Starting phenix.real_space_refine
on Wed Mar  4 04:19:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6y5k_10700/03_2026/6y5k_10700.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6y5k_10700/03_2026/6y5k_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_10700/03_2026/6y5k_10700.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6y5k_10700/03_2026/6y5k_10700.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6y5k_10700/03_2026/6y5k_10700.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6y5k_10700/03_2026/6y5k_10700.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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:
    C, E, D, F
  Time building chain proxies: 2.22, per 1000 atoms: 0.21
  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: 0.89
  Conformation dependent library (CDL) restraints added in 601.0 milliseconds
  

  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: 0.39
  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: 1.69

  Time building geometry restraints manager: 1.23 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}

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:             6.520
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.280
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.370
-------------------------------------------------------------------------------
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 : 10.37
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.002   0.000   ARG E 255 
 TYR   0.012   0.002   TYR C 178 
 PHE   0.007   0.001   PHE A  79 
 TRP   0.012   0.001   TRP A 222 
 HIS   0.002   0.001   HIS E 184 

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

*********************** 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  : 0.420 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 TYR cc_start: 0.8238 (m-80) cc_final: 0.7729 (m-80)
REVERT: B   58 LYS cc_start: 0.9360 (mtmt) cc_final: 0.9087 (mttm)
REVERT: B   61 GLU cc_start: 0.8922 (pp20) cc_final: 0.8556 (pp20)
REVERT: B   64 HIS cc_start: 0.8925 (m-70) cc_final: 0.8625 (m-70)
REVERT: B   86 ASP cc_start: 0.8259 (t0) cc_final: 0.7850 (t0)
REVERT: C   98 TYR cc_start: 0.8956 (t80) cc_final: 0.8244 (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: 0.6661 (t80)
REVERT: E   98 TYR cc_start: 0.8297 (t80) cc_final: 0.7880 (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: 0.9089 (ptpp)
REVERT: D   62 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8602 (mmtt)
REVERT: D   64 HIS cc_start: 0.8922 (m-70) cc_final: 0.8519 (m90)
REVERT: D   86 ASP cc_start: 0.8450 (t0) cc_final: 0.8010 (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   58 LYS cc_start: 0.9404 (mtmt) cc_final: 0.9203 (ptpp)
REVERT: F   59 THR cc_start: 0.9595 (p) cc_final: 0.8947 (p)
REVERT: F   63 PHE cc_start: 0.9340 (m-10) cc_final: 0.9049 (m-80)
REVERT: F   64 HIS cc_start: 0.8930 (m-70) cc_final: 0.8560 (m90)
REVERT: F   66 ILE cc_start: 0.9704 (mt) cc_final: 0.9415 (mt)
REVERT: F   70 PHE cc_start: 0.8781 (m-80) cc_final: 0.8216 (m-80)
REVERT: F   78 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8499 (mm-40)
  outliers start: 0
  outliers final: 0
  residues processed: 279
  average time/residue: 0.1358
  time to fit residues: 48.7423
Evaluate side-chains
  160 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    0.0870
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0870
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:   10.0000
   overall best weight:    0.5136

-------------------------------------------------------------------------------
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 298 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 298 ASN
E 173 ASN
E 184 HIS
E 197 GLN
E 216 ASN
E 298 ASN
D 104 ASN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 159 HIS
F 104 ASN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.087090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.058075 restraints weight = 46115.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.058123 restraints weight = 22998.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.058362 restraints weight = 19321.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.059013 restraints weight = 15934.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.059157 restraints weight = 14529.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  10845  Z= 0.112
  Angle     :  0.554   7.336  14730  Z= 0.294
  Chirality :  0.044   0.148   1650
  Planarity :  0.004   0.046   1917
  Dihedral  :  4.769  34.353   1569
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.21), residues: 1323
  helix:  1.60 (0.24), residues: 399
  sheet:  0.19 (0.35), residues: 240
  loop : -2.12 (0.18), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 163 
 TYR   0.012   0.001   TYR E 100 
 PHE   0.030   0.002   PHE B  70 
 TRP   0.025   0.002   TRP C 180 
 HIS   0.007   0.001   HIS F 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (10824)
  covalent geometry    : angle       0.54952 (14685)
  SS BOND              : bond        0.00242 (   18)
  SS BOND              : angle       1.52305 (   36)
  hydrogen bonds       : bond        0.03172 (  483)
  hydrogen bonds       : angle       4.04117 ( 1359)
  link_NAG-ASN         : bond        0.00271 (    3)
  link_NAG-ASN         : angle       0.53745 (    9)

*********************** 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
  220 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.404 
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: symmetry clash
REVERT: A   79 PHE cc_start: 0.8719 (m-80) cc_final: 0.8447 (m-80)
REVERT: A  137 ASN cc_start: 0.9489 (m-40) cc_final: 0.8774 (p0)
REVERT: A  233 TYR cc_start: 0.8033 (m-80) cc_final: 0.7752 (m-80)
REVERT: B   54 ARG cc_start: 0.9380 (mtp85) cc_final: 0.8701 (ptm-80)
REVERT: B   58 LYS cc_start: 0.9409 (mtmt) cc_final: 0.9115 (mttm)
REVERT: B   64 HIS cc_start: 0.8923 (m-70) cc_final: 0.8676 (m-70)
REVERT: B   86 ASP cc_start: 0.8791 (t0) cc_final: 0.8202 (t0)
REVERT: B  117 LYS cc_start: 0.9841 (tptt) cc_final: 0.9623 (tptp)
REVERT: B  133 MET cc_start: 0.7671 (ptt) cc_final: 0.7213 (ppp)
REVERT: C   70 LEU cc_start: 0.7930 (tp) cc_final: 0.7549 (mt)
REVERT: C   98 TYR cc_start: 0.8883 (t80) cc_final: 0.8172 (t80)
REVERT: C  137 ASN cc_start: 0.9505 (m-40) cc_final: 0.8933 (p0)
REVERT: C  184 HIS cc_start: 0.7969 (m-70) cc_final: 0.7565 (m90)
REVERT: C  233 TYR cc_start: 0.7918 (m-80) cc_final: 0.7649 (m-80)
REVERT: E   50 LYS cc_start: 0.8397 (mttt) cc_final: 0.7966 (tptm)
REVERT: E   70 LEU cc_start: 0.8059 (tp) cc_final: 0.7820 (mt)
REVERT: E   87 PHE cc_start: 0.6284 (t80) cc_final: 0.5605 (t80)
REVERT: E   98 TYR cc_start: 0.8389 (t80) cc_final: 0.7944 (t80)
REVERT: D   58 LYS cc_start: 0.9451 (mtmt) cc_final: 0.9110 (ptpp)
REVERT: D   64 HIS cc_start: 0.8950 (m-70) cc_final: 0.8549 (m-70)
REVERT: D   86 ASP cc_start: 0.8780 (t0) cc_final: 0.8219 (t0)
REVERT: D   90 ASP cc_start: 0.9105 (m-30) cc_final: 0.8857 (m-30)
REVERT: D  108 ILE cc_start: 0.9710 (mt) cc_final: 0.9509 (tt)
REVERT: D  126 LEU cc_start: 0.9475 (tt) cc_final: 0.9272 (tt)
REVERT: F   59 THR cc_start: 0.9578 (p) cc_final: 0.8810 (p)
REVERT: F   63 PHE cc_start: 0.9338 (m-10) cc_final: 0.8958 (m-80)
REVERT: F   66 ILE cc_start: 0.9612 (mt) cc_final: 0.9356 (mt)
REVERT: F   70 PHE cc_start: 0.8858 (m-80) cc_final: 0.8329 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.1462
  time to fit residues: 41.6407
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  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 4 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 126 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 91 optimal weight:    6.9990
   chunk 96 optimal weight:   10.0000
   chunk 107 optimal weight:    0.5980
   chunk 112 optimal weight:    1.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 285 ASN
B  64 HIS
B 104 ASN
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 ASN
C  75 HIS
C 285 ASN
E  75 HIS
E 184 HIS
E 285 ASN
D  60 ASN
D  64 HIS
D 104 ASN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 146 ASN
F  64 HIS
F 104 ASN
F 146 ASN
F 159 HIS

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.087920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.061186 restraints weight = 52924.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.059225 restraints weight = 29641.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.059641 restraints weight = 26867.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.060678 restraints weight = 22562.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.060305 restraints weight = 20021.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  10845  Z= 0.242
  Angle     :  0.653   8.142  14730  Z= 0.352
  Chirality :  0.046   0.199   1650
  Planarity :  0.005   0.088   1917
  Dihedral  :  5.535  47.084   1569
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.71 %
    Favored  : 95.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.21), residues: 1323
  helix:  1.37 (0.24), residues: 402
  sheet: -0.11 (0.32), residues: 267
  loop : -1.81 (0.20), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F 124 
 TYR   0.026   0.002   TYR B  83 
 PHE   0.014   0.002   PHE D  70 
 TRP   0.023   0.002   TRP A 127 
 HIS   0.009   0.001   HIS F 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 (10824)
  covalent geometry    : angle       0.64673 (14685)
  SS BOND              : bond        0.00783 (   18)
  SS BOND              : angle       1.84941 (   36)
  hydrogen bonds       : bond        0.03754 (  483)
  hydrogen bonds       : angle       4.64469 ( 1359)
  link_NAG-ASN         : bond        0.00370 (    3)
  link_NAG-ASN         : angle       1.39540 (    9)

*********************** 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
  183 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 0.428 
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  137 ASN cc_start: 0.9369 (m-40) cc_final: 0.8533 (p0)
REVERT: B   54 ARG cc_start: 0.9030 (mtp85) cc_final: 0.8458 (mtp-110)
REVERT: B   58 LYS cc_start: 0.9251 (mtmt) cc_final: 0.8985 (mttm)
REVERT: B   64 HIS cc_start: 0.8682 (m170) cc_final: 0.8280 (m-70)
REVERT: B   86 ASP cc_start: 0.8265 (t0) cc_final: 0.7855 (t0)
REVERT: B  118 LEU cc_start: 0.9635 (pp) cc_final: 0.9298 (pp)
REVERT: B  133 MET cc_start: 0.7782 (ptt) cc_final: 0.7235 (ppp)
REVERT: C   70 LEU cc_start: 0.7880 (tp) cc_final: 0.7620 (mt)
REVERT: C   98 TYR cc_start: 0.8789 (t80) cc_final: 0.8345 (t80)
REVERT: C  233 TYR cc_start: 0.8197 (m-80) cc_final: 0.7697 (m-80)
REVERT: E   98 TYR cc_start: 0.8638 (t80) cc_final: 0.8235 (t80)
REVERT: D   39 LYS cc_start: 0.9687 (mmtm) cc_final: 0.9425 (mmtm)
REVERT: D   54 ARG cc_start: 0.9046 (mtp85) cc_final: 0.8810 (mtp-110)
REVERT: D   58 LYS cc_start: 0.9262 (mtmt) cc_final: 0.8748 (ptpp)
REVERT: D   62 LYS cc_start: 0.9221 (mptt) cc_final: 0.8937 (mmtp)
REVERT: D   86 ASP cc_start: 0.8214 (t0) cc_final: 0.7802 (t0)
REVERT: D   90 ASP cc_start: 0.8696 (m-30) cc_final: 0.8460 (m-30)
REVERT: F   59 THR cc_start: 0.9347 (p) cc_final: 0.8401 (p)
REVERT: F   62 LYS cc_start: 0.9228 (mmtt) cc_final: 0.8734 (mmmm)
REVERT: F   63 PHE cc_start: 0.9124 (m-10) cc_final: 0.8698 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 183
  average time/residue: 0.1410
  time to fit residues: 33.7484
Evaluate side-chains
  126 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   chunk 84 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 99 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 107 optimal weight:    0.6980
   chunk 90 optimal weight:    5.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 184 HIS
B 104 ASN
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 HIS
E 184 HIS
D  60 ASN
D  64 HIS
D  78 GLN
D 104 ASN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.089222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.062318 restraints weight = 52255.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.060279 restraints weight = 33483.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.060419 restraints weight = 31115.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.060814 restraints weight = 24162.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.060958 restraints weight = 21941.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.4229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10845  Z= 0.132
  Angle     :  0.556   7.066  14730  Z= 0.294
  Chirality :  0.044   0.165   1650
  Planarity :  0.004   0.040   1917
  Dihedral  :  4.869  37.632   1569
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  1.77 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.21), residues: 1323
  helix:  1.65 (0.24), residues: 402
  sheet:  0.07 (0.34), residues: 240
  loop : -1.61 (0.20), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 123 
 TYR   0.010   0.001   TYR B  83 
 PHE   0.012   0.001   PHE D  70 
 TRP   0.019   0.002   TRP C 127 
 HIS   0.016   0.001   HIS D  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10824)
  covalent geometry    : angle       0.55059 (14685)
  SS BOND              : bond        0.00479 (   18)
  SS BOND              : angle       1.56436 (   36)
  hydrogen bonds       : bond        0.03191 (  483)
  hydrogen bonds       : angle       4.25851 ( 1359)
  link_NAG-ASN         : bond        0.00248 (    3)
  link_NAG-ASN         : angle       0.87471 (    9)

*********************** 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
  199 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 195
  time to evaluate  : 0.476 
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  137 ASN cc_start: 0.9378 (m-40) cc_final: 0.8586 (p0)
REVERT: A  233 TYR cc_start: 0.8438 (m-80) cc_final: 0.8179 (m-80)
REVERT: B   54 ARG cc_start: 0.9116 (mtp85) cc_final: 0.8780 (ptm-80)
REVERT: B   64 HIS cc_start: 0.8600 (m170) cc_final: 0.8070 (m-70)
REVERT: B   65 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8596 (pm20)
REVERT: B   68 LYS cc_start: 0.9364 (mmtm) cc_final: 0.9094 (mmtm)
REVERT: B   86 ASP cc_start: 0.8525 (t0) cc_final: 0.7947 (t0)
REVERT: B  133 MET cc_start: 0.7846 (ptt) cc_final: 0.7326 (ppp)
REVERT: C   70 LEU cc_start: 0.7882 (tp) cc_final: 0.7146 (pp)
REVERT: C   98 TYR cc_start: 0.8934 (t80) cc_final: 0.8438 (t80)
REVERT: C  100 TYR cc_start: 0.7211 (p90) cc_final: 0.6959 (p90)
REVERT: C  137 ASN cc_start: 0.9423 (m-40) cc_final: 0.8886 (p0)
REVERT: C  233 TYR cc_start: 0.8232 (m-80) cc_final: 0.7750 (m-80)
REVERT: E   50 LYS cc_start: 0.8747 (mttt) cc_final: 0.8323 (mmtt)
REVERT: E   98 TYR cc_start: 0.7154 (t80) cc_final: 0.6622 (t80)
REVERT: E  100 TYR cc_start: 0.5155 (p90) cc_final: 0.4899 (p90)
REVERT: E  222 TRP cc_start: 0.7180 (t-100) cc_final: 0.6866 (t-100)
REVERT: D   39 LYS cc_start: 0.9733 (mmtm) cc_final: 0.9468 (mmmt)
REVERT: D   42 GLN cc_start: 0.9516 (mt0) cc_final: 0.9151 (mt0)
REVERT: D   54 ARG cc_start: 0.9129 (mtp85) cc_final: 0.8843 (ptm-80)
REVERT: D   58 LYS cc_start: 0.9367 (mtmt) cc_final: 0.8871 (ptpp)
REVERT: D   61 GLU cc_start: 0.8765 (pp20) cc_final: 0.8432 (pp20)
REVERT: D   62 LYS cc_start: 0.9151 (mptt) cc_final: 0.8944 (mmtt)
REVERT: D   86 ASP cc_start: 0.8371 (t0) cc_final: 0.7904 (t0)
REVERT: D   90 ASP cc_start: 0.8696 (m-30) cc_final: 0.8466 (m-30)
REVERT: D  133 MET cc_start: 0.7720 (ptt) cc_final: 0.7382 (ppp)
REVERT: F   59 THR cc_start: 0.9396 (p) cc_final: 0.8535 (p)
REVERT: F   61 GLU cc_start: 0.8745 (pp20) cc_final: 0.7945 (pp20)
REVERT: F   62 LYS cc_start: 0.9199 (mmtt) cc_final: 0.8860 (mmtt)
REVERT: F   63 PHE cc_start: 0.9127 (m-10) cc_final: 0.8811 (m-80)
REVERT: F   69 GLU cc_start: 0.8868 (mp0) cc_final: 0.8660 (mp0)
  outliers start: 4
  outliers final: 2
  residues processed: 197
  average time/residue: 0.1388
  time to fit residues: 35.9925
Evaluate side-chains
  137 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 134
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 128 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 125 optimal weight:    0.7980
   chunk 44 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 93 optimal weight:    7.9990
   chunk 22 optimal weight:    0.8980
   chunk 40 optimal weight:   10.0000
   chunk 57 optimal weight:    9.9990
   chunk 16 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    1.7386

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

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

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.086062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.060468 restraints weight = 52747.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.058000 restraints weight = 31019.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.058700 restraints weight = 28460.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.059030 restraints weight = 22989.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.059068 restraints weight = 21999.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.4924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  10845  Z= 0.243
  Angle     :  0.660   8.606  14730  Z= 0.352
  Chirality :  0.047   0.201   1650
  Planarity :  0.004   0.042   1917
  Dihedral  :  5.523  45.421   1569
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.21), residues: 1323
  helix:  1.35 (0.24), residues: 402
  sheet: -0.32 (0.30), residues: 273
  loop : -1.68 (0.21), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG F 163 
 TYR   0.019   0.002   TYR F  83 
 PHE   0.010   0.002   PHE F  70 
 TRP   0.020   0.002   TRP C 127 
 HIS   0.008   0.001   HIS D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 (10824)
  covalent geometry    : angle       0.64913 (14685)
  SS BOND              : bond        0.00661 (   18)
  SS BOND              : angle       2.44054 (   36)
  hydrogen bonds       : bond        0.03770 (  483)
  hydrogen bonds       : angle       4.80196 ( 1359)
  link_NAG-ASN         : bond        0.00394 (    3)
  link_NAG-ASN         : angle       1.47289 (    9)

*********************** 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
  178 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.478 
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  137 ASN cc_start: 0.9317 (m-40) cc_final: 0.8502 (p0)
REVERT: A  231 SER cc_start: 0.8546 (t) cc_final: 0.8343 (t)
REVERT: A  233 TYR cc_start: 0.8332 (m-80) cc_final: 0.8080 (m-80)
REVERT: B   58 LYS cc_start: 0.9369 (mtmt) cc_final: 0.8897 (mttm)
REVERT: B   62 LYS cc_start: 0.9278 (mmtt) cc_final: 0.8963 (mmtt)
REVERT: B   64 HIS cc_start: 0.8792 (m170) cc_final: 0.8317 (m90)
REVERT: B   86 ASP cc_start: 0.8758 (t0) cc_final: 0.8175 (t0)
REVERT: B   90 ASP cc_start: 0.9084 (m-30) cc_final: 0.8820 (m-30)
REVERT: B  115 MET cc_start: 0.9084 (tpt) cc_final: 0.8730 (ttt)
REVERT: B  118 LEU cc_start: 0.9633 (pp) cc_final: 0.9431 (pp)
REVERT: B  133 MET cc_start: 0.7900 (ptt) cc_final: 0.7383 (ppp)
REVERT: C   98 TYR cc_start: 0.8902 (t80) cc_final: 0.8445 (t80)
REVERT: C  184 HIS cc_start: 0.8179 (m-70) cc_final: 0.7974 (m90)
REVERT: C  231 SER cc_start: 0.8591 (m) cc_final: 0.7886 (m)
REVERT: C  233 TYR cc_start: 0.8265 (m-80) cc_final: 0.7873 (m-80)
REVERT: E   50 LYS cc_start: 0.8806 (mttt) cc_final: 0.8205 (mmmt)
REVERT: E   98 TYR cc_start: 0.7629 (t80) cc_final: 0.7133 (t80)
REVERT: D   54 ARG cc_start: 0.9146 (mtp85) cc_final: 0.8577 (mtp-110)
REVERT: D   58 LYS cc_start: 0.9383 (mtmt) cc_final: 0.9024 (mttm)
REVERT: D   67 GLU cc_start: 0.9275 (pt0) cc_final: 0.8670 (pp20)
REVERT: D   86 ASP cc_start: 0.8448 (t0) cc_final: 0.8029 (t0)
REVERT: D   90 ASP cc_start: 0.8881 (m-30) cc_final: 0.8620 (m-30)
REVERT: D  133 MET cc_start: 0.7888 (ptt) cc_final: 0.7590 (ppp)
REVERT: F   59 THR cc_start: 0.9422 (p) cc_final: 0.8437 (p)
REVERT: F   63 PHE cc_start: 0.9253 (m-10) cc_final: 0.8894 (m-80)
REVERT: F  133 MET cc_start: 0.7996 (ptt) cc_final: 0.7591 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1418
  time to fit residues: 33.0701
Evaluate side-chains
  128 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 131 optimal weight:    0.3980
   chunk 34 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 130 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 109 optimal weight:    0.8980
   chunk 86 optimal weight:    5.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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
F 104 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.088302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.061746 restraints weight = 52037.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.059674 restraints weight = 28409.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.060225 restraints weight = 26704.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.060583 restraints weight = 21816.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.060611 restraints weight = 20394.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.4997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10845  Z= 0.124
  Angle     :  0.580  11.544  14730  Z= 0.302
  Chirality :  0.044   0.164   1650
  Planarity :  0.004   0.043   1917
  Dihedral  :  4.749  34.757   1569
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.22), residues: 1323
  helix:  1.64 (0.25), residues: 402
  sheet:  0.07 (0.34), residues: 228
  loop : -1.60 (0.20), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 207 
 TYR   0.009   0.001   TYR A 302 
 PHE   0.007   0.001   PHE F  70 
 TRP   0.017   0.001   TRP C 127 
 HIS   0.010   0.001   HIS F 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10824)
  covalent geometry    : angle       0.57252 (14685)
  SS BOND              : bond        0.00605 (   18)
  SS BOND              : angle       1.91209 (   36)
  hydrogen bonds       : bond        0.03146 (  483)
  hydrogen bonds       : angle       4.37661 ( 1359)
  link_NAG-ASN         : bond        0.00270 (    3)
  link_NAG-ASN         : angle       0.92494 (    9)

*********************** 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
  186 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.406 
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   98 TYR cc_start: 0.7851 (t80) cc_final: 0.7585 (t80)
REVERT: A  137 ASN cc_start: 0.9309 (m-40) cc_final: 0.8552 (p0)
REVERT: A  280 GLU cc_start: 0.8814 (mp0) cc_final: 0.8417 (pm20)
REVERT: A  288 ILE cc_start: 0.9041 (mt) cc_final: 0.8705 (mt)
REVERT: B   64 HIS cc_start: 0.8521 (m170) cc_final: 0.8106 (m-70)
REVERT: B   69 GLU cc_start: 0.8760 (mp0) cc_final: 0.8486 (mp0)
REVERT: B   86 ASP cc_start: 0.8368 (t0) cc_final: 0.7867 (t0)
REVERT: B   90 ASP cc_start: 0.8874 (m-30) cc_final: 0.8672 (m-30)
REVERT: B  133 MET cc_start: 0.7765 (ptt) cc_final: 0.7318 (ppp)
REVERT: C   70 LEU cc_start: 0.7768 (tp) cc_final: 0.7017 (pp)
REVERT: C   98 TYR cc_start: 0.8950 (t80) cc_final: 0.8400 (t80)
REVERT: C  184 HIS cc_start: 0.8019 (m-70) cc_final: 0.7801 (m90)
REVERT: C  231 SER cc_start: 0.8490 (m) cc_final: 0.7814 (m)
REVERT: C  233 TYR cc_start: 0.8215 (m-80) cc_final: 0.7823 (m-80)
REVERT: C  261 ARG cc_start: 0.4686 (mtt90) cc_final: 0.3327 (ppt90)
REVERT: E   50 LYS cc_start: 0.8802 (mttt) cc_final: 0.8353 (tptm)
REVERT: D   54 ARG cc_start: 0.9008 (mtp85) cc_final: 0.8771 (ptm-80)
REVERT: D   58 LYS cc_start: 0.9319 (mtmt) cc_final: 0.9099 (ptpp)
REVERT: D   64 HIS cc_start: 0.8615 (m170) cc_final: 0.8226 (m90)
REVERT: D   86 ASP cc_start: 0.8186 (t0) cc_final: 0.7750 (t0)
REVERT: D   90 ASP cc_start: 0.8679 (m-30) cc_final: 0.8453 (m-30)
REVERT: D  133 MET cc_start: 0.7864 (ptt) cc_final: 0.7576 (ppp)
REVERT: F   42 GLN cc_start: 0.9398 (mt0) cc_final: 0.9064 (mt0)
REVERT: F   59 THR cc_start: 0.9334 (p) cc_final: 0.8341 (p)
REVERT: F   63 PHE cc_start: 0.9019 (m-10) cc_final: 0.8705 (m-80)
REVERT: F   66 ILE cc_start: 0.9594 (mt) cc_final: 0.9197 (mt)
REVERT: F   69 GLU cc_start: 0.8783 (mp0) cc_final: 0.8481 (mp0)
REVERT: F   70 PHE cc_start: 0.8410 (m-80) cc_final: 0.8029 (m-80)
REVERT: F   86 ASP cc_start: 0.8237 (t0) cc_final: 0.7641 (t0)
REVERT: F   90 ASP cc_start: 0.8924 (m-30) cc_final: 0.8693 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1363
  time to fit residues: 33.3993
Evaluate side-chains
  135 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
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 18 optimal weight:    9.9990
   chunk 64 optimal weight:    0.2980
   chunk 100 optimal weight:    3.9990
   chunk 101 optimal weight:    0.4980
   chunk 57 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 55 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 17 optimal weight:    8.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
** B  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 104 ASN
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 GLN
E 184 HIS
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  60 ASN
F 104 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.079807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.048165 restraints weight = 48574.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.050615 restraints weight = 23883.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.051982 restraints weight = 15889.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.052668 restraints weight = 12771.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.052980 restraints weight = 11489.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.5613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067  10845  Z= 0.272
  Angle     :  0.704   9.721  14730  Z= 0.372
  Chirality :  0.048   0.209   1650
  Planarity :  0.005   0.045   1917
  Dihedral  :  5.660  49.370   1569
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 16.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.21), residues: 1323
  helix:  1.25 (0.24), residues: 402
  sheet: -0.50 (0.31), residues: 252
  loop : -1.81 (0.20), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 163 
 TYR   0.017   0.002   TYR F  83 
 PHE   0.018   0.002   PHE C 120 
 TRP   0.023   0.002   TRP C 127 
 HIS   0.012   0.002   HIS F 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 (10824)
  covalent geometry    : angle       0.69570 (14685)
  SS BOND              : bond        0.00822 (   18)
  SS BOND              : angle       2.10180 (   36)
  hydrogen bonds       : bond        0.03988 (  483)
  hydrogen bonds       : angle       5.00981 ( 1359)
  link_NAG-ASN         : bond        0.00515 (    3)
  link_NAG-ASN         : angle       1.66938 (    9)

*********************** 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
  172 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.417 
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: A  137 ASN cc_start: 0.9391 (m-40) cc_final: 0.8694 (p0)
REVERT: A  280 GLU cc_start: 0.8970 (mp0) cc_final: 0.8493 (pm20)
REVERT: A  288 ILE cc_start: 0.9049 (mt) cc_final: 0.8730 (mt)
REVERT: B   58 LYS cc_start: 0.9543 (mtmt) cc_final: 0.9146 (mttm)
REVERT: B   62 LYS cc_start: 0.9326 (mmtt) cc_final: 0.9092 (mttm)
REVERT: B   64 HIS cc_start: 0.8991 (m170) cc_final: 0.8540 (m90)
REVERT: B   86 ASP cc_start: 0.8499 (t0) cc_final: 0.8017 (t0)
REVERT: B   90 ASP cc_start: 0.8812 (m-30) cc_final: 0.8585 (m-30)
REVERT: B  133 MET cc_start: 0.7793 (ptt) cc_final: 0.7355 (ppp)
REVERT: C   98 TYR cc_start: 0.8973 (t80) cc_final: 0.8496 (t80)
REVERT: C  231 SER cc_start: 0.8636 (m) cc_final: 0.8075 (m)
REVERT: C  233 TYR cc_start: 0.8399 (m-80) cc_final: 0.8025 (m-80)
REVERT: E   50 LYS cc_start: 0.8808 (mttt) cc_final: 0.8298 (tptp)
REVERT: E  233 TYR cc_start: 0.8431 (m-80) cc_final: 0.8207 (m-80)
REVERT: D   58 LYS cc_start: 0.9524 (mtmt) cc_final: 0.9147 (ptpt)
REVERT: D   62 LYS cc_start: 0.9331 (mmtm) cc_final: 0.9094 (mmtt)
REVERT: D   64 HIS cc_start: 0.8935 (m170) cc_final: 0.8389 (m90)
REVERT: D   67 GLU cc_start: 0.9361 (pt0) cc_final: 0.8778 (pp20)
REVERT: D   86 ASP cc_start: 0.8467 (t0) cc_final: 0.8037 (t0)
REVERT: D   90 ASP cc_start: 0.8624 (m-30) cc_final: 0.8413 (m-30)
REVERT: D  133 MET cc_start: 0.7825 (ptt) cc_final: 0.7237 (ppp)
REVERT: F   59 THR cc_start: 0.9587 (p) cc_final: 0.8885 (p)
REVERT: F   62 LYS cc_start: 0.9391 (mmtt) cc_final: 0.9083 (mttp)
REVERT: F   63 PHE cc_start: 0.9365 (m-10) cc_final: 0.8999 (m-80)
REVERT: F  133 MET cc_start: 0.7844 (ptt) cc_final: 0.7459 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1235
  time to fit residues: 28.4457
Evaluate side-chains
  129 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0980
   chunk 78 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 121 optimal weight:    0.1980
   chunk 122 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 4 optimal weight:    0.3980
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
B  60 ASN
B  78 GLN
B 104 ASN
B 105 GLN
D 125 GLN
** F  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  60 ASN
F 104 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.088358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.061921 restraints weight = 51454.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.060010 restraints weight = 27919.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.060650 restraints weight = 25629.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.060848 restraints weight = 22023.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.060874 restraints weight = 20121.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.5588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10845  Z= 0.115
  Angle     :  0.609  10.487  14730  Z= 0.315
  Chirality :  0.044   0.162   1650
  Planarity :  0.004   0.043   1917
  Dihedral  :  4.609  34.997   1569
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.22), residues: 1323
  helix:  1.66 (0.25), residues: 408
  sheet:  0.05 (0.33), residues: 234
  loop : -1.63 (0.21), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 163 
 TYR   0.007   0.001   TYR B  94 
 PHE   0.007   0.001   PHE F  70 
 TRP   0.015   0.001   TRP C 127 
 HIS   0.008   0.001   HIS F 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10824)
  covalent geometry    : angle       0.60171 (14685)
  SS BOND              : bond        0.00454 (   18)
  SS BOND              : angle       1.99025 (   36)
  hydrogen bonds       : bond        0.03079 (  483)
  hydrogen bonds       : angle       4.43147 ( 1359)
  link_NAG-ASN         : bond        0.00280 (    3)
  link_NAG-ASN         : angle       1.01086 (    9)

*********************** 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
  188 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.411 
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   50 LYS cc_start: 0.8862 (mttt) cc_final: 0.8387 (ttmt)
REVERT: A   98 TYR cc_start: 0.8207 (t80) cc_final: 0.7780 (t80)
REVERT: A  137 ASN cc_start: 0.9328 (m-40) cc_final: 0.8567 (p0)
REVERT: A  280 GLU cc_start: 0.8644 (mp0) cc_final: 0.8168 (pm20)
REVERT: B   58 LYS cc_start: 0.9330 (mtmt) cc_final: 0.9110 (ptpp)
REVERT: B   59 THR cc_start: 0.9384 (p) cc_final: 0.8558 (p)
REVERT: B   63 PHE cc_start: 0.9066 (m-10) cc_final: 0.8796 (m-80)
REVERT: B   64 HIS cc_start: 0.8628 (m170) cc_final: 0.8252 (m90)
REVERT: B   65 GLN cc_start: 0.9039 (pm20) cc_final: 0.8827 (pm20)
REVERT: B   86 ASP cc_start: 0.8504 (t0) cc_final: 0.8055 (t0)
REVERT: B  114 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8987 (tm-30)
REVERT: B  133 MET cc_start: 0.7798 (ptt) cc_final: 0.7424 (ppp)
REVERT: C   98 TYR cc_start: 0.8948 (t80) cc_final: 0.8430 (t80)
REVERT: C  231 SER cc_start: 0.8466 (m) cc_final: 0.7743 (m)
REVERT: C  233 TYR cc_start: 0.8247 (m-80) cc_final: 0.7926 (m-80)
REVERT: E   50 LYS cc_start: 0.8728 (mttt) cc_final: 0.8274 (tptm)
REVERT: E  222 TRP cc_start: 0.7347 (t-100) cc_final: 0.6894 (t-100)
REVERT: D   54 ARG cc_start: 0.9118 (mtp85) cc_final: 0.8846 (mtp-110)
REVERT: D   58 LYS cc_start: 0.9359 (mtmt) cc_final: 0.9025 (ptpp)
REVERT: D   59 THR cc_start: 0.9344 (p) cc_final: 0.8700 (p)
REVERT: D   64 HIS cc_start: 0.8695 (m170) cc_final: 0.8325 (m90)
REVERT: D   86 ASP cc_start: 0.8365 (t0) cc_final: 0.7920 (t0)
REVERT: D   90 ASP cc_start: 0.8789 (m-30) cc_final: 0.8538 (m-30)
REVERT: D  133 MET cc_start: 0.7926 (ptt) cc_final: 0.7495 (ppp)
REVERT: F   59 THR cc_start: 0.9395 (p) cc_final: 0.8382 (p)
REVERT: F   66 ILE cc_start: 0.9609 (mt) cc_final: 0.9268 (mt)
REVERT: F   70 PHE cc_start: 0.8556 (m-80) cc_final: 0.8105 (m-80)
REVERT: F   86 ASP cc_start: 0.8390 (t0) cc_final: 0.7783 (t0)
REVERT: F   90 ASP cc_start: 0.9020 (m-30) cc_final: 0.8754 (m-30)
REVERT: F  133 MET cc_start: 0.7843 (ptt) cc_final: 0.7490 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1291
  time to fit residues: 32.2431
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  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0040
   chunk 4 optimal weight:    0.7980
   chunk 85 optimal weight:    7.9990
   chunk 100 optimal weight:    0.3980
   chunk 51 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 0 optimal weight:    2.9990
   chunk 114 optimal weight:    2.9990
   overall best weight:    1.0394

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 298 ASN
B  60 ASN
B 104 ASN
D 104 ASN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 104 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.087123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.060631 restraints weight = 51850.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.058813 restraints weight = 28012.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.059402 restraints weight = 25382.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.059526 restraints weight = 21932.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.059570 restraints weight = 20295.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.5772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10845  Z= 0.164
  Angle     :  0.639  12.189  14730  Z= 0.336
  Chirality :  0.046   0.189   1650
  Planarity :  0.005   0.101   1917
  Dihedral  :  4.851  46.153   1569
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.22), residues: 1323
  helix:  1.53 (0.24), residues: 408
  sheet: -0.27 (0.32), residues: 252
  loop : -1.61 (0.21), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG D 124 
 TYR   0.010   0.001   TYR F  83 
 PHE   0.011   0.001   PHE D  63 
 TRP   0.015   0.001   TRP C 127 
 HIS   0.008   0.001   HIS F 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (10824)
  covalent geometry    : angle       0.63401 (14685)
  SS BOND              : bond        0.00611 (   18)
  SS BOND              : angle       1.67912 (   36)
  hydrogen bonds       : bond        0.03394 (  483)
  hydrogen bonds       : angle       4.64641 ( 1359)
  link_NAG-ASN         : bond        0.00312 (    3)
  link_NAG-ASN         : angle       1.15453 (    9)

*********************** 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
  191 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.409 
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   98 TYR cc_start: 0.8203 (t80) cc_final: 0.7723 (t80)
REVERT: A  137 ASN cc_start: 0.9337 (m-40) cc_final: 0.8584 (p0)
REVERT: A  280 GLU cc_start: 0.8775 (mp0) cc_final: 0.8225 (pm20)
REVERT: B   59 THR cc_start: 0.9387 (p) cc_final: 0.8624 (p)
REVERT: B   62 LYS cc_start: 0.9208 (mmtt) cc_final: 0.8931 (mmtt)
REVERT: B   63 PHE cc_start: 0.9023 (m-10) cc_final: 0.8720 (m-80)
REVERT: B   64 HIS cc_start: 0.8683 (m170) cc_final: 0.8223 (m90)
REVERT: B   66 ILE cc_start: 0.9688 (mt) cc_final: 0.9211 (mt)
REVERT: B   69 GLU cc_start: 0.8889 (mp0) cc_final: 0.8663 (mp0)
REVERT: B   70 PHE cc_start: 0.8560 (m-80) cc_final: 0.8046 (m-80)
REVERT: B   86 ASP cc_start: 0.8512 (t0) cc_final: 0.7981 (t0)
REVERT: B   90 ASP cc_start: 0.9035 (m-30) cc_final: 0.8751 (m-30)
REVERT: B  133 MET cc_start: 0.7814 (ptt) cc_final: 0.7432 (ppp)
REVERT: C   98 TYR cc_start: 0.8951 (t80) cc_final: 0.8449 (t80)
REVERT: C  231 SER cc_start: 0.8458 (m) cc_final: 0.7745 (m)
REVERT: C  233 TYR cc_start: 0.8298 (m-80) cc_final: 0.7969 (m-80)
REVERT: C  320 MET cc_start: 0.7185 (ptp) cc_final: 0.6874 (ptp)
REVERT: E   50 LYS cc_start: 0.8759 (mttt) cc_final: 0.8291 (tptm)
REVERT: E  260 MET cc_start: 0.6798 (ptp) cc_final: 0.6573 (pmm)
REVERT: D   59 THR cc_start: 0.9350 (p) cc_final: 0.8566 (p)
REVERT: D   64 HIS cc_start: 0.8827 (m170) cc_final: 0.8302 (m90)
REVERT: D   67 GLU cc_start: 0.9277 (pt0) cc_final: 0.8701 (pp20)
REVERT: D   69 GLU cc_start: 0.8914 (mp0) cc_final: 0.8689 (mp0)
REVERT: D   86 ASP cc_start: 0.8411 (t0) cc_final: 0.7962 (t0)
REVERT: D   90 ASP cc_start: 0.8807 (m-30) cc_final: 0.8554 (m-30)
REVERT: D  133 MET cc_start: 0.7917 (ptt) cc_final: 0.7446 (ppp)
REVERT: F   59 THR cc_start: 0.9397 (p) cc_final: 0.8206 (p)
REVERT: F   66 ILE cc_start: 0.9629 (mt) cc_final: 0.9317 (mt)
REVERT: F   70 PHE cc_start: 0.8575 (m-80) cc_final: 0.8177 (m-80)
REVERT: F   86 ASP cc_start: 0.8431 (t0) cc_final: 0.7823 (t0)
REVERT: F   90 ASP cc_start: 0.9026 (m-30) cc_final: 0.8765 (m-30)
REVERT: F  133 MET cc_start: 0.7915 (ptt) cc_final: 0.7611 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.1241
  time to fit residues: 31.7630
Evaluate side-chains
  138 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 83 optimal weight:    9.9990
   chunk 101 optimal weight:    0.0670
   chunk 120 optimal weight:    0.6980
   chunk 121 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   overall best weight:    0.6718

-------------------------------------------------------------------------------
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 104 ASN
** F  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 104 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.088255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.061611 restraints weight = 51713.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.059630 restraints weight = 27521.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.060265 restraints weight = 25693.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.060419 restraints weight = 21624.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.060475 restraints weight = 20306.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.5867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10845  Z= 0.126
  Angle     :  0.623   8.852  14730  Z= 0.329
  Chirality :  0.045   0.178   1650
  Planarity :  0.004   0.045   1917
  Dihedral  :  4.524  36.281   1569
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.22), residues: 1323
  helix:  1.65 (0.24), residues: 408
  sheet:  0.00 (0.33), residues: 246
  loop : -1.62 (0.22), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D 127 
 TYR   0.007   0.001   TYR E 308 
 PHE   0.008   0.001   PHE D  63 
 TRP   0.020   0.001   TRP C 153 
 HIS   0.008   0.001   HIS F 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (10824)
  covalent geometry    : angle       0.62096 (14685)
  SS BOND              : bond        0.00611 (   18)
  SS BOND              : angle       1.02628 (   36)
  hydrogen bonds       : bond        0.03238 (  483)
  hydrogen bonds       : angle       4.49752 ( 1359)
  link_NAG-ASN         : bond        0.00280 (    3)
  link_NAG-ASN         : angle       0.97553 (    9)

********************** 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
  190 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.478 
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: A   98 TYR cc_start: 0.8262 (t80) cc_final: 0.7792 (t80)
REVERT: A  137 ASN cc_start: 0.9350 (m-40) cc_final: 0.8587 (p0)
REVERT: B   58 LYS cc_start: 0.9330 (mtmt) cc_final: 0.8916 (ptpp)
REVERT: B   59 THR cc_start: 0.9415 (p) cc_final: 0.8719 (p)
REVERT: B   61 GLU cc_start: 0.8846 (pp20) cc_final: 0.8427 (pp20)
REVERT: B   64 HIS cc_start: 0.8670 (m170) cc_final: 0.8464 (m-70)
REVERT: B   65 GLN cc_start: 0.9115 (pm20) cc_final: 0.8850 (pm20)
REVERT: B   66 ILE cc_start: 0.9641 (mt) cc_final: 0.9276 (mt)
REVERT: B   70 PHE cc_start: 0.8575 (m-80) cc_final: 0.8055 (m-80)
REVERT: B   86 ASP cc_start: 0.8528 (t0) cc_final: 0.7982 (t0)
REVERT: B   90 ASP cc_start: 0.8946 (m-30) cc_final: 0.8705 (m-30)
REVERT: B  114 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8994 (tm-30)
REVERT: B  133 MET cc_start: 0.7816 (ptt) cc_final: 0.7459 (ppp)
REVERT: C   70 LEU cc_start: 0.7616 (tp) cc_final: 0.6764 (pp)
REVERT: C   98 TYR cc_start: 0.8966 (t80) cc_final: 0.8451 (t80)
REVERT: C  233 TYR cc_start: 0.8279 (m-80) cc_final: 0.7930 (m-80)
REVERT: C  320 MET cc_start: 0.7142 (ptp) cc_final: 0.6833 (ptp)
REVERT: E   50 LYS cc_start: 0.8717 (mttt) cc_final: 0.8150 (mmmt)
REVERT: E  260 MET cc_start: 0.7009 (ptp) cc_final: 0.6768 (pmm)
REVERT: D   54 ARG cc_start: 0.9146 (mtp85) cc_final: 0.8919 (mtp-110)
REVERT: D   59 THR cc_start: 0.9366 (p) cc_final: 0.8569 (p)
REVERT: D   64 HIS cc_start: 0.8820 (m170) cc_final: 0.8363 (m90)
REVERT: D   66 ILE cc_start: 0.9667 (mt) cc_final: 0.9464 (mt)
REVERT: D   70 PHE cc_start: 0.8511 (m-80) cc_final: 0.8009 (m-80)
REVERT: D   86 ASP cc_start: 0.8425 (t0) cc_final: 0.7961 (t0)
REVERT: D   90 ASP cc_start: 0.8810 (m-30) cc_final: 0.8556 (m-30)
REVERT: D  123 ARG cc_start: 0.9620 (pmt-80) cc_final: 0.9387 (pmt-80)
REVERT: D  133 MET cc_start: 0.7875 (ptt) cc_final: 0.7427 (ppp)
REVERT: F   59 THR cc_start: 0.9375 (p) cc_final: 0.8473 (p)
REVERT: F   64 HIS cc_start: 0.8753 (m170) cc_final: 0.8326 (m90)
REVERT: F   66 ILE cc_start: 0.9623 (mt) cc_final: 0.9306 (mt)
REVERT: F   70 PHE cc_start: 0.8546 (m-80) cc_final: 0.7986 (m-80)
REVERT: F   86 ASP cc_start: 0.8411 (t0) cc_final: 0.7796 (t0)
REVERT: F   90 ASP cc_start: 0.9049 (m-30) cc_final: 0.8800 (m-30)
REVERT: F  133 MET cc_start: 0.7879 (ptt) cc_final: 0.7604 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1287
  time to fit residues: 32.7515
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  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 14 optimal weight:    0.0270
   chunk 85 optimal weight:    7.9990
   chunk 58 optimal weight:    0.0570
   chunk 34 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 118 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0050
   chunk 45 optimal weight:    3.9990
   chunk 123 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   chunk 101 optimal weight:    2.9990
   overall best weight:    0.2570

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.089457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.063714 restraints weight = 51186.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.061956 restraints weight = 31277.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.061890 restraints weight = 31753.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.061985 restraints weight = 27673.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.062414 restraints weight = 22940.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.5995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  10845  Z= 0.108
  Angle     :  0.629   9.399  14730  Z= 0.335
  Chirality :  0.045   0.231   1650
  Planarity :  0.004   0.038   1917
  Dihedral  :  4.225  34.390   1569
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  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 : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.23), residues: 1323
  helix:  1.63 (0.25), residues: 405
  sheet:  0.05 (0.34), residues: 234
  loop : -1.33 (0.22), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 127 
 TYR   0.009   0.001   TYR E 308 
 PHE   0.059   0.002   PHE F  63 
 TRP   0.022   0.001   TRP C 153 
 HIS   0.006   0.001   HIS F 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (10824)
  covalent geometry    : angle       0.62861 (14685)
  SS BOND              : bond        0.00420 (   18)
  SS BOND              : angle       0.90054 (   36)
  hydrogen bonds       : bond        0.03343 (  483)
  hydrogen bonds       : angle       4.39719 ( 1359)
  link_NAG-ASN         : bond        0.00196 (    3)
  link_NAG-ASN         : angle       0.66746 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2281.82 seconds
wall clock time: 40 minutes 8.36 seconds (2408.36 seconds total)