Starting phenix.real_space_refine
on Mon Jul 28 23:23:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6y5k_10700/07_2025/6y5k_10700.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6y5k_10700/07_2025/6y5k_10700.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6y5k_10700/07_2025/6y5k_10700.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6y5k_10700/07_2025/6y5k_10700.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6y5k_10700/07_2025/6y5k_10700.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6y5k_10700/07_2025/6y5k_10700.cif"
  }
  resolution = 4.2
  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=   0.003 sd=   0.062
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    6609      2.51       5
     N    1854      2.21       5
     O    2097      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10614
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2414
          Classifications: {'peptide': 312}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 292}
    Chain: "B"
      Number of atoms: 1096
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 1096
          Classifications: {'peptide': 133}
          Link IDs: {'TRANS': 132}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    D, F, C, E
  Time building chain proxies: 6.52, per 1000 atoms: 0.61
  Number of scatterers: 10614
  At special positions: 0
  Unit cell: (101.091, 98.917, 159.789, 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      54     16.00
     O    2097      8.00
     N    1854      7.00
     C    6609      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  14 " - pdb=" SG  CYS B 137 " distance=1.75
    Simple disulfide: pdb=" SG  CYS A  52 " - pdb=" SG  CYS A 277 " distance=2.46
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A  76 " distance=2.00
    Simple disulfide: pdb=" SG  CYS A  97 " - pdb=" SG  CYS A 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 281 " - pdb=" SG  CYS A 305 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 144 " - pdb=" SG  CYS B 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  14 " - pdb=" SG  CYS D 137 " distance=1.79
    Simple disulfide: pdb=" SG  CYS E  14 " - pdb=" SG  CYS F 137 " distance=1.78
    Simple disulfide: pdb=" SG  CYS C  52 " - pdb=" SG  CYS C 277 " distance=2.46
    Simple disulfide: pdb=" SG  CYS E  52 " - pdb=" SG  CYS E 277 " distance=2.46
    Simple disulfide: pdb=" SG  CYS C  64 " - pdb=" SG  CYS C  76 " distance=2.00
    Simple disulfide: pdb=" SG  CYS E  64 " - pdb=" SG  CYS E  76 " distance=2.00
    Simple disulfide: pdb=" SG  CYS C  97 " - pdb=" SG  CYS C 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  97 " - pdb=" SG  CYS E 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 281 " - pdb=" SG  CYS C 305 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 281 " - pdb=" SG  CYS E 305 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 144 " - pdb=" SG  CYS D 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 144 " - pdb=" SG  CYS F 148 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 401 " - " ASN A  38 "
      " NAG C 401 " - " ASN C  38 "
      " NAG E 401 " - " ASN E  38 "
  Time building additional restraints: 2.72
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2490

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 36 sheets defined
      32.1% alpha, 18.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 72
    Processing helix  chain 'A' and resid 73 through 80
      removed outlier: 4.117A  pdb=" N   ASP A  77 " --> pdb=" O   PRO A  74 " (cutoff:3.500A)
      removed outlier: 5.578A  pdb=" N   VAL A  78 " --> pdb=" O   HIS A  75 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   GLN A  80 " --> pdb=" O   ASP A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 114
    Processing helix  chain 'A' and resid 187 through 195
      removed outlier: 3.699A  pdb=" N   GLN A 191 " --> pdb=" O   THR A 187 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   THR A 192 " --> pdb=" O   ASN A 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 126
    Processing helix  chain 'B' and resid 145 through 154
      removed outlier: 3.800A  pdb=" N   ILE B 149 " --> pdb=" O   ASP B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 169
    Processing helix  chain 'C' and resid 65 through 72
    Processing helix  chain 'C' and resid 73 through 80
      removed outlier: 4.116A  pdb=" N   ASP C  77 " --> pdb=" O   PRO C  74 " (cutoff:3.500A)
      removed outlier: 5.577A  pdb=" N   VAL C  78 " --> pdb=" O   HIS C  75 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLN C  80 " --> pdb=" O   ASP C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 114
    Processing helix  chain 'C' and resid 187 through 195
      removed outlier: 3.699A  pdb=" N   GLN C 191 " --> pdb=" O   THR C 187 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   THR C 192 " --> pdb=" O   ASN C 188 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 65 through 72
    Processing helix  chain 'E' and resid 73 through 80
      removed outlier: 4.116A  pdb=" N   ASP E  77 " --> pdb=" O   PRO E  74 " (cutoff:3.500A)
      removed outlier: 5.578A  pdb=" N   VAL E  78 " --> pdb=" O   HIS E  75 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   GLN E  80 " --> pdb=" O   ASP E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 104 through 114
    Processing helix  chain 'E' and resid 187 through 195
      removed outlier: 3.700A  pdb=" N   GLN E 191 " --> pdb=" O   THR E 187 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   THR E 192 " --> pdb=" O   ASN E 188 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 38 through 126
    Processing helix  chain 'D' and resid 145 through 154
      removed outlier: 3.800A  pdb=" N   ILE D 149 " --> pdb=" O   ASP D 145 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 162 through 169
    Processing helix  chain 'F' and resid 38 through 126
    Processing helix  chain 'F' and resid 145 through 154
      removed outlier: 3.800A  pdb=" N   ILE F 149 " --> pdb=" O   ASP F 145 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 162 through 169
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27
      removed outlier: 3.619A  pdb=" N   THR A  24 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41
    Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44
    Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 52
      removed outlier: 5.964A  pdb=" N   ILE A  51 " --> pdb=" O   ASP A 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 61
      removed outlier: 6.519A  pdb=" N   LEU A  59 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 122
      removed outlier: 6.703A  pdb=" N   GLY A 256 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   ILE A 179 " --> pdb=" O   GLY A 256 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 131
    Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141
      removed outlier: 7.494A  pdb=" N   ALA A 138 " --> pdb=" O   GLY A 144 " (cutoff:3.500A)
      removed outlier: 10.924A  pdb=" N   GLY A 144 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153
    Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169
    Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 288
      removed outlier: 4.184A  pdb=" N   CYS A 281 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 130 through 132
    Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 27
      removed outlier: 3.619A  pdb=" N   THR C  24 " --> pdb=" O   VAL C  36 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41
    Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44
    Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 52
      removed outlier: 5.965A  pdb=" N   ILE C  51 " --> pdb=" O   ASP C 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 61
      removed outlier: 6.519A  pdb=" N   LEU C  59 " --> pdb=" O   VAL C  88 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 122
      removed outlier: 6.703A  pdb=" N   GLY C 256 " --> pdb=" O   ILE C 179 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   ILE C 179 " --> pdb=" O   GLY C 256 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 130 through 131
    Processing sheet with id=AC2, first strand: chain 'C' and resid 136 through 141
      removed outlier: 7.495A  pdb=" N   ALA C 138 " --> pdb=" O   GLY C 144 " (cutoff:3.500A)
      removed outlier: 10.925A  pdb=" N   GLY C 144 " --> pdb=" O   ALA C 138 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 151 through 153
    Processing sheet with id=AC4, first strand: chain 'C' and resid 164 through 169
    Processing sheet with id=AC5, first strand: chain 'C' and resid 286 through 288
      removed outlier: 4.184A  pdb=" N   CYS C 281 " --> pdb=" O   ILE C 288 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'E' and resid 24 through 27
      removed outlier: 3.619A  pdb=" N   THR E  24 " --> pdb=" O   VAL E  36 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'E' and resid 39 through 41
    Processing sheet with id=AC8, first strand: chain 'E' and resid 43 through 44
    Processing sheet with id=AC9, first strand: chain 'E' and resid 51 through 52
      removed outlier: 5.964A  pdb=" N   ILE E  51 " --> pdb=" O   ASP E 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC9
    Processing sheet with id=AD1, first strand: chain 'E' and resid 58 through 61
      removed outlier: 6.519A  pdb=" N   LEU E  59 " --> pdb=" O   VAL E  88 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'E' and resid 120 through 122
      removed outlier: 6.702A  pdb=" N   GLY E 256 " --> pdb=" O   ILE E 179 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   ILE E 179 " --> pdb=" O   GLY E 256 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'E' and resid 130 through 131
    Processing sheet with id=AD4, first strand: chain 'E' and resid 136 through 141
      removed outlier: 7.494A  pdb=" N   ALA E 138 " --> pdb=" O   GLY E 144 " (cutoff:3.500A)
      removed outlier: 10.924A  pdb=" N   GLY E 144 " --> pdb=" O   ALA E 138 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'E' and resid 151 through 153
    Processing sheet with id=AD6, first strand: chain 'E' and resid 164 through 169
    Processing sheet with id=AD7, first strand: chain 'E' and resid 286 through 288
      removed outlier: 4.184A  pdb=" N   CYS E 281 " --> pdb=" O   ILE E 288 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'D' and resid 130 through 132
    Processing sheet with id=AD9, first strand: chain 'F' and resid 130 through 132

    483 hydrogen bonds defined for protein.
    1359 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.84

  Time building geometry restraints manager: 3.23 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: 3567
        1.34 -     1.46: 2442
        1.46 -     1.59: 4743
        1.59 -     1.71: 0
        1.71 -     1.83: 72
  Bond restraints: 10824
  Sorted by residual:
  bond pdb=" N   CYS A 305 "
       pdb=" CA  CYS A 305 "
    ideal  model  delta    sigma   weight residual
    1.455  1.492 -0.036 1.17e-02 7.31e+03 9.71e+00
  bond pdb=" N   CYS C 305 "
       pdb=" CA  CYS C 305 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.17e-02 7.31e+03 9.44e+00
  bond pdb=" N   CYS E 305 "
       pdb=" CA  CYS E 305 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.17e-02 7.31e+03 9.32e+00
  bond pdb=" N   LYS C  50 "
       pdb=" CA  LYS C  50 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.23e-02 6.61e+03 7.22e+00
  bond pdb=" N   LYS E  50 "
       pdb=" CA  LYS E  50 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.033 1.23e-02 6.61e+03 7.15e+00
  ... (remaining 10819 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 14282
        2.06 -     4.12: 359
        4.12 -     6.17: 35
        6.17 -     8.23: 3
        8.23 -    10.29: 6
  Bond angle restraints: 14685
  Sorted by residual:
  angle pdb=" C   CYS C 305 "
        pdb=" CA  CYS C 305 "
        pdb=" CB  CYS C 305 "
      ideal   model   delta    sigma   weight residual
     110.47  104.21    6.26 1.77e+00 3.19e-01 1.25e+01
  angle pdb=" C   CYS A 305 "
        pdb=" CA  CYS A 305 "
        pdb=" CB  CYS A 305 "
      ideal   model   delta    sigma   weight residual
     110.47  104.21    6.26 1.77e+00 3.19e-01 1.25e+01
  angle pdb=" C   CYS E 305 "
        pdb=" CA  CYS E 305 "
        pdb=" CB  CYS E 305 "
      ideal   model   delta    sigma   weight residual
     110.47  104.22    6.25 1.77e+00 3.19e-01 1.25e+01
  angle pdb=" O   CYS C  76 "
        pdb=" C   CYS C  76 "
        pdb=" N   ASP C  77 "
      ideal   model   delta    sigma   weight residual
     121.99  125.98   -3.99 1.24e+00 6.50e-01 1.03e+01
  angle pdb=" O   CYS E  76 "
        pdb=" C   CYS E  76 "
        pdb=" N   ASP E  77 "
      ideal   model   delta    sigma   weight residual
     121.99  125.97   -3.98 1.24e+00 6.50e-01 1.03e+01
  ... (remaining 14680 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.15: 6035
       17.15 -    34.31: 446
       34.31 -    51.46: 145
       51.46 -    68.61: 16
       68.61 -    85.76: 12
  Dihedral angle restraints: 6654
    sinusoidal: 2790
      harmonic: 3864
  Sorted by residual:
  dihedral pdb=" CB  CYS E  14 "
           pdb=" SG  CYS E  14 "
           pdb=" SG  CYS F 137 "
           pdb=" CB  CYS F 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -159.46   73.46     1      1.00e+01 1.00e-02 6.87e+01
  dihedral pdb=" CB  CYS C  14 "
           pdb=" SG  CYS C  14 "
           pdb=" SG  CYS D 137 "
           pdb=" CB  CYS D 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.92   72.92     1      1.00e+01 1.00e-02 6.78e+01
  dihedral pdb=" CB  CYS A  14 "
           pdb=" SG  CYS A  14 "
           pdb=" SG  CYS B 137 "
           pdb=" CB  CYS B 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.43   72.43     1      1.00e+01 1.00e-02 6.70e+01
  ... (remaining 6651 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1252
       0.050 -    0.100: 291
       0.100 -    0.150: 80
       0.150 -    0.200: 23
       0.200 -    0.250: 4
  Chirality restraints: 1650
  Sorted by residual:
  chirality pdb=" CA  CYS A 305 "
            pdb=" N   CYS A 305 "
            pdb=" C   CYS A 305 "
            pdb=" CB  CYS A 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  CYS E 305 "
            pdb=" N   CYS E 305 "
            pdb=" C   CYS E 305 "
            pdb=" CB  CYS E 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  CYS C 305 "
            pdb=" N   CYS C 305 "
            pdb=" C   CYS C 305 "
            pdb=" CB  CYS C 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.54e+00
  ... (remaining 1647 not shown)

  Planarity restraints: 1920
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 190 "    0.014 2.00e-02 2.50e+03   2.75e-02 7.55e+00
        pdb=" C   GLU A 190 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   GLU A 190 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLN A 191 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU E 190 "    0.014 2.00e-02 2.50e+03   2.74e-02 7.49e+00
        pdb=" C   GLU E 190 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   GLU E 190 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLN E 191 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 190 "    0.014 2.00e-02 2.50e+03   2.73e-02 7.46e+00
        pdb=" C   GLU C 190 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   GLU C 190 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLN C 191 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1917 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 197
        2.66 -     3.22: 9844
        3.22 -     3.78: 16679
        3.78 -     4.34: 22090
        4.34 -     4.90: 35982
  Nonbonded interactions: 84792
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C  24 "
            pdb=" O   VAL C  36 "
     model   vdw
     2.096 3.040
  nonbonded pdb=" OG1 THR A  24 "
            pdb=" O   VAL A  36 "
     model   vdw
     2.097 3.040
  nonbonded pdb=" OG1 THR E  24 "
            pdb=" O   VAL E  36 "
     model   vdw
     2.097 3.040
  nonbonded pdb=" NH1 ARG D  76 "
            pdb=" OE2 GLU F  74 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OD1 ASP C 275 "
            pdb=" N   THR C 276 "
     model   vdw
     2.196 3.120
  ... (remaining 84787 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             45.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.200
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   76.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
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      :  0.009   0.424  10845  Z= 0.472
  Angle     :  0.912  30.104  14730  Z= 0.497
  Chirality :  0.051   0.250   1650
  Planarity :  0.004   0.043   1917
  Dihedral  : 13.059  85.764   4110
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.20), residues: 1323
  helix:  0.39 (0.23), residues: 408
  sheet: -0.52 (0.31), residues: 267
  loop : -2.93 (0.17), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 222 
 HIS   0.002   0.001   HIS E 184 
 PHE   0.007   0.001   PHE A  79 
 TYR   0.012   0.002   TYR C 178 
 ARG   0.002   0.000   ARG E 255 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00085 (    3)
  link_NAG-ASN         : angle       1.96379 (    9)
  hydrogen bonds       : bond        0.11396 (  483)
  hydrogen bonds       : angle       4.76415 ( 1359)
  SS BOND              : bond        0.20298 (   18)
  SS BOND              : angle      10.22057 (   36)
  covalent geometry    : bond        0.00393 (10824)
  covalent geometry    : angle       0.75841 (14685)

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

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

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 TYR cc_start: 0.8238 (m-80) cc_final: 0.7727 (m-80)
REVERT: B   58 LYS cc_start: 0.9360 (mtmt) cc_final: 0.9094 (mttm)
REVERT: B   64 HIS cc_start: 0.8925 (m-70) cc_final: 0.8573 (m-70)
REVERT: B   65 GLN cc_start: 0.9440 (mm-40) cc_final: 0.8796 (tp-100)
REVERT: B   66 ILE cc_start: 0.9717 (mt) cc_final: 0.9499 (mt)
REVERT: B   69 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8491 (mt-10)
REVERT: B   86 ASP cc_start: 0.8260 (t0) cc_final: 0.7850 (t0)
REVERT: C   98 TYR cc_start: 0.8956 (t80) cc_final: 0.8240 (t80)
REVERT: C  137 ASN cc_start: 0.9480 (m-40) cc_final: 0.9038 (p0)
REVERT: E   50 LYS cc_start: 0.8581 (mttt) cc_final: 0.8120 (tptm)
REVERT: E   87 PHE cc_start: 0.7100 (t80) cc_final: 0.6662 (t80)
REVERT: E   98 TYR cc_start: 0.8297 (t80) cc_final: 0.7881 (t80)
REVERT: E  233 TYR cc_start: 0.7983 (m-80) cc_final: 0.7715 (m-80)
REVERT: D   39 LYS cc_start: 0.9733 (mptt) cc_final: 0.9515 (mmtm)
REVERT: D   58 LYS cc_start: 0.9461 (mtmt) cc_final: 0.9051 (mttm)
REVERT: D   62 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8598 (mmtt)
REVERT: D   64 HIS cc_start: 0.8922 (m-70) cc_final: 0.8518 (m90)
REVERT: D   86 ASP cc_start: 0.8450 (t0) cc_final: 0.8011 (t0)
REVERT: D  108 ILE cc_start: 0.9723 (mt) cc_final: 0.9434 (tt)
REVERT: F   38 LEU cc_start: 0.9521 (pt) cc_final: 0.9318 (pt)
REVERT: F   39 LYS cc_start: 0.9736 (mptt) cc_final: 0.9515 (mmtm)
REVERT: F   55 VAL cc_start: 0.9734 (m) cc_final: 0.9441 (m)
REVERT: F   58 LYS cc_start: 0.9404 (mtmt) cc_final: 0.9135 (mttm)
REVERT: F   59 THR cc_start: 0.9595 (p) cc_final: 0.8865 (p)
REVERT: F   63 PHE cc_start: 0.9340 (m-10) cc_final: 0.9002 (m-80)
REVERT: F   64 HIS cc_start: 0.8930 (m-70) cc_final: 0.8520 (m90)
REVERT: F   65 GLN cc_start: 0.9404 (mm-40) cc_final: 0.8907 (tp-100)
REVERT: F   66 ILE cc_start: 0.9704 (mt) cc_final: 0.9377 (mt)
REVERT: F   69 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8398 (mm-30)
REVERT: F   70 PHE cc_start: 0.8781 (m-80) cc_final: 0.8220 (m-80)
REVERT: F   78 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8497 (mm-40)
  outliers start: 0
  outliers final: 0
  residues processed: 279
  average time/residue: 0.3421
  time to fit residues: 123.0280
Evaluate side-chains
  149 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    0.5980
   chunk 100 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 77 optimal weight:    0.5980
   chunk 119 optimal weight:    0.0970
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
A 184 HIS
A 197 GLN
A 216 ASN
A 285 ASN
B 104 ASN
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 HIS
C 173 ASN
C 184 HIS
C 197 GLN
C 216 ASN
C 285 ASN
C 298 ASN
E 173 ASN
E 184 HIS
E 197 GLN
E 216 ASN
E 285 ASN
D  64 HIS
D 104 ASN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 146 ASN
D 159 HIS
F 104 ASN
F 146 ASN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.085379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.056925 restraints weight = 45980.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.056465 restraints weight = 23541.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.056624 restraints weight = 21721.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  10845  Z= 0.164
  Angle     :  0.578   7.313  14730  Z= 0.307
  Chirality :  0.044   0.168   1650
  Planarity :  0.004   0.041   1917
  Dihedral  :  5.027  37.432   1569
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.21), residues: 1323
  helix:  1.59 (0.24), residues: 399
  sheet:  0.20 (0.34), residues: 246
  loop : -2.17 (0.18), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C 180 
 HIS   0.008   0.001   HIS F 106 
 PHE   0.029   0.002   PHE B  70 
 TYR   0.017   0.002   TYR B  83 
 ARG   0.007   0.001   ARG B 163 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00316 (    3)
  link_NAG-ASN         : angle       0.77037 (    9)
  hydrogen bonds       : bond        0.03271 (  483)
  hydrogen bonds       : angle       4.16939 ( 1359)
  SS BOND              : bond        0.00291 (   18)
  SS BOND              : angle       1.52152 (   36)
  covalent geometry    : bond        0.00347 (10824)
  covalent geometry    : angle       0.57343 (14685)

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

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

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 1.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8817 (m-80) cc_final: 0.8541 (m-80)
REVERT: A  137 ASN cc_start: 0.9463 (m-40) cc_final: 0.8704 (p0)
REVERT: A  233 TYR cc_start: 0.8050 (m-80) cc_final: 0.7807 (m-80)
REVERT: B   54 ARG cc_start: 0.9346 (mtp85) cc_final: 0.8711 (mtp85)
REVERT: B   58 LYS cc_start: 0.9355 (mtmt) cc_final: 0.8817 (mttm)
REVERT: B   61 GLU cc_start: 0.8962 (pp20) cc_final: 0.8448 (pp20)
REVERT: B   62 LYS cc_start: 0.9098 (mmtt) cc_final: 0.8605 (mmtt)
REVERT: B   64 HIS cc_start: 0.8971 (m-70) cc_final: 0.8687 (m90)
REVERT: B   86 ASP cc_start: 0.8684 (t0) cc_final: 0.8115 (t0)
REVERT: B  117 LYS cc_start: 0.9831 (tptt) cc_final: 0.9603 (tptp)
REVERT: B  133 MET cc_start: 0.7797 (ptt) cc_final: 0.7268 (ppp)
REVERT: C   70 LEU cc_start: 0.8036 (tp) cc_final: 0.7654 (mt)
REVERT: C   98 TYR cc_start: 0.8862 (t80) cc_final: 0.8184 (t80)
REVERT: C  137 ASN cc_start: 0.9487 (m-40) cc_final: 0.8889 (p0)
REVERT: C  184 HIS cc_start: 0.8028 (m-70) cc_final: 0.7712 (m90)
REVERT: C  233 TYR cc_start: 0.7990 (m-80) cc_final: 0.7718 (m-80)
REVERT: E   50 LYS cc_start: 0.8483 (mttt) cc_final: 0.8024 (tptm)
REVERT: E   87 PHE cc_start: 0.6366 (t80) cc_final: 0.5707 (t80)
REVERT: E   98 TYR cc_start: 0.8518 (t80) cc_final: 0.8066 (t80)
REVERT: D   39 LYS cc_start: 0.9747 (mptt) cc_final: 0.9529 (mmtm)
REVERT: D   58 LYS cc_start: 0.9428 (mtmt) cc_final: 0.8987 (mttm)
REVERT: D   86 ASP cc_start: 0.8647 (t0) cc_final: 0.8077 (t0)
REVERT: D  126 LEU cc_start: 0.9471 (tt) cc_final: 0.9266 (tt)
REVERT: F   58 LYS cc_start: 0.9372 (mtmt) cc_final: 0.9105 (mttm)
REVERT: F   59 THR cc_start: 0.9565 (p) cc_final: 0.8720 (p)
REVERT: F   63 PHE cc_start: 0.9297 (m-10) cc_final: 0.8938 (m-80)
REVERT: F   86 ASP cc_start: 0.8674 (t0) cc_final: 0.8428 (t0)
REVERT: F  117 LYS cc_start: 0.9815 (tptt) cc_final: 0.9609 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.4409
  time to fit residues: 121.5527
Evaluate side-chains
  148 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9990
   chunk 93 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0980
   chunk 33 optimal weight:    0.9980
   chunk 118 optimal weight:    0.4980
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  75 HIS
A 184 HIS
A 298 ASN
B  64 HIS
** B  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 104 ASN
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  75 HIS
E  75 HIS
E 184 HIS
D  64 HIS
D 104 ASN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  64 HIS
** F  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 104 ASN
** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.091414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.065037 restraints weight = 51590.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.062814 restraints weight = 31533.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.063442 restraints weight = 27944.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10845  Z= 0.113
  Angle     :  0.547   6.534  14730  Z= 0.290
  Chirality :  0.043   0.149   1650
  Planarity :  0.004   0.065   1917
  Dihedral  :  4.700  34.879   1569
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.11 %
    Favored  : 96.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.22), residues: 1323
  helix:  1.78 (0.25), residues: 399
  sheet:  0.35 (0.34), residues: 246
  loop : -1.76 (0.20), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 127 
 HIS   0.012   0.001   HIS D  64 
 PHE   0.017   0.001   PHE D  70 
 TYR   0.009   0.001   TYR B  83 
 ARG   0.007   0.001   ARG B 123 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00252 (    3)
  link_NAG-ASN         : angle       0.60878 (    9)
  hydrogen bonds       : bond        0.03048 (  483)
  hydrogen bonds       : angle       4.05556 ( 1359)
  SS BOND              : bond        0.00212 (   18)
  SS BOND              : angle       1.71621 (   36)
  covalent geometry    : bond        0.00247 (10824)
  covalent geometry    : angle       0.54138 (14685)

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

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

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 ASN cc_start: 0.9337 (m-40) cc_final: 0.8476 (p0)
REVERT: B   54 ARG cc_start: 0.8972 (mtp85) cc_final: 0.8441 (mtp-110)
REVERT: B   58 LYS cc_start: 0.9248 (mtmt) cc_final: 0.8983 (mttm)
REVERT: B   64 HIS cc_start: 0.8660 (m170) cc_final: 0.8199 (m-70)
REVERT: B   86 ASP cc_start: 0.8407 (t0) cc_final: 0.7831 (t0)
REVERT: B  118 LEU cc_start: 0.9623 (pp) cc_final: 0.9343 (pp)
REVERT: B  133 MET cc_start: 0.7642 (ptt) cc_final: 0.7142 (ppp)
REVERT: C   70 LEU cc_start: 0.7885 (tp) cc_final: 0.7511 (mt)
REVERT: C   98 TYR cc_start: 0.8743 (t80) cc_final: 0.8288 (t80)
REVERT: C  137 ASN cc_start: 0.9389 (m-40) cc_final: 0.8731 (p0)
REVERT: C  233 TYR cc_start: 0.8132 (m-80) cc_final: 0.7646 (m-80)
REVERT: E   50 LYS cc_start: 0.8619 (mttt) cc_final: 0.8216 (tptm)
REVERT: E   98 TYR cc_start: 0.8461 (t80) cc_final: 0.7974 (t80)
REVERT: E  100 TYR cc_start: 0.5472 (p90) cc_final: 0.5237 (p90)
REVERT: D   54 ARG cc_start: 0.8987 (mtp85) cc_final: 0.8490 (mtp-110)
REVERT: D   58 LYS cc_start: 0.9397 (mtmt) cc_final: 0.9155 (mttm)
REVERT: D   62 LYS cc_start: 0.9338 (mmtt) cc_final: 0.8894 (mmmt)
REVERT: D   86 ASP cc_start: 0.8295 (t0) cc_final: 0.7729 (t0)
REVERT: F   58 LYS cc_start: 0.9274 (mtmt) cc_final: 0.8709 (ptpt)
REVERT: F   59 THR cc_start: 0.9346 (p) cc_final: 0.8477 (p)
REVERT: F   61 GLU cc_start: 0.8614 (pp20) cc_final: 0.7619 (pp20)
REVERT: F   62 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8602 (mmtt)
REVERT: F   63 PHE cc_start: 0.9055 (m-10) cc_final: 0.8712 (m-80)
REVERT: F   66 ILE cc_start: 0.9586 (mt) cc_final: 0.9325 (mt)
REVERT: F   70 PHE cc_start: 0.8546 (m-80) cc_final: 0.8104 (m-80)
REVERT: F   86 ASP cc_start: 0.8363 (t0) cc_final: 0.7886 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 208
  average time/residue: 0.2841
  time to fit residues: 77.5479
Evaluate side-chains
  136 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 118 optimal weight:    7.9990
   chunk 76 optimal weight:    0.7980
   chunk 114 optimal weight:    2.9990
   chunk 85 optimal weight:    9.9990
   chunk 45 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 128 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 96 optimal weight:    6.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 184 HIS
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  53 ASN
** B  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 104 ASN
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 ASN
C 184 HIS
E 184 HIS
E 298 ASN
D  53 ASN
D  60 ASN
D 104 ASN
F  53 ASN
F  60 ASN
** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.080041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.048458 restraints weight = 48676.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.050967 restraints weight = 23754.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.052361 restraints weight = 15644.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.4889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.066  10845  Z= 0.327
  Angle     :  0.751   9.172  14730  Z= 0.407
  Chirality :  0.050   0.230   1650
  Planarity :  0.006   0.082   1917
  Dihedral  :  6.222  49.633   1569
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 18.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.45 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.20), residues: 1323
  helix:  0.77 (0.24), residues: 402
  sheet: -0.42 (0.30), residues: 273
  loop : -1.90 (0.20), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 127 
 HIS   0.010   0.002   HIS D 106 
 PHE   0.013   0.002   PHE C 120 
 TYR   0.027   0.002   TYR F  83 
 ARG   0.009   0.001   ARG D 123 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00478 (    3)
  link_NAG-ASN         : angle       1.90805 (    9)
  hydrogen bonds       : bond        0.04454 (  483)
  hydrogen bonds       : angle       5.31511 ( 1359)
  SS BOND              : bond        0.01326 (   18)
  SS BOND              : angle       2.18000 (   36)
  covalent geometry    : bond        0.00677 (10824)
  covalent geometry    : angle       0.74324 (14685)

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

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

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 ASN cc_start: 0.9424 (m-40) cc_final: 0.8759 (p0)
REVERT: A  190 GLU cc_start: 0.9164 (pt0) cc_final: 0.8839 (pt0)
REVERT: A  231 SER cc_start: 0.8666 (t) cc_final: 0.8406 (t)
REVERT: A  233 TYR cc_start: 0.8546 (m-80) cc_final: 0.8110 (m-80)
REVERT: A  320 MET cc_start: 0.5306 (ptm) cc_final: 0.4842 (ptp)
REVERT: B   68 LYS cc_start: 0.9470 (mmtm) cc_final: 0.9154 (mmtm)
REVERT: B   78 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8884 (mm-40)
REVERT: B   86 ASP cc_start: 0.8545 (t0) cc_final: 0.8122 (t0)
REVERT: B   90 ASP cc_start: 0.8914 (m-30) cc_final: 0.8700 (m-30)
REVERT: B  133 MET cc_start: 0.7888 (ptt) cc_final: 0.7369 (ppp)
REVERT: C   70 LEU cc_start: 0.7533 (tp) cc_final: 0.7004 (mt)
REVERT: C   98 TYR cc_start: 0.8919 (t80) cc_final: 0.8401 (t80)
REVERT: C  100 TYR cc_start: 0.7354 (p90) cc_final: 0.7144 (p90)
REVERT: C  231 SER cc_start: 0.8770 (m) cc_final: 0.8231 (m)
REVERT: C  233 TYR cc_start: 0.8410 (m-80) cc_final: 0.7934 (m-80)
REVERT: C  261 ARG cc_start: 0.4896 (mtt90) cc_final: 0.3624 (ptt90)
REVERT: E   50 LYS cc_start: 0.8783 (mttt) cc_final: 0.8322 (tptm)
REVERT: E  100 TYR cc_start: 0.5704 (p90) cc_final: 0.5482 (p90)
REVERT: D   54 ARG cc_start: 0.9444 (mtp85) cc_final: 0.8855 (mtp-110)
REVERT: D   58 LYS cc_start: 0.9593 (mtmt) cc_final: 0.9294 (mttm)
REVERT: D   62 LYS cc_start: 0.9324 (mmtt) cc_final: 0.9077 (mmmt)
REVERT: D   67 GLU cc_start: 0.9435 (pt0) cc_final: 0.8833 (pp20)
REVERT: D   78 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8841 (mm-40)
REVERT: D   86 ASP cc_start: 0.8589 (t0) cc_final: 0.8136 (t0)
REVERT: D   90 ASP cc_start: 0.8829 (m-30) cc_final: 0.8565 (m-30)
REVERT: F   58 LYS cc_start: 0.9506 (mtmt) cc_final: 0.9125 (mtmt)
REVERT: F   59 THR cc_start: 0.9618 (p) cc_final: 0.9063 (p)
REVERT: F   63 PHE cc_start: 0.9518 (m-10) cc_final: 0.9117 (m-80)
REVERT: F   86 ASP cc_start: 0.8549 (t0) cc_final: 0.8251 (t0)
REVERT: F  133 MET cc_start: 0.7898 (ptt) cc_final: 0.7460 (ptt)
  outliers start: 1
  outliers final: 1
  residues processed: 176
  average time/residue: 0.3134
  time to fit residues: 72.9387
Evaluate side-chains
  138 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 88 optimal weight:   10.0000
   chunk 124 optimal weight:    0.9990
   chunk 116 optimal weight:    2.9990
   chunk 8 optimal weight:    8.9990
   chunk 55 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
B 104 ASN
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 184 HIS
D 104 ASN
D 125 GLN
F  60 ASN
F 104 ASN
** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.088310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.061649 restraints weight = 51456.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.059470 restraints weight = 28402.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.059880 restraints weight = 26721.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.4920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10845  Z= 0.146
  Angle     :  0.577   8.387  14730  Z= 0.302
  Chirality :  0.045   0.170   1650
  Planarity :  0.004   0.035   1917
  Dihedral  :  4.993  35.334   1569
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.21), residues: 1323
  helix:  1.41 (0.24), residues: 402
  sheet: -0.18 (0.33), residues: 228
  loop : -1.73 (0.20), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 127 
 HIS   0.009   0.001   HIS F 106 
 PHE   0.013   0.001   PHE B  63 
 TYR   0.010   0.001   TYR F  83 
 ARG   0.007   0.000   ARG B 163 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00283 (    3)
  link_NAG-ASN         : angle       1.12708 (    9)
  hydrogen bonds       : bond        0.03269 (  483)
  hydrogen bonds       : angle       4.47881 ( 1359)
  SS BOND              : bond        0.00638 (   18)
  SS BOND              : angle       1.92939 (   36)
  covalent geometry    : bond        0.00314 (10824)
  covalent geometry    : angle       0.56959 (14685)

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

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

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 TYR cc_start: 0.7926 (t80) cc_final: 0.7675 (t80)
REVERT: A  137 ASN cc_start: 0.9287 (m-40) cc_final: 0.8489 (p0)
REVERT: A  231 SER cc_start: 0.8599 (t) cc_final: 0.8319 (t)
REVERT: A  233 TYR cc_start: 0.8187 (m-80) cc_final: 0.7867 (m-80)
REVERT: B   58 LYS cc_start: 0.9244 (mtmt) cc_final: 0.8663 (mttm)
REVERT: B   59 THR cc_start: 0.9357 (p) cc_final: 0.8526 (p)
REVERT: B   61 GLU cc_start: 0.8594 (pp20) cc_final: 0.8199 (pp20)
REVERT: B   86 ASP cc_start: 0.8423 (t0) cc_final: 0.7967 (t0)
REVERT: B   90 ASP cc_start: 0.8943 (m-30) cc_final: 0.8739 (m-30)
REVERT: B  133 MET cc_start: 0.7828 (ptt) cc_final: 0.7390 (ppp)
REVERT: C   70 LEU cc_start: 0.7438 (tp) cc_final: 0.7132 (mt)
REVERT: C   98 TYR cc_start: 0.8911 (t80) cc_final: 0.8432 (t80)
REVERT: C  100 TYR cc_start: 0.7293 (p90) cc_final: 0.7087 (p90)
REVERT: C  184 HIS cc_start: 0.7988 (m-70) cc_final: 0.7740 (m90)
REVERT: C  231 SER cc_start: 0.8514 (m) cc_final: 0.7888 (m)
REVERT: C  233 TYR cc_start: 0.8237 (m-80) cc_final: 0.7876 (m-80)
REVERT: E   50 LYS cc_start: 0.8808 (mttt) cc_final: 0.8366 (tptm)
REVERT: D   39 LYS cc_start: 0.9712 (mmtm) cc_final: 0.9424 (mmmt)
REVERT: D   42 GLN cc_start: 0.9439 (mt0) cc_final: 0.8972 (mt0)
REVERT: D   62 LYS cc_start: 0.9305 (mmtt) cc_final: 0.9028 (mmmt)
REVERT: D   63 PHE cc_start: 0.8975 (m-10) cc_final: 0.8761 (m-80)
REVERT: D   67 GLU cc_start: 0.9178 (pt0) cc_final: 0.8917 (pt0)
REVERT: D   68 LYS cc_start: 0.9399 (mmtm) cc_final: 0.9112 (mmtm)
REVERT: D   86 ASP cc_start: 0.8223 (t0) cc_final: 0.7780 (t0)
REVERT: D   90 ASP cc_start: 0.8672 (m-30) cc_final: 0.8411 (m-30)
REVERT: F   42 GLN cc_start: 0.9382 (mt0) cc_final: 0.9051 (mt0)
REVERT: F   58 LYS cc_start: 0.9260 (mtmt) cc_final: 0.9053 (ptpt)
REVERT: F   59 THR cc_start: 0.9282 (p) cc_final: 0.8364 (p)
REVERT: F   63 PHE cc_start: 0.9057 (m-10) cc_final: 0.8746 (m-80)
REVERT: F   66 ILE cc_start: 0.9562 (mt) cc_final: 0.9137 (mt)
REVERT: F   70 PHE cc_start: 0.8412 (m-80) cc_final: 0.7991 (m-80)
REVERT: F   86 ASP cc_start: 0.8152 (t0) cc_final: 0.7569 (t0)
REVERT: F   90 ASP cc_start: 0.8922 (m-30) cc_final: 0.8577 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.3402
  time to fit residues: 87.8156
Evaluate side-chains
  146 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 107 optimal weight:    0.6980
   chunk 123 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0980
   chunk 1 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 109 optimal weight:    2.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B  64 HIS
B 104 ASN
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 184 HIS
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 104 ASN
** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.088781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.062132 restraints weight = 51627.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.059600 restraints weight = 34518.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.060033 restraints weight = 32899.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.5122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10845  Z= 0.124
  Angle     :  0.579  11.967  14730  Z= 0.304
  Chirality :  0.044   0.162   1650
  Planarity :  0.004   0.077   1917
  Dihedral  :  4.703  34.453   1569
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.22), residues: 1323
  helix:  1.68 (0.25), residues: 402
  sheet:  0.03 (0.32), residues: 243
  loop : -1.55 (0.21), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 127 
 HIS   0.020   0.001   HIS B  64 
 PHE   0.021   0.001   PHE B  63 
 TYR   0.008   0.001   TYR B  83 
 ARG   0.005   0.000   ARG B 163 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00247 (    3)
  link_NAG-ASN         : angle       0.85155 (    9)
  hydrogen bonds       : bond        0.03196 (  483)
  hydrogen bonds       : angle       4.36915 ( 1359)
  SS BOND              : bond        0.00488 (   18)
  SS BOND              : angle       1.80987 (   36)
  covalent geometry    : bond        0.00266 (10824)
  covalent geometry    : angle       0.57224 (14685)

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

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

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 TYR cc_start: 0.8080 (t80) cc_final: 0.7731 (t80)
REVERT: A  137 ASN cc_start: 0.9293 (m-40) cc_final: 0.8524 (p0)
REVERT: A  280 GLU cc_start: 0.8941 (mp0) cc_final: 0.8372 (pm20)
REVERT: A  288 ILE cc_start: 0.8921 (mt) cc_final: 0.8459 (mt)
REVERT: B   58 LYS cc_start: 0.9266 (mtmt) cc_final: 0.8974 (mttm)
REVERT: B   59 THR cc_start: 0.9533 (p) cc_final: 0.8630 (p)
REVERT: B   62 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8820 (mmmt)
REVERT: B   66 ILE cc_start: 0.9629 (mt) cc_final: 0.9230 (mt)
REVERT: B   70 PHE cc_start: 0.8571 (m-80) cc_final: 0.8132 (m-80)
REVERT: B   86 ASP cc_start: 0.8651 (t0) cc_final: 0.8129 (t0)
REVERT: B  133 MET cc_start: 0.7846 (ptt) cc_final: 0.7425 (ppp)
REVERT: C   70 LEU cc_start: 0.7465 (tp) cc_final: 0.7164 (mt)
REVERT: C   98 TYR cc_start: 0.8945 (t80) cc_final: 0.8476 (t80)
REVERT: C  100 TYR cc_start: 0.7307 (p90) cc_final: 0.7082 (p90)
REVERT: C  233 TYR cc_start: 0.8220 (m-80) cc_final: 0.7868 (m-80)
REVERT: C  261 ARG cc_start: 0.4784 (mtt90) cc_final: 0.2923 (ptt90)
REVERT: E   50 LYS cc_start: 0.8747 (mttt) cc_final: 0.8283 (tptm)
REVERT: E  222 TRP cc_start: 0.7286 (t-100) cc_final: 0.6967 (t-100)
REVERT: D   39 LYS cc_start: 0.9737 (mmtm) cc_final: 0.9453 (mmmt)
REVERT: D   42 GLN cc_start: 0.9435 (mt0) cc_final: 0.8996 (mt0)
REVERT: D   86 ASP cc_start: 0.8420 (t0) cc_final: 0.7954 (t0)
REVERT: D   90 ASP cc_start: 0.8745 (m-30) cc_final: 0.8491 (m-30)
REVERT: D  118 LEU cc_start: 0.9721 (pp) cc_final: 0.9487 (pp)
REVERT: D  133 MET cc_start: 0.7923 (ptt) cc_final: 0.7430 (mpp)
REVERT: F   42 GLN cc_start: 0.9392 (mt0) cc_final: 0.9055 (mt0)
REVERT: F   59 THR cc_start: 0.9309 (p) cc_final: 0.8708 (p)
REVERT: F   63 PHE cc_start: 0.9133 (m-10) cc_final: 0.8882 (m-80)
REVERT: F   66 ILE cc_start: 0.9605 (mt) cc_final: 0.9376 (mt)
REVERT: F   70 PHE cc_start: 0.8554 (m-80) cc_final: 0.8162 (m-80)
REVERT: F   86 ASP cc_start: 0.8390 (t0) cc_final: 0.7735 (t0)
REVERT: F   90 ASP cc_start: 0.8991 (m-30) cc_final: 0.8650 (m-30)
REVERT: F  133 MET cc_start: 0.7855 (ptt) cc_final: 0.7499 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.3951
  time to fit residues: 102.1503
Evaluate side-chains
  150 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0000
   chunk 123 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 115 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 96 optimal weight:    9.9990
   chunk 106 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.3790

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

Flipped N/Q/H residues before XYZ refinement:
B  60 ASN
B  78 GLN
B 104 ASN
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 HIS
E 184 HIS
D 104 ASN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 104 ASN
** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.086828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.060302 restraints weight = 52607.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.058231 restraints weight = 29594.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.058873 restraints weight = 27412.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.5542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10845  Z= 0.199
  Angle     :  0.636  10.092  14730  Z= 0.336
  Chirality :  0.046   0.189   1650
  Planarity :  0.004   0.035   1917
  Dihedral  :  5.253  47.149   1569
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.57 (0.22), residues: 1323
  helix:  1.51 (0.25), residues: 402
  sheet: -0.37 (0.32), residues: 252
  loop : -1.62 (0.21), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 127 
 HIS   0.009   0.001   HIS F 106 
 PHE   0.042   0.002   PHE B  63 
 TYR   0.013   0.002   TYR F  83 
 ARG   0.004   0.000   ARG D 123 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00407 (    3)
  link_NAG-ASN         : angle       1.32114 (    9)
  hydrogen bonds       : bond        0.03668 (  483)
  hydrogen bonds       : angle       4.66988 ( 1359)
  SS BOND              : bond        0.00671 (   18)
  SS BOND              : angle       1.76759 (   36)
  covalent geometry    : bond        0.00422 (10824)
  covalent geometry    : angle       0.62959 (14685)

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

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

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 TYR cc_start: 0.8149 (t80) cc_final: 0.7732 (t80)
REVERT: A  137 ASN cc_start: 0.9292 (m-40) cc_final: 0.8521 (p0)
REVERT: B   58 LYS cc_start: 0.9161 (mtmt) cc_final: 0.8751 (mttm)
REVERT: B   62 LYS cc_start: 0.9354 (mmtt) cc_final: 0.9017 (mmtt)
REVERT: B   66 ILE cc_start: 0.9635 (mt) cc_final: 0.9161 (mt)
REVERT: B   70 PHE cc_start: 0.8608 (m-80) cc_final: 0.7782 (m-80)
REVERT: B   86 ASP cc_start: 0.8646 (t0) cc_final: 0.8223 (t0)
REVERT: B  133 MET cc_start: 0.7900 (ptt) cc_final: 0.7532 (ppp)
REVERT: C   70 LEU cc_start: 0.7488 (tp) cc_final: 0.7190 (mt)
REVERT: C   98 TYR cc_start: 0.8964 (t80) cc_final: 0.8504 (t80)
REVERT: C  100 TYR cc_start: 0.7227 (p90) cc_final: 0.7008 (p90)
REVERT: C  231 SER cc_start: 0.8531 (m) cc_final: 0.7822 (m)
REVERT: C  233 TYR cc_start: 0.8271 (m-80) cc_final: 0.7929 (m-80)
REVERT: E   50 LYS cc_start: 0.8772 (mttt) cc_final: 0.8210 (mmmt)
REVERT: E  222 TRP cc_start: 0.7269 (t-100) cc_final: 0.6909 (t-100)
REVERT: D   58 LYS cc_start: 0.9419 (mtmt) cc_final: 0.9191 (mttm)
REVERT: D   67 GLU cc_start: 0.9232 (pt0) cc_final: 0.8658 (pp20)
REVERT: D   86 ASP cc_start: 0.8390 (t0) cc_final: 0.7933 (t0)
REVERT: D   90 ASP cc_start: 0.8842 (m-30) cc_final: 0.8520 (m-30)
REVERT: D  117 LYS cc_start: 0.9778 (ptpp) cc_final: 0.9537 (pttm)
REVERT: D  133 MET cc_start: 0.7977 (ptt) cc_final: 0.7593 (mpp)
REVERT: F   59 THR cc_start: 0.9498 (p) cc_final: 0.8531 (p)
REVERT: F   63 PHE cc_start: 0.9203 (m-10) cc_final: 0.8895 (m-80)
REVERT: F   64 HIS cc_start: 0.8615 (m170) cc_final: 0.8233 (m90)
REVERT: F   65 GLN cc_start: 0.9301 (pm20) cc_final: 0.9063 (pm20)
REVERT: F   66 ILE cc_start: 0.9652 (mt) cc_final: 0.8954 (mt)
REVERT: F   69 GLU cc_start: 0.8931 (mp0) cc_final: 0.8721 (pm20)
REVERT: F   70 PHE cc_start: 0.8551 (m-80) cc_final: 0.8180 (m-80)
REVERT: F  133 MET cc_start: 0.7956 (ptt) cc_final: 0.7649 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2628
  time to fit residues: 64.3243
Evaluate side-chains
  145 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 117 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 126 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 122 optimal weight:    0.8980
   chunk 72 optimal weight:    0.4980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
** B  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 104 ASN
B 105 GLN
D  78 GLN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 104 ASN
** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.087774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.060977 restraints weight = 51575.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.058505 restraints weight = 28461.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.058926 restraints weight = 27608.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.5722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10845  Z= 0.152
  Angle     :  0.587   9.445  14730  Z= 0.309
  Chirality :  0.045   0.169   1650
  Planarity :  0.004   0.036   1917
  Dihedral  :  4.810  35.522   1569
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.43 (0.22), residues: 1323
  helix:  1.59 (0.25), residues: 408
  sheet: -0.31 (0.32), residues: 252
  loop : -1.53 (0.22), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 153 
 HIS   0.007   0.001   HIS F 106 
 PHE   0.033   0.001   PHE B  63 
 TYR   0.009   0.001   TYR B  83 
 ARG   0.004   0.000   ARG D 123 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00320 (    3)
  link_NAG-ASN         : angle       1.09211 (    9)
  hydrogen bonds       : bond        0.03276 (  483)
  hydrogen bonds       : angle       4.55207 ( 1359)
  SS BOND              : bond        0.00625 (   18)
  SS BOND              : angle       1.21465 (   36)
  covalent geometry    : bond        0.00323 (10824)
  covalent geometry    : angle       0.58447 (14685)

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

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

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 TYR cc_start: 0.8268 (t80) cc_final: 0.7820 (t80)
REVERT: A  137 ASN cc_start: 0.9337 (m-40) cc_final: 0.8604 (p0)
REVERT: A  280 GLU cc_start: 0.8931 (mp0) cc_final: 0.8456 (pm20)
REVERT: A  288 ILE cc_start: 0.8951 (mt) cc_final: 0.8514 (mt)
REVERT: B   62 LYS cc_start: 0.9398 (mmtt) cc_final: 0.9120 (mmtt)
REVERT: B   66 ILE cc_start: 0.9617 (mt) cc_final: 0.9080 (mt)
REVERT: B   70 PHE cc_start: 0.8459 (m-80) cc_final: 0.7188 (m-80)
REVERT: B   86 ASP cc_start: 0.8515 (t0) cc_final: 0.7988 (t0)
REVERT: B   90 ASP cc_start: 0.9006 (m-30) cc_final: 0.8770 (m-30)
REVERT: B  133 MET cc_start: 0.7887 (ptt) cc_final: 0.7544 (ppp)
REVERT: C   70 LEU cc_start: 0.7483 (tp) cc_final: 0.7238 (mt)
REVERT: C   98 TYR cc_start: 0.9026 (t80) cc_final: 0.8582 (t80)
REVERT: C  100 TYR cc_start: 0.7321 (p90) cc_final: 0.7055 (p90)
REVERT: C  231 SER cc_start: 0.8493 (m) cc_final: 0.7834 (m)
REVERT: C  233 TYR cc_start: 0.8317 (m-80) cc_final: 0.7972 (m-80)
REVERT: E   50 LYS cc_start: 0.8765 (mttt) cc_final: 0.8297 (tptm)
REVERT: E  222 TRP cc_start: 0.7389 (t-100) cc_final: 0.7043 (t-100)
REVERT: D   62 LYS cc_start: 0.9205 (mmtm) cc_final: 0.8953 (mmtt)
REVERT: D   63 PHE cc_start: 0.9095 (m-10) cc_final: 0.8791 (m-80)
REVERT: D   67 GLU cc_start: 0.9234 (pt0) cc_final: 0.8981 (pt0)
REVERT: D   68 LYS cc_start: 0.9402 (mmtm) cc_final: 0.9120 (mmtm)
REVERT: D   86 ASP cc_start: 0.8334 (t0) cc_final: 0.7876 (t0)
REVERT: D   90 ASP cc_start: 0.8777 (m-30) cc_final: 0.8481 (m-30)
REVERT: D  115 MET cc_start: 0.9017 (tpt) cc_final: 0.8655 (tpt)
REVERT: D  118 LEU cc_start: 0.9730 (pp) cc_final: 0.9270 (pp)
REVERT: D  133 MET cc_start: 0.8040 (ptt) cc_final: 0.7672 (mpp)
REVERT: F   39 LYS cc_start: 0.9714 (mmtm) cc_final: 0.9409 (mmmt)
REVERT: F   42 GLN cc_start: 0.9361 (mt0) cc_final: 0.8860 (mt0)
REVERT: F   59 THR cc_start: 0.9512 (p) cc_final: 0.8598 (p)
REVERT: F   63 PHE cc_start: 0.9141 (m-10) cc_final: 0.8907 (m-80)
REVERT: F   64 HIS cc_start: 0.8545 (m170) cc_final: 0.8193 (m-70)
REVERT: F   65 GLN cc_start: 0.9223 (pm20) cc_final: 0.8837 (pm20)
REVERT: F   66 ILE cc_start: 0.9628 (mt) cc_final: 0.8609 (mt)
REVERT: F   70 PHE cc_start: 0.8500 (m-80) cc_final: 0.7708 (m-80)
REVERT: F   86 ASP cc_start: 0.8300 (t0) cc_final: 0.7706 (t0)
REVERT: F   90 ASP cc_start: 0.9006 (m-30) cc_final: 0.8759 (m-30)
REVERT: F  133 MET cc_start: 0.8004 (ptt) cc_final: 0.7714 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.2719
  time to fit residues: 68.2392
Evaluate side-chains
  148 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 5 optimal weight:    0.1980
   chunk 74 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 45 optimal weight:    3.9990
   chunk 114 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 113 optimal weight:    0.8980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
B 104 ASN
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 104 ASN
** F 159 HIS ** 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 = 0.4053 r_free = 0.4053 target = 0.086917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.060933 restraints weight = 52822.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.058649 restraints weight = 29017.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.059190 restraints weight = 27148.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.5939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10845  Z= 0.182
  Angle     :  0.624   9.892  14730  Z= 0.330
  Chirality :  0.046   0.181   1650
  Planarity :  0.004   0.040   1917
  Dihedral  :  4.907  33.971   1569
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.57 (0.22), residues: 1323
  helix:  1.38 (0.25), residues: 408
  sheet: -0.33 (0.32), residues: 252
  loop : -1.57 (0.22), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 127 
 HIS   0.008   0.001   HIS F 106 
 PHE   0.029   0.002   PHE B  63 
 TYR   0.012   0.001   TYR B  83 
 ARG   0.003   0.000   ARG B 163 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00355 (    3)
  link_NAG-ASN         : angle       1.29669 (    9)
  hydrogen bonds       : bond        0.03604 (  483)
  hydrogen bonds       : angle       4.77527 ( 1359)
  SS BOND              : bond        0.00740 (   18)
  SS BOND              : angle       1.42165 (   36)
  covalent geometry    : bond        0.00386 (10824)
  covalent geometry    : angle       0.62003 (14685)

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

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

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LYS cc_start: 0.9008 (mttt) cc_final: 0.8467 (tttp)
REVERT: A   98 TYR cc_start: 0.8186 (t80) cc_final: 0.7733 (t80)
REVERT: A  137 ASN cc_start: 0.9316 (m-40) cc_final: 0.8549 (p0)
REVERT: A  280 GLU cc_start: 0.8979 (mp0) cc_final: 0.8535 (pm20)
REVERT: A  288 ILE cc_start: 0.9014 (mt) cc_final: 0.8541 (mt)
REVERT: B   62 LYS cc_start: 0.9409 (mmtt) cc_final: 0.9127 (mmtt)
REVERT: B   86 ASP cc_start: 0.8342 (t0) cc_final: 0.7835 (t0)
REVERT: B   90 ASP cc_start: 0.8981 (m-30) cc_final: 0.8726 (m-30)
REVERT: B  133 MET cc_start: 0.7817 (ptt) cc_final: 0.7427 (ppp)
REVERT: C   98 TYR cc_start: 0.8944 (t80) cc_final: 0.8531 (t80)
REVERT: C  100 TYR cc_start: 0.7210 (p90) cc_final: 0.6961 (p90)
REVERT: C  231 SER cc_start: 0.8448 (m) cc_final: 0.7737 (m)
REVERT: C  233 TYR cc_start: 0.8268 (m-80) cc_final: 0.7959 (m-80)
REVERT: E   50 LYS cc_start: 0.8789 (mttt) cc_final: 0.8318 (tptm)
REVERT: E  222 TRP cc_start: 0.7253 (t-100) cc_final: 0.6879 (t-100)
REVERT: D   58 LYS cc_start: 0.9369 (mtmt) cc_final: 0.9126 (mttm)
REVERT: D   63 PHE cc_start: 0.9155 (m-10) cc_final: 0.8805 (m-80)
REVERT: D   64 HIS cc_start: 0.8719 (m170) cc_final: 0.8397 (m-70)
REVERT: D   69 GLU cc_start: 0.8962 (mp0) cc_final: 0.8740 (mp0)
REVERT: D   86 ASP cc_start: 0.8296 (t0) cc_final: 0.7846 (t0)
REVERT: D   90 ASP cc_start: 0.8772 (m-30) cc_final: 0.8459 (m-30)
REVERT: D  114 GLU cc_start: 0.9297 (tm-30) cc_final: 0.9069 (tm-30)
REVERT: D  118 LEU cc_start: 0.9556 (pp) cc_final: 0.9349 (pp)
REVERT: D  133 MET cc_start: 0.7914 (ptt) cc_final: 0.7647 (mpp)
REVERT: F   39 LYS cc_start: 0.9699 (mmtm) cc_final: 0.9486 (mmmt)
REVERT: F   59 THR cc_start: 0.9517 (p) cc_final: 0.8631 (p)
REVERT: F   63 PHE cc_start: 0.9193 (m-10) cc_final: 0.8912 (m-80)
REVERT: F   64 HIS cc_start: 0.8557 (m170) cc_final: 0.8161 (m-70)
REVERT: F   65 GLN cc_start: 0.9206 (pm20) cc_final: 0.8926 (pm20)
REVERT: F   86 ASP cc_start: 0.8247 (t0) cc_final: 0.7688 (t0)
REVERT: F   90 ASP cc_start: 0.8996 (m-30) cc_final: 0.8714 (m-30)
REVERT: F  133 MET cc_start: 0.7857 (ptt) cc_final: 0.7597 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.2621
  time to fit residues: 65.5016
Evaluate side-chains
  149 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 129 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 85 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
B 104 ASN
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 104 ASN
** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.087689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.061901 restraints weight = 51891.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.059437 restraints weight = 30844.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.059426 restraints weight = 30632.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.6046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10845  Z= 0.148
  Angle     :  0.610   9.213  14730  Z= 0.324
  Chirality :  0.045   0.166   1650
  Planarity :  0.004   0.040   1917
  Dihedral  :  4.666  34.463   1569
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.22), residues: 1323
  helix:  1.46 (0.25), residues: 408
  sheet: -0.24 (0.32), residues: 252
  loop : -1.53 (0.22), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP C  84 
 HIS   0.007   0.001   HIS F 106 
 PHE   0.026   0.001   PHE B  63 
 TYR   0.008   0.001   TYR F  83 
 ARG   0.004   0.000   ARG D 123 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00290 (    3)
  link_NAG-ASN         : angle       1.13740 (    9)
  hydrogen bonds       : bond        0.03466 (  483)
  hydrogen bonds       : angle       4.66961 ( 1359)
  SS BOND              : bond        0.00618 (   18)
  SS BOND              : angle       1.18080 (   36)
  covalent geometry    : bond        0.00319 (10824)
  covalent geometry    : angle       0.60784 (14685)

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

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

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2646 Ramachandran restraints generated.
    1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LYS cc_start: 0.8955 (mttt) cc_final: 0.8541 (tttp)
REVERT: A   98 TYR cc_start: 0.8328 (t80) cc_final: 0.7809 (t80)
REVERT: A  137 ASN cc_start: 0.9359 (m-40) cc_final: 0.8614 (p0)
REVERT: A  280 GLU cc_start: 0.8991 (mp0) cc_final: 0.8570 (pm20)
REVERT: A  288 ILE cc_start: 0.9010 (mt) cc_final: 0.8556 (mt)
REVERT: B   62 LYS cc_start: 0.9455 (mmtt) cc_final: 0.9154 (mmtt)
REVERT: B   64 HIS cc_start: 0.8724 (m90) cc_final: 0.8466 (m-70)
REVERT: B   69 GLU cc_start: 0.8910 (mp0) cc_final: 0.8680 (mp0)
REVERT: B   86 ASP cc_start: 0.8610 (t0) cc_final: 0.8012 (t0)
REVERT: B   90 ASP cc_start: 0.8991 (m-30) cc_final: 0.8774 (m-30)
REVERT: B  133 MET cc_start: 0.7829 (ptt) cc_final: 0.7459 (ppp)
REVERT: C   70 LEU cc_start: 0.7272 (tp) cc_final: 0.7014 (mt)
REVERT: C   98 TYR cc_start: 0.9018 (t80) cc_final: 0.8556 (t80)
REVERT: C  100 TYR cc_start: 0.7268 (p90) cc_final: 0.7005 (p90)
REVERT: C  231 SER cc_start: 0.8457 (m) cc_final: 0.7781 (m)
REVERT: C  233 TYR cc_start: 0.8311 (m-80) cc_final: 0.8000 (m-80)
REVERT: E   50 LYS cc_start: 0.8790 (mttt) cc_final: 0.8351 (tptm)
REVERT: E  222 TRP cc_start: 0.7283 (t-100) cc_final: 0.6920 (t-100)
REVERT: D   63 PHE cc_start: 0.9108 (m-10) cc_final: 0.8849 (m-80)
REVERT: D   64 HIS cc_start: 0.8691 (m170) cc_final: 0.8262 (m-70)
REVERT: D   68 LYS cc_start: 0.9412 (mmtm) cc_final: 0.9061 (mmtm)
REVERT: D   86 ASP cc_start: 0.8285 (t0) cc_final: 0.7815 (t0)
REVERT: D   90 ASP cc_start: 0.8715 (m-30) cc_final: 0.8438 (m-30)
REVERT: D  117 LYS cc_start: 0.9711 (ptpp) cc_final: 0.9467 (pttm)
REVERT: D  118 LEU cc_start: 0.9629 (pp) cc_final: 0.9316 (pp)
REVERT: D  133 MET cc_start: 0.7951 (ptt) cc_final: 0.7705 (mpp)
REVERT: F   39 LYS cc_start: 0.9711 (mmtm) cc_final: 0.9432 (mmmt)
REVERT: F   42 GLN cc_start: 0.9363 (mt0) cc_final: 0.8859 (mt0)
REVERT: F   64 HIS cc_start: 0.8548 (m170) cc_final: 0.8114 (m-70)
REVERT: F   65 GLN cc_start: 0.9155 (pm20) cc_final: 0.8866 (pm20)
REVERT: F   70 PHE cc_start: 0.8337 (m-80) cc_final: 0.7838 (m-80)
REVERT: F   86 ASP cc_start: 0.8170 (t0) cc_final: 0.7589 (t0)
REVERT: F   90 ASP cc_start: 0.8975 (m-30) cc_final: 0.8734 (m-30)
REVERT: F  133 MET cc_start: 0.7871 (ptt) cc_final: 0.7662 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.2726
  time to fit residues: 67.4769
Evaluate side-chains
  153 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 57 optimal weight:    9.9990
   chunk 92 optimal weight:    5.9990
   chunk 75 optimal weight:   10.0000
   chunk 55 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 102 optimal weight:    0.0060
   chunk 21 optimal weight:   10.0000
   chunk 85 optimal weight:    0.0040
   chunk 81 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.9612

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

Flipped N/Q/H residues before XYZ refinement:
B 104 ASN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 104 ASN
** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.087276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.061254 restraints weight = 51379.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.058969 restraints weight = 29230.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.059545 restraints weight = 28059.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.6195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10845  Z= 0.155
  Angle     :  0.610   8.832  14730  Z= 0.326
  Chirality :  0.045   0.192   1650
  Planarity :  0.004   0.038   1917
  Dihedral  :  4.575  34.462   1569
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.08 %
    Favored  : 99.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.22), residues: 1323
  helix:  1.37 (0.25), residues: 408
  sheet: -0.16 (0.33), residues: 252
  loop : -1.53 (0.22), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  84 
 HIS   0.007   0.001   HIS F 106 
 PHE   0.053   0.002   PHE F  63 
 TYR   0.010   0.001   TYR B  83 
 ARG   0.005   0.000   ARG B 123 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00309 (    3)
  link_NAG-ASN         : angle       1.10985 (    9)
  hydrogen bonds       : bond        0.03498 (  483)
  hydrogen bonds       : angle       4.63655 ( 1359)
  SS BOND              : bond        0.00623 (   18)
  SS BOND              : angle       1.17653 (   36)
  covalent geometry    : bond        0.00333 (10824)
  covalent geometry    : angle       0.60759 (14685)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5187.38 seconds
wall clock time: 95 minutes 28.54 seconds (5728.54 seconds total)