry    : bond        0.00520 ( 8487)
  covalent geometry    : angle       0.73040 (11553)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
REVERT: H   87 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.5850 (mpp)
REVERT: H   88 ASP cc_start: 0.7200 (p0) cc_final: 0.6871 (p0)
REVERT: H  160 TYR cc_start: 0.6469 (p90) cc_final: 0.6098 (p90)
REVERT: L  168 ASP cc_start: 0.7116 (m-30) cc_final: 0.6861 (m-30)
REVERT: L  171 ASP cc_start: 0.6350 (t0) cc_final: 0.5961 (p0)
REVERT: M   64 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7830 (mmtm)
REVERT: N    4 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7430 (tpp)
  outliers start: 25
  outliers final: 13
  residues processed: 106
  average time/residue: 1.2604
  time to fit residues: 142.6109
Evaluate side-chains
  100 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 TYR
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain M residue   11 LEU
Chi-restraints excluded: chain M residue   22 CYS
Chi-restraints excluded: chain M residue   64 LYS
Chi-restraints excluded: chain M residue  140 THR
Chi-restraints excluded: chain M residue  191 VAL
Chi-restraints excluded: chain N residue    4 MET
Chi-restraints excluded: chain N residue   18 ARG
Chi-restraints excluded: chain N residue   21 ILE
Chi-restraints excluded: chain N residue  138 LEU
Chi-restraints excluded: chain N residue  188 TYR
Chi-restraints excluded: chain N residue  208 THR
Chi-restraints excluded: chain N residue  210 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 86 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 88 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 105 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
M 180 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.148069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.124458 restraints weight = 24526.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3955 rms_B_bonded: 2.63
r_work: 0.3837 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3733 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8502  Z= 0.157
  Angle     :  0.690  15.449  11584  Z= 0.356
  Chirality :  0.046   0.172   1290
  Planarity :  0.006   0.073   1488
  Dihedral  :  5.378  43.313   1189
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 16.61 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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: -0.10 (0.27), residues: 1071
  helix: -2.90 (0.64), residues: 40
  sheet:  1.09 (0.26), residues: 409
  loop : -0.68 (0.26), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 450 
 HIS   0.006   0.001   HIS A 519 
 PHE   0.022   0.002   PHE A 391 
 TYR   0.018   0.002   TYR L 141 
 ARG   0.012   0.001   ARG L  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00018 (    1)
  link_NAG-ASN         : angle       1.34851 (    3)
  hydrogen bonds       : bond        0.03289 (  313)
  hydrogen bonds       : angle       5.76391 (  879)
  SS BOND              : bond        0.00548 (   14)
  SS BOND              : angle       2.90765 (   28)
  covalent geometry    : bond        0.00371 ( 8487)
  covalent geometry    : angle       0.67547 (11553)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 88
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
REVERT: A  385 PHE cc_start: 0.5771 (OUTLIER) cc_final: 0.5466 (m-80)
REVERT: A  408 ASN cc_start: 0.7356 (p0) cc_final: 0.7125 (t0)
REVERT: H   87 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.5912 (mpp)
REVERT: H  160 TYR cc_start: 0.6471 (p90) cc_final: 0.5874 (p90)
REVERT: L  171 ASP cc_start: 0.6275 (t0) cc_final: 0.5936 (p0)
REVERT: N    4 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7529 (tpp)
  outliers start: 27
  outliers final: 14
  residues processed: 107
  average time/residue: 1.2497
  time to fit residues: 143.3535
Evaluate side-chains
  100 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 TYR
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain H residue   68 ARG
Chi-restraints excluded: chain H residue   87 MET
Chi-restraints excluded: chain L residue  210 PHE
Chi-restraints excluded: chain M residue   11 LEU
Chi-restraints excluded: chain M residue  104 LEU
Chi-restraints excluded: chain M residue  140 THR
Chi-restraints excluded: chain M residue  191 VAL
Chi-restraints excluded: chain N residue    4 MET
Chi-restraints excluded: chain N residue   18 ARG
Chi-restraints excluded: chain N residue   21 ILE
Chi-restraints excluded: chain N residue  138 LEU
Chi-restraints excluded: chain N residue  188 TYR
Chi-restraints excluded: chain N residue  208 THR
Chi-restraints excluded: chain N residue  210 SER
Chi-restraints excluded: chain N residue  211 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 88 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 40 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
H  67 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.146880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.120637 restraints weight = 39162.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 3.58
r_work: 0.3784 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3786 r_free = 0.3786    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3786 r_free = 0.3786    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   8502  Z= 0.198
  Angle     :  0.725  14.972  11584  Z= 0.375
  Chirality :  0.047   0.167   1290
  Planarity :  0.006   0.073   1488
  Dihedral  :  5.596  42.774   1189
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 17.26 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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: -0.20 (0.26), residues: 1071
  helix: -2.96 (0.62), residues: 40
  sheet:  1.02 (0.25), residues: 409
  loop : -0.76 (0.26), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 114 
 HIS   0.007   0.001   HIS A 519 
 PHE   0.022   0.002   PHE A 391 
 TYR   0.022   0.002   TYR L 141 
 ARG   0.013   0.001   ARG L  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00053 (    1)
  link_NAG-ASN         : angle       1.36204 (    3)
  hydrogen bonds       : bond        0.03579 (  313)
  hydrogen bonds       : angle       5.94264 (  879)
  SS BOND              : bond        0.00606 (   14)
  SS BOND              : angle       2.89489 (   28)
  covalent geometry    : bond        0.00464 ( 8487)
  covalent geometry    : angle       0.71147 (11553)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 89
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
REVERT: A  385 PHE cc_start: 0.5658 (OUTLIER) cc_final: 0.5353 (m-80)
REVERT: H   84 MET cc_start: 0.7885 (ttp) cc_final: 0.7468 (ttm)
REVERT: H   88 ASP cc_start: 0.7093 (p0) cc_final: 0.6753 (p0)
REVERT: H  160 TYR cc_start: 0.6446 (p90) cc_final: 0.5938 (p90)
REVERT: L  171 ASP cc_start: 0.6351 (t0) cc_final: 0.6082 (p0)
REVERT: N    4 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7453 (tpp)
  outliers start: 29
  outliers final: 16
  residues processed: 109
  average time/residue: 1.1930
  time to fit residues: 138.9826
Evaluate side-chains
  101 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 TYR
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain H residue   68 ARG
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain M residue   11 LEU
Chi-restraints excluded: chain M residue   22 CYS
Chi-restraints excluded: chain M residue  104 LEU
Chi-restraints excluded: chain M residue  140 THR
Chi-restraints excluded: chain M residue  191 VAL
Chi-restraints excluded: chain N residue    4 MET
Chi-restraints excluded: chain N residue   18 ARG
Chi-restraints excluded: chain N residue   21 ILE
Chi-restraints excluded: chain N residue  131 THR
Chi-restraints excluded: chain N residue  138 LEU
Chi-restraints excluded: chain N residue  188 TYR
Chi-restraints excluded: chain N residue  208 THR
Chi-restraints excluded: chain N residue  210 SER
Chi-restraints excluded: chain N residue  211 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   chunk 104 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 62 optimal weight:    9.9990
   chunk 58 optimal weight:    0.3980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
H  67 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.148285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.123645 restraints weight = 32915.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 3.21
r_work: 0.3822 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3823
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3823 r_free = 0.3823    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3823 r_free = 0.3823    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3823
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8502  Z= 0.144
  Angle     :  0.714  17.509  11584  Z= 0.364
  Chirality :  0.046   0.172   1290
  Planarity :  0.006   0.071   1488
  Dihedral  :  5.363  41.400   1189
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 18.33 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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: -0.14 (0.26), residues: 1071
  helix: -2.91 (0.64), residues: 40
  sheet:  1.04 (0.26), residues: 410
  loop : -0.70 (0.26), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 450 
 HIS   0.005   0.001   HIS A 519 
 PHE   0.017   0.002   PHE A 388 
 TYR   0.020   0.002   TYR N 142 
 ARG   0.014   0.001   ARG L  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00012 (    1)
  link_NAG-ASN         : angle       1.24208 (    3)
  hydrogen bonds       : bond        0.03229 (  313)
  hydrogen bonds       : angle       5.70153 (  879)
  SS BOND              : bond        0.00543 (   14)
  SS BOND              : angle       3.17369 (   28)
  covalent geometry    : bond        0.00340 ( 8487)
  covalent geometry    : angle       0.69710 (11553)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
REVERT: H  160 TYR cc_start: 0.6431 (p90) cc_final: 0.5934 (p90)
REVERT: L  171 ASP cc_start: 0.6212 (t0) cc_final: 0.5947 (p0)
REVERT: L  191 LYS cc_start: 0.5495 (tppt) cc_final: 0.4302 (tppt)
REVERT: N    4 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7409 (tpp)
  outliers start: 20
  outliers final: 13
  residues processed: 103
  average time/residue: 1.1621
  time to fit residues: 128.3204
Evaluate side-chains
  96 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 TYR
Chi-restraints excluded: chain H residue   68 ARG
Chi-restraints excluded: chain L residue  210 PHE
Chi-restraints excluded: chain M residue   11 LEU
Chi-restraints excluded: chain M residue  104 LEU
Chi-restraints excluded: chain M residue  140 THR
Chi-restraints excluded: chain M residue  191 VAL
Chi-restraints excluded: chain N residue    4 MET
Chi-restraints excluded: chain N residue   21 ILE
Chi-restraints excluded: chain N residue  131 THR
Chi-restraints excluded: chain N residue  138 LEU
Chi-restraints excluded: chain N residue  188 TYR
Chi-restraints excluded: chain N residue  208 THR
Chi-restraints excluded: chain N residue  210 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
H  67 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.147952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.122994 restraints weight = 22303.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 2.28
r_work: 0.3866 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3769 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3769
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3769 r_free = 0.3769    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3769 r_free = 0.3769    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3769
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8502  Z= 0.157
  Angle     :  0.719  16.775  11584  Z= 0.368
  Chirality :  0.046   0.172   1290
  Planarity :  0.006   0.071   1488
  Dihedral  :  5.347  40.486   1189
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 18.86 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.26), residues: 1071
  helix: -2.89 (0.65), residues: 40
  sheet:  1.04 (0.26), residues: 410
  loop : -0.73 (0.26), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 450 
 HIS   0.005   0.001   HIS A 519 
 PHE   0.024   0.002   PHE N 141 
 TYR   0.026   0.002   TYR N 142 
 ARG   0.015   0.001   ARG L  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00020 (    1)
  link_NAG-ASN         : angle       1.13591 (    3)
  hydrogen bonds       : bond        0.03285 (  313)
  hydrogen bonds       : angle       5.67701 (  879)
  SS BOND              : bond        0.00544 (   14)
  SS BOND              : angle       3.13258 (   28)
  covalent geometry    : bond        0.00373 ( 8487)
  covalent geometry    : angle       0.70272 (11553)

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
REVERT: H   88 ASP cc_start: 0.7092 (p0) cc_final: 0.6552 (p0)
REVERT: H   90 GLU cc_start: 0.7565 (pp20) cc_final: 0.7345 (pm20)
REVERT: H  160 TYR cc_start: 0.6503 (p90) cc_final: 0.5962 (p90)
REVERT: L  171 ASP cc_start: 0.6327 (t0) cc_final: 0.6018 (p0)
REVERT: L  191 LYS cc_start: 0.5732 (tppt) cc_final: 0.4690 (tppt)
REVERT: N    4 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7466 (tpp)
  outliers start: 17
  outliers final: 13
  residues processed: 95
  average time/residue: 1.1514
  time to fit residues: 117.2575
Evaluate side-chains
  95 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   68 ARG
Chi-restraints excluded: chain L residue  210 PHE
Chi-restraints excluded: chain M residue   11 LEU
Chi-restraints excluded: chain M residue  104 LEU
Chi-restraints excluded: chain M residue  140 THR
Chi-restraints excluded: chain M residue  191 VAL
Chi-restraints excluded: chain N residue    4 MET
Chi-restraints excluded: chain N residue   18 ARG
Chi-restraints excluded: chain N residue  131 THR
Chi-restraints excluded: chain N residue  138 LEU
Chi-restraints excluded: chain N residue  188 TYR
Chi-restraints excluded: chain N residue  208 THR
Chi-restraints excluded: chain N residue  210 SER
Chi-restraints excluded: chain N residue  211 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 50 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   chunk 89 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 90 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
H  67 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.148813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.123704 restraints weight = 33420.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 3.17
r_work: 0.3828 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3829
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3829 r_free = 0.3829    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3829 r_free = 0.3829    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3829
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8502  Z= 0.133
  Angle     :  0.701  15.886  11584  Z= 0.358
  Chirality :  0.046   0.184   1290
  Planarity :  0.006   0.069   1488
  Dihedral  :  5.186  39.506   1189
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 19.19 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    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: -0.06 (0.27), residues: 1071
  helix: -2.91 (0.65), residues: 40
  sheet:  1.03 (0.25), residues: 431
  loop : -0.65 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 450 
 HIS   0.005   0.001   HIS A 519 
 PHE   0.024   0.002   PHE N 141 
 TYR   0.026   0.002   TYR N 142 
 ARG   0.013   0.001   ARG L  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00034 (    1)
  link_NAG-ASN         : angle       1.07140 (    3)
  hydrogen bonds       : bond        0.03071 (  313)
  hydrogen bonds       : angle       5.49030 (  879)
  SS BOND              : bond        0.00466 (   14)
  SS BOND              : angle       3.07235 (   28)
  covalent geometry    : bond        0.00315 ( 8487)
  covalent geometry    : angle       0.68535 (11553)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8885.33 seconds
wall clock time: 152 minutes 11.40 seconds (9131.40 seconds total)