Starting phenix.real_space_refine
on Sun Apr  5 05:39:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m3s_63607/04_2026/9m3s_63607.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m3s_63607/04_2026/9m3s_63607.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m3s_63607/04_2026/9m3s_63607.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m3s_63607/04_2026/9m3s_63607.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m3s_63607/04_2026/9m3s_63607.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m3s_63607/04_2026/9m3s_63607.cif"
  }
  resolution = 2.83
  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=   0.002 sd=   0.031
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      57      5.16       5
     C    5370      2.51       5
     N    1453      2.21       5
     O    1571      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8451
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "A"
      Number of atoms: 1919
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1919
          Classifications: {'peptide': 234}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "R"
      Number of atoms: 2521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2521
          Classifications: {'peptide': 315}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 302}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'HSM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.52, per 1000 atoms: 0.18
  Number of scatterers: 8451
  At special positions: 0
  Unit cell: (79.872, 99.84, 138.112, 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      57     16.00
     O    1571      8.00
     N    1453      7.00
     C    5370      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  14 " - pdb=" SG  CYS R  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  22 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 190 " 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
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 340.2 milliseconds
  

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2018

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      43.3% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 23
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.599A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.692A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 13 through 36
    Processing helix  chain 'A' and resid 37 through 40
      removed outlier: 3.915A  pdb=" N   THR A  40 " --> pdb=" O   ALA A  37 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 37 through 40'
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.811A  pdb=" N   LYS A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 101
      removed outlier: 3.774A  pdb=" N   ASN A 101 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 145 through 156
      removed outlier: 3.508A  pdb=" N   GLY A 156 " --> pdb=" O   LYS A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.067A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 170
      removed outlier: 3.524A  pdb=" N   ALA A 168 " --> pdb=" O   PRO A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 205
      removed outlier: 3.909A  pdb=" N   ILE A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY A 205 " --> pdb=" O   SER A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'R' and resid 28 through 60
      removed outlier: 4.050A  pdb=" N   THR R  33 " --> pdb=" O   VAL R  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 61 through 64
      removed outlier: 3.891A  pdb=" N   GLN R  64 " --> pdb=" O   LYS R  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 61 through 64'
    Processing helix  chain 'R' and resid 65 through 85
    Processing helix  chain 'R' and resid 85 through 95
      removed outlier: 3.944A  pdb=" N   ILE R  91 " --> pdb=" O   PRO R  87 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 101 through 135
      removed outlier: 4.210A  pdb=" N   LEU R 107 " --> pdb=" O   THR R 103 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 144
    Processing helix  chain 'R' and resid 145 through 169
    Processing helix  chain 'R' and resid 171 through 175
    Processing helix  chain 'R' and resid 177 through 185
    Processing helix  chain 'R' and resid 195 through 207
    Processing helix  chain 'R' and resid 207 through 234
    Processing helix  chain 'R' and resid 252 through 279
      removed outlier: 3.632A  pdb=" N   LYS R 256 " --> pdb=" O   ARG R 252 " (cutoff:3.500A)
      Proline residue:  R 271  - end of helix
    Processing helix  chain 'R' and resid 280 through 283
    Processing helix  chain 'R' and resid 287 through 310
      Proline residue:  R 306  - end of helix
    Processing helix  chain 'R' and resid 313 through 325
    Processing helix  chain 'R' and resid 332 through 336
      removed outlier: 3.597A  pdb=" N   ASP R 335 " --> pdb=" O   ASN R 332 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.638A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.661A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.467A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.943A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.290A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.434A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 4.407A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.487A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.819A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 69 through 75
      removed outlier: 4.727A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 8.234A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 5.741A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)

    441 hydrogen bonds defined for protein.
    1278 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: 1.21

  Time building geometry restraints manager: 1.08 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.32: 1519
        1.32 -     1.45: 2290
        1.45 -     1.57: 4744
        1.57 -     1.69: 0
        1.69 -     1.81: 81
  Bond restraints: 8634
  Sorted by residual:
  bond pdb=" N   VAL R  84 "
       pdb=" CA  VAL R  84 "
    ideal  model  delta    sigma   weight residual
    1.459  1.501 -0.042 9.10e-03 1.21e+04 2.13e+01
  bond pdb=" CA  SER B 161 "
       pdb=" CB  SER B 161 "
    ideal  model  delta    sigma   weight residual
    1.534  1.474  0.060 1.60e-02 3.91e+03 1.41e+01
  bond pdb=" CA  SER B 316 "
       pdb=" CB  SER B 316 "
    ideal  model  delta    sigma   weight residual
    1.531  1.478  0.053 1.56e-02 4.11e+03 1.18e+01
  bond pdb=" N   ASP B 247 "
       pdb=" CA  ASP B 247 "
    ideal  model  delta    sigma   weight residual
    1.455  1.492 -0.036 1.25e-02 6.40e+03 8.47e+00
  bond pdb=" N   PRO R 271 "
       pdb=" CA  PRO R 271 "
    ideal  model  delta    sigma   weight residual
    1.472  1.433  0.039 1.34e-02 5.57e+03 8.31e+00
  ... (remaining 8629 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 11376
        1.68 -     3.36: 286
        3.36 -     5.03: 41
        5.03 -     6.71: 4
        6.71 -     8.39: 3
  Bond angle restraints: 11710
  Sorted by residual:
  angle pdb=" N   ARG N  67 "
        pdb=" CA  ARG N  67 "
        pdb=" C   ARG N  67 "
      ideal   model   delta    sigma   weight residual
     114.62  107.61    7.01 1.14e+00 7.69e-01 3.78e+01
  angle pdb=" N   GLN A 236 "
        pdb=" CA  GLN A 236 "
        pdb=" C   GLN A 236 "
      ideal   model   delta    sigma   weight residual
     110.97  106.70    4.27 1.09e+00 8.42e-01 1.54e+01
  angle pdb=" C   PHE N 108 "
        pdb=" N   ASP N 109 "
        pdb=" CA  ASP N 109 "
      ideal   model   delta    sigma   weight residual
     122.83  117.00    5.83 1.54e+00 4.22e-01 1.43e+01
  angle pdb=" N   ASN R 301 "
        pdb=" CA  ASN R 301 "
        pdb=" C   ASN R 301 "
      ideal   model   delta    sigma   weight residual
     111.07  107.23    3.84 1.07e+00 8.73e-01 1.29e+01
  angle pdb=" C   ARG N  67 "
        pdb=" CA  ARG N  67 "
        pdb=" CB  ARG N  67 "
      ideal   model   delta    sigma   weight residual
     109.28  113.72   -4.44 1.33e+00 5.65e-01 1.12e+01
  ... (remaining 11705 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 4706
       17.81 -    35.61: 330
       35.61 -    53.42: 72
       53.42 -    71.23: 15
       71.23 -    89.03: 3
  Dihedral angle restraints: 5126
    sinusoidal: 2004
      harmonic: 3122
  Sorted by residual:
  dihedral pdb=" CB  CYS R  22 "
           pdb=" SG  CYS R  22 "
           pdb=" SG  CYS R 186 "
           pdb=" CB  CYS R 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -129.24   43.24     1      1.00e+01 1.00e-02 2.61e+01
  dihedral pdb=" CD  ARG B  52 "
           pdb=" NE  ARG B  52 "
           pdb=" CZ  ARG B  52 "
           pdb=" NH1 ARG B  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -38.22   38.22     1      1.00e+01 1.00e-02 2.06e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   59.33   33.67     1      1.00e+01 1.00e-02 1.61e+01
  ... (remaining 5123 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1122
       0.059 -    0.119: 180
       0.119 -    0.178: 18
       0.178 -    0.237: 2
       0.237 -    0.297: 1
  Chirality restraints: 1323
  Sorted by residual:
  chirality pdb=" CA  ILE B  81 "
            pdb=" N   ILE B  81 "
            pdb=" C   ILE B  81 "
            pdb=" CB  ILE B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.73   -0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CA  ARG N  98 "
            pdb=" N   ARG N  98 "
            pdb=" C   ARG N  98 "
            pdb=" CB  ARG N  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CB  ILE R 282 "
            pdb=" CA  ILE R 282 "
            pdb=" CG1 ILE R 282 "
            pdb=" CG2 ILE R 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.20 2.00e-01 2.50e+01 9.84e-01
  ... (remaining 1320 not shown)

  Planarity restraints: 1490
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  52 "   -0.665 9.50e-02 1.11e+02   2.98e-01 5.41e+01
        pdb=" NE  ARG B  52 "    0.041 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  52 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  52 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  52 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG N  98 "   -0.424 9.50e-02 1.11e+02   1.90e-01 2.21e+01
        pdb=" NE  ARG N  98 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ  ARG N  98 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG N  98 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG N  98 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG N  72 "   -0.314 9.50e-02 1.11e+02   1.41e-01 1.22e+01
        pdb=" NE  ARG N  72 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG N  72 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG N  72 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG N  72 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1487 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 2018
        2.79 -     3.32: 8080
        3.32 -     3.85: 14497
        3.85 -     4.37: 17191
        4.37 -     4.90: 29795
  Nonbonded interactions: 71581
  Sorted by model distance:
  nonbonded pdb=" OG1 THR R  46 "
            pdb=" OG1 THR R 303 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OG1 THR B  34 "
            pdb=" O   LEU B 300 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.354 3.040
  ... (remaining 71576 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.720
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8639  Z= 0.228
  Angle     :  0.597   8.390  11720  Z= 0.375
  Chirality :  0.044   0.297   1323
  Planarity :  0.011   0.298   1490
  Dihedral  : 13.134  89.031   3093
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.03 (0.27), residues: 1057
  helix:  2.07 (0.27), residues: 399
  sheet:  0.06 (0.36), residues: 217
  loop : -0.21 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 251 
 TYR   0.025   0.001   TYR R  36 
 PHE   0.011   0.001   PHE R  15 
 TRP   0.013   0.002   TRP B 169 
 HIS   0.010   0.001   HIS R 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8634)
  covalent geometry    : angle       0.59731 (11710)
  SS BOND              : bond        0.00096 (    5)
  SS BOND              : angle       0.41839 (   10)
  hydrogen bonds       : bond        0.16726 (  441)
  hydrogen bonds       : angle       6.72687 ( 1278)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 LYS cc_start: 0.7876 (tttm) cc_final: 0.7649 (tttm)
REVERT: A  145 LYS cc_start: 0.8208 (mttm) cc_final: 0.8002 (mttp)
REVERT: A  147 ASP cc_start: 0.7562 (p0) cc_final: 0.7347 (p0)
REVERT: A  195 ASP cc_start: 0.7515 (m-30) cc_final: 0.7250 (m-30)
REVERT: A  230 ASP cc_start: 0.7460 (m-30) cc_final: 0.7133 (m-30)
REVERT: R  282 ILE cc_start: 0.8277 (mm) cc_final: 0.8023 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.5165
  time to fit residues: 123.2176
Evaluate side-chains
  198 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0770
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
C  18 GLN
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.124092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.109883 restraints weight = 11652.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.86
r_work: 0.3344 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8639  Z= 0.155
  Angle     :  0.510   5.424  11720  Z= 0.278
  Chirality :  0.043   0.144   1323
  Planarity :  0.004   0.045   1490
  Dihedral  :  4.262  39.279   1171
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  9.55 %
    Favored  : 89.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.21 (0.27), residues: 1057
  helix:  2.33 (0.26), residues: 408
  sheet: -0.00 (0.33), residues: 231
  loop : -0.20 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 251 
 TYR   0.022   0.001   TYR R  36 
 PHE   0.013   0.002   PHE B 199 
 TRP   0.017   0.002   TRP B 169 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8634)
  covalent geometry    : angle       0.50985 (11710)
  SS BOND              : bond        0.00195 (    5)
  SS BOND              : angle       0.67629 (   10)
  hydrogen bonds       : bond        0.04464 (  441)
  hydrogen bonds       : angle       5.19601 ( 1278)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 216
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: B  134 ARG cc_start: 0.7212 (pmt-80) cc_final: 0.6735 (pmt-80)
REVERT: N   57 SER cc_start: 0.8448 (t) cc_final: 0.8001 (p)
REVERT: A   49 ASP cc_start: 0.8010 (m-30) cc_final: 0.7750 (m-30)
REVERT: A   73 LYS cc_start: 0.8186 (tttm) cc_final: 0.7864 (tttm)
REVERT: A  117 ARG cc_start: 0.8163 (mtp180) cc_final: 0.7867 (mtp-110)
REVERT: A  147 ASP cc_start: 0.8120 (p0) cc_final: 0.7811 (p0)
REVERT: A  170 TYR cc_start: 0.8723 (t80) cc_final: 0.8466 (t80)
REVERT: A  195 ASP cc_start: 0.7920 (m-30) cc_final: 0.7642 (m-30)
REVERT: A  230 ASP cc_start: 0.7803 (m-30) cc_final: 0.7549 (m-30)
REVERT: R  160 ILE cc_start: 0.8244 (mm) cc_final: 0.8036 (mm)
  outliers start: 12
  outliers final: 7
  residues processed: 219
  average time/residue: 0.5143
  time to fit residues: 120.1543
Evaluate side-chains
  209 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 202
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain R residue   91 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 90 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   chunk 95 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.121363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.106782 restraints weight = 11612.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.88
r_work: 0.3310 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8639  Z= 0.217
  Angle     :  0.530   8.120  11720  Z= 0.285
  Chirality :  0.044   0.144   1323
  Planarity :  0.004   0.044   1490
  Dihedral  :  4.560  46.803   1171
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.03 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.21 (0.27), residues: 1057
  helix:  2.28 (0.26), residues: 403
  sheet: -0.05 (0.33), residues: 237
  loop : -0.06 (0.33), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 251 
 TYR   0.023   0.001   TYR R  36 
 PHE   0.018   0.002   PHE R 272 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 8634)
  covalent geometry    : angle       0.52957 (11710)
  SS BOND              : bond        0.00237 (    5)
  SS BOND              : angle       0.60717 (   10)
  hydrogen bonds       : bond        0.04522 (  441)
  hydrogen bonds       : angle       5.20567 ( 1278)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 216
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: B   50 THR cc_start: 0.8104 (m) cc_final: 0.7900 (t)
REVERT: B  101 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8216 (mtp)
REVERT: B  134 ARG cc_start: 0.7302 (pmt-80) cc_final: 0.6818 (pmt-80)
REVERT: B  303 ASP cc_start: 0.7733 (m-30) cc_final: 0.7389 (m-30)
REVERT: N   57 SER cc_start: 0.8421 (t) cc_final: 0.7956 (p)
REVERT: A   26 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7333 (m-30)
REVERT: A   49 ASP cc_start: 0.8055 (m-30) cc_final: 0.7779 (m-30)
REVERT: A   73 LYS cc_start: 0.8141 (tttm) cc_final: 0.7797 (tttm)
REVERT: A  145 LYS cc_start: 0.8394 (mttp) cc_final: 0.8067 (mttt)
REVERT: A  147 ASP cc_start: 0.8135 (p0) cc_final: 0.7790 (p0)
REVERT: A  170 TYR cc_start: 0.8711 (t80) cc_final: 0.8478 (t80)
REVERT: A  195 ASP cc_start: 0.8009 (m-30) cc_final: 0.7747 (m-30)
REVERT: R  160 ILE cc_start: 0.8297 (mm) cc_final: 0.8057 (mp)
  outliers start: 18
  outliers final: 10
  residues processed: 225
  average time/residue: 0.5127
  time to fit residues: 123.1508
Evaluate side-chains
  215 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 203
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  181 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 94 optimal weight:    0.5980
   chunk 78 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0060
   chunk 100 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
A 131 ASN
R  62 GLN
R 301 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.122609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.108112 restraints weight = 11764.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.87
r_work: 0.3328 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8639  Z= 0.138
  Angle     :  0.483   6.120  11720  Z= 0.262
  Chirality :  0.042   0.139   1323
  Planarity :  0.004   0.045   1490
  Dihedral  :  4.321  38.468   1171
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.66 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.32 (0.27), residues: 1057
  helix:  2.46 (0.26), residues: 403
  sheet:  0.03 (0.32), residues: 235
  loop : -0.11 (0.33), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 251 
 TYR   0.018   0.001   TYR R  36 
 PHE   0.015   0.001   PHE R 272 
 TRP   0.015   0.002   TRP A  96 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8634)
  covalent geometry    : angle       0.48270 (11710)
  SS BOND              : bond        0.00153 (    5)
  SS BOND              : angle       0.56763 (   10)
  hydrogen bonds       : bond        0.04013 (  441)
  hydrogen bonds       : angle       5.01633 ( 1278)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 220
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: B  101 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8152 (mtp)
REVERT: B  134 ARG cc_start: 0.7303 (pmt-80) cc_final: 0.7072 (pmt-80)
REVERT: B  212 ASP cc_start: 0.8020 (t0) cc_final: 0.7801 (t0)
REVERT: N   34 MET cc_start: 0.8431 (mmm) cc_final: 0.8099 (mmm)
REVERT: N   57 SER cc_start: 0.8440 (t) cc_final: 0.7996 (p)
REVERT: A   26 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7309 (m-30)
REVERT: A   49 ASP cc_start: 0.8012 (m-30) cc_final: 0.7773 (m-30)
REVERT: A   73 LYS cc_start: 0.8089 (tttm) cc_final: 0.7778 (tttm)
REVERT: A  147 ASP cc_start: 0.8093 (p0) cc_final: 0.7792 (p0)
REVERT: A  161 GLU cc_start: 0.7849 (mp0) cc_final: 0.7612 (mp0)
REVERT: A  170 TYR cc_start: 0.8697 (t80) cc_final: 0.8429 (t80)
REVERT: A  195 ASP cc_start: 0.7946 (m-30) cc_final: 0.7676 (m-30)
REVERT: A  199 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7412 (mtm-85)
REVERT: R   50 ASN cc_start: 0.7918 (m-40) cc_final: 0.7617 (m110)
REVERT: R   84 VAL cc_start: 0.8296 (m) cc_final: 0.7957 (p)
REVERT: R   99 TYR cc_start: 0.8024 (m-80) cc_final: 0.7732 (m-80)
REVERT: R  283 ASN cc_start: 0.8213 (t0) cc_final: 0.7876 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 227
  average time/residue: 0.4981
  time to fit residues: 120.9983
Evaluate side-chains
  219 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 205
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  181 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0170
   chunk 55 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 73 optimal weight:    9.9990
   chunk 80 optimal weight:    0.9990
   chunk 101 optimal weight:    0.0980
   chunk 33 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
A 116 ASN
A 131 ASN
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.123366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.108862 restraints weight = 11661.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.87
r_work: 0.3334 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8639  Z= 0.124
  Angle     :  0.466   5.608  11720  Z= 0.254
  Chirality :  0.041   0.139   1323
  Planarity :  0.004   0.044   1490
  Dihedral  :  4.165  34.035   1171
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.85 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.35 (0.27), residues: 1057
  helix:  2.52 (0.26), residues: 403
  sheet:  0.01 (0.33), residues: 230
  loop : -0.11 (0.32), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 251 
 TYR   0.016   0.001   TYR R  36 
 PHE   0.013   0.001   PHE R 272 
 TRP   0.013   0.001   TRP A  96 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8634)
  covalent geometry    : angle       0.46560 (11710)
  SS BOND              : bond        0.00136 (    5)
  SS BOND              : angle       0.53447 (   10)
  hydrogen bonds       : bond        0.03839 (  441)
  hydrogen bonds       : angle       4.89052 ( 1278)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 212
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: B  134 ARG cc_start: 0.7336 (pmt-80) cc_final: 0.7064 (pmt-80)
REVERT: B  212 ASP cc_start: 0.8010 (t0) cc_final: 0.7792 (t0)
REVERT: N   57 SER cc_start: 0.8417 (t) cc_final: 0.7982 (p)
REVERT: N   67 ARG cc_start: 0.7765 (ttp80) cc_final: 0.7497 (ttp80)
REVERT: A   26 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7282 (m-30)
REVERT: A   49 ASP cc_start: 0.8038 (m-30) cc_final: 0.7754 (m-30)
REVERT: A   73 LYS cc_start: 0.8069 (tttm) cc_final: 0.7736 (tttm)
REVERT: A  114 ASP cc_start: 0.7824 (t0) cc_final: 0.7587 (t0)
REVERT: A  117 ARG cc_start: 0.8015 (mtp180) cc_final: 0.7710 (mtp-110)
REVERT: A  147 ASP cc_start: 0.8068 (p0) cc_final: 0.7841 (p0)
REVERT: A  161 GLU cc_start: 0.7805 (mp0) cc_final: 0.7592 (mp0)
REVERT: A  195 ASP cc_start: 0.7908 (m-30) cc_final: 0.7660 (m-30)
REVERT: A  199 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7418 (mtm-85)
REVERT: R   50 ASN cc_start: 0.7833 (m-40) cc_final: 0.7513 (m110)
REVERT: R   84 VAL cc_start: 0.8312 (m) cc_final: 0.7964 (p)
REVERT: R  283 ASN cc_start: 0.8226 (t0) cc_final: 0.7905 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 220
  average time/residue: 0.5033
  time to fit residues: 118.0301
Evaluate side-chains
  230 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 217
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  220 ASP
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  181 ILE
Chi-restraints excluded: chain R residue  197 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
N  35 ASN
A 116 ASN
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.121932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.107392 restraints weight = 11542.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.85
r_work: 0.3314 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8639  Z= 0.197
  Angle     :  0.507   5.517  11720  Z= 0.273
  Chirality :  0.043   0.139   1323
  Planarity :  0.004   0.043   1490
  Dihedral  :  4.308  38.738   1171
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.16 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.26 (0.27), residues: 1057
  helix:  2.31 (0.26), residues: 407
  sheet: -0.09 (0.33), residues: 230
  loop : -0.01 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 251 
 TYR   0.020   0.001   TYR R  36 
 PHE   0.015   0.002   PHE B 199 
 TRP   0.023   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 8634)
  covalent geometry    : angle       0.50660 (11710)
  SS BOND              : bond        0.00177 (    5)
  SS BOND              : angle       0.50102 (   10)
  hydrogen bonds       : bond        0.04200 (  441)
  hydrogen bonds       : angle       4.99910 ( 1278)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 220
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: B  134 ARG cc_start: 0.7308 (pmt-80) cc_final: 0.7034 (pmt-80)
REVERT: B  212 ASP cc_start: 0.8020 (t0) cc_final: 0.7796 (t0)
REVERT: B  303 ASP cc_start: 0.7789 (m-30) cc_final: 0.7458 (m-30)
REVERT: A   26 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7321 (m-30)
REVERT: A   49 ASP cc_start: 0.8015 (m-30) cc_final: 0.7745 (m-30)
REVERT: A   73 LYS cc_start: 0.8101 (tttm) cc_final: 0.7772 (tttm)
REVERT: A  111 ASP cc_start: 0.8103 (t0) cc_final: 0.7831 (t70)
REVERT: A  114 ASP cc_start: 0.7832 (t0) cc_final: 0.7429 (t0)
REVERT: A  117 ARG cc_start: 0.8048 (mtp180) cc_final: 0.7815 (mtp180)
REVERT: A  147 ASP cc_start: 0.8069 (p0) cc_final: 0.7746 (p0)
REVERT: A  161 GLU cc_start: 0.7838 (mp0) cc_final: 0.7628 (mp0)
REVERT: A  170 TYR cc_start: 0.8695 (t80) cc_final: 0.8490 (t80)
REVERT: A  196 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7291 (mm-30)
REVERT: A  199 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7220 (mtm-85)
REVERT: R   84 VAL cc_start: 0.8397 (m) cc_final: 0.8050 (p)
REVERT: R   99 TYR cc_start: 0.8025 (m-80) cc_final: 0.7713 (m-80)
REVERT: R  160 ILE cc_start: 0.8284 (mm) cc_final: 0.8057 (mp)
  outliers start: 20
  outliers final: 14
  residues processed: 227
  average time/residue: 0.5002
  time to fit residues: 121.3456
Evaluate side-chains
  235 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 220
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  181 ILE
Chi-restraints excluded: chain R residue  300 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 50 optimal weight:    6.9990
   chunk 68 optimal weight:    0.8980
   chunk 66 optimal weight:    0.1980
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    9.9990
   chunk 97 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
A 116 ASN
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.122039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.107334 restraints weight = 11761.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 1.87
r_work: 0.3316 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8639  Z= 0.175
  Angle     :  0.498   5.624  11720  Z= 0.269
  Chirality :  0.042   0.137   1323
  Planarity :  0.004   0.044   1490
  Dihedral  :  4.310  38.109   1171
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.92 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.27 (0.27), residues: 1057
  helix:  2.26 (0.26), residues: 409
  sheet:  0.07 (0.34), residues: 223
  loop : -0.06 (0.32), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 251 
 TYR   0.019   0.001   TYR R  36 
 PHE   0.014   0.001   PHE R 272 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 8634)
  covalent geometry    : angle       0.49770 (11710)
  SS BOND              : bond        0.00165 (    5)
  SS BOND              : angle       0.50825 (   10)
  hydrogen bonds       : bond        0.04150 (  441)
  hydrogen bonds       : angle       4.98328 ( 1278)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 214
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: B  134 ARG cc_start: 0.7300 (pmt-80) cc_final: 0.6998 (pmt-80)
REVERT: B  212 ASP cc_start: 0.8068 (t0) cc_final: 0.7826 (t0)
REVERT: B  303 ASP cc_start: 0.7793 (m-30) cc_final: 0.7460 (m-30)
REVERT: N   34 MET cc_start: 0.8372 (mmm) cc_final: 0.8147 (mmm)
REVERT: A   26 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7291 (m-30)
REVERT: A   49 ASP cc_start: 0.8028 (m-30) cc_final: 0.7757 (m-30)
REVERT: A   61 ARG cc_start: 0.6362 (mpp-170) cc_final: 0.5906 (mpp-170)
REVERT: A   73 LYS cc_start: 0.8114 (tttm) cc_final: 0.7774 (tttm)
REVERT: A  111 ASP cc_start: 0.8142 (t0) cc_final: 0.7755 (t70)
REVERT: A  114 ASP cc_start: 0.7794 (t0) cc_final: 0.7374 (t70)
REVERT: A  117 ARG cc_start: 0.8038 (mtp180) cc_final: 0.7789 (mtp180)
REVERT: A  145 LYS cc_start: 0.8409 (mttt) cc_final: 0.8121 (mttp)
REVERT: A  147 ASP cc_start: 0.8080 (p0) cc_final: 0.7741 (p0)
REVERT: A  161 GLU cc_start: 0.7829 (mp0) cc_final: 0.7613 (mp0)
REVERT: A  195 ASP cc_start: 0.7915 (m-30) cc_final: 0.7542 (m-30)
REVERT: A  196 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7319 (mm-30)
REVERT: A  199 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7174 (mtm-85)
REVERT: R   84 VAL cc_start: 0.8396 (m) cc_final: 0.8055 (p)
REVERT: R   99 TYR cc_start: 0.8025 (m-80) cc_final: 0.7726 (m-80)
REVERT: R  160 ILE cc_start: 0.8275 (mm) cc_final: 0.8052 (mp)
  outliers start: 20
  outliers final: 16
  residues processed: 221
  average time/residue: 0.5184
  time to fit residues: 122.1543
Evaluate side-chains
  232 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 215
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  181 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 101 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
B 340 ASN
A 101 ASN
A 116 ASN
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.122430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.107802 restraints weight = 11533.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.85
r_work: 0.3323 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8639  Z= 0.157
  Angle     :  0.493   7.284  11720  Z= 0.265
  Chirality :  0.042   0.138   1323
  Planarity :  0.004   0.045   1490
  Dihedral  :  4.266  37.121   1171
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.02 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.30 (0.27), residues: 1057
  helix:  2.29 (0.26), residues: 409
  sheet:  0.10 (0.34), residues: 221
  loop : -0.07 (0.32), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 251 
 TYR   0.017   0.001   TYR R  36 
 PHE   0.013   0.001   PHE R 272 
 TRP   0.018   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8634)
  covalent geometry    : angle       0.49295 (11710)
  SS BOND              : bond        0.00154 (    5)
  SS BOND              : angle       0.49384 (   10)
  hydrogen bonds       : bond        0.04050 (  441)
  hydrogen bonds       : angle       4.95176 ( 1278)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 213
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: B  134 ARG cc_start: 0.7294 (pmt-80) cc_final: 0.6964 (pmt-80)
REVERT: B  212 ASP cc_start: 0.8058 (t0) cc_final: 0.7821 (t0)
REVERT: B  303 ASP cc_start: 0.7803 (m-30) cc_final: 0.7475 (m-30)
REVERT: A   26 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7283 (m-30)
REVERT: A   49 ASP cc_start: 0.8029 (m-30) cc_final: 0.7781 (m-30)
REVERT: A   61 ARG cc_start: 0.6376 (mpp-170) cc_final: 0.5912 (mpp-170)
REVERT: A   73 LYS cc_start: 0.8117 (tttm) cc_final: 0.7777 (tttm)
REVERT: A  111 ASP cc_start: 0.8124 (t0) cc_final: 0.7715 (t70)
REVERT: A  114 ASP cc_start: 0.7790 (t0) cc_final: 0.7403 (t70)
REVERT: A  117 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7654 (mtp-110)
REVERT: A  145 LYS cc_start: 0.8401 (mttt) cc_final: 0.8029 (mttp)
REVERT: A  147 ASP cc_start: 0.8068 (p0) cc_final: 0.7742 (p0)
REVERT: A  195 ASP cc_start: 0.7867 (m-30) cc_final: 0.7560 (m-30)
REVERT: A  199 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7454 (mtm-85)
REVERT: A  223 ASN cc_start: 0.8196 (m110) cc_final: 0.7961 (m-40)
REVERT: R   84 VAL cc_start: 0.8378 (m) cc_final: 0.8036 (p)
REVERT: R   99 TYR cc_start: 0.8024 (m-80) cc_final: 0.7675 (m-80)
REVERT: R  160 ILE cc_start: 0.8268 (mm) cc_final: 0.8038 (mp)
  outliers start: 22
  outliers final: 17
  residues processed: 222
  average time/residue: 0.5045
  time to fit residues: 119.3419
Evaluate side-chains
  234 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 216
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  181 ILE
Chi-restraints excluded: chain R residue  300 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   chunk 69 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0040
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.123129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.108614 restraints weight = 11708.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 1.85
r_work: 0.3343 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8639  Z= 0.122
  Angle     :  0.477   6.253  11720  Z= 0.257
  Chirality :  0.041   0.141   1323
  Planarity :  0.004   0.045   1490
  Dihedral  :  4.111  32.161   1171
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 18.89 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.35 (0.27), residues: 1057
  helix:  2.40 (0.26), residues: 409
  sheet:  0.03 (0.33), residues: 229
  loop : -0.05 (0.33), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 169 
 TYR   0.013   0.001   TYR R  36 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.003   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8634)
  covalent geometry    : angle       0.47709 (11710)
  SS BOND              : bond        0.00123 (    5)
  SS BOND              : angle       0.47813 (   10)
  hydrogen bonds       : bond        0.03802 (  441)
  hydrogen bonds       : angle       4.85297 ( 1278)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 207
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: B  134 ARG cc_start: 0.7293 (pmt-80) cc_final: 0.6977 (pmt-80)
REVERT: B  212 ASP cc_start: 0.8048 (t0) cc_final: 0.7803 (t0)
REVERT: B  303 ASP cc_start: 0.7778 (m-30) cc_final: 0.7448 (m-30)
REVERT: B  314 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7581 (ttt180)
REVERT: N   34 MET cc_start: 0.8344 (mmm) cc_final: 0.8066 (mmm)
REVERT: N   57 SER cc_start: 0.8378 (t) cc_final: 0.7966 (p)
REVERT: A   26 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7316 (m-30)
REVERT: A   49 ASP cc_start: 0.8004 (m-30) cc_final: 0.7776 (m-30)
REVERT: A   73 LYS cc_start: 0.8067 (tttm) cc_final: 0.7716 (tttm)
REVERT: A  117 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7673 (mtp-110)
REVERT: A  147 ASP cc_start: 0.8045 (p0) cc_final: 0.7741 (p0)
REVERT: A  195 ASP cc_start: 0.7806 (m-30) cc_final: 0.7512 (m-30)
REVERT: A  196 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7354 (mm-30)
REVERT: A  199 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7135 (mtm-85)
REVERT: A  223 ASN cc_start: 0.8176 (m110) cc_final: 0.7950 (m-40)
REVERT: R   50 ASN cc_start: 0.7805 (m-40) cc_final: 0.7521 (m110)
REVERT: R   84 VAL cc_start: 0.8336 (m) cc_final: 0.7977 (p)
REVERT: R   99 TYR cc_start: 0.7966 (m-80) cc_final: 0.7601 (m-80)
REVERT: R  148 VAL cc_start: 0.8285 (t) cc_final: 0.8064 (p)
REVERT: R  283 ASN cc_start: 0.8168 (t0) cc_final: 0.7871 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 214
  average time/residue: 0.5305
  time to fit residues: 120.8528
Evaluate side-chains
  214 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 200
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  181 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0980
   chunk 43 optimal weight:    0.8980
   chunk 95 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
B 340 ASN
A 116 ASN
A 131 ASN
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.122564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.108115 restraints weight = 11565.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.83
r_work: 0.3333 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8639  Z= 0.152
  Angle     :  0.494   6.287  11720  Z= 0.267
  Chirality :  0.042   0.138   1323
  Planarity :  0.004   0.044   1490
  Dihedral  :  4.163  33.704   1171
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.44 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.31 (0.27), residues: 1057
  helix:  2.33 (0.26), residues: 409
  sheet:  0.07 (0.33), residues: 221
  loop : -0.06 (0.32), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 251 
 TYR   0.015   0.001   TYR R  36 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 8634)
  covalent geometry    : angle       0.49361 (11710)
  SS BOND              : bond        0.00141 (    5)
  SS BOND              : angle       0.46710 (   10)
  hydrogen bonds       : bond        0.03959 (  441)
  hydrogen bonds       : angle       4.87675 ( 1278)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 204
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 ARG cc_start: 0.7304 (pmt-80) cc_final: 0.6921 (pmt-80)
REVERT: B  212 ASP cc_start: 0.8049 (t0) cc_final: 0.7797 (t0)
REVERT: B  303 ASP cc_start: 0.7779 (m-30) cc_final: 0.7482 (m-30)
REVERT: B  314 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7626 (ttt180)
REVERT: N   34 MET cc_start: 0.8368 (mmm) cc_final: 0.8080 (mmm)
REVERT: A   26 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7283 (m-30)
REVERT: A   49 ASP cc_start: 0.8002 (m-30) cc_final: 0.7783 (m-30)
REVERT: A   73 LYS cc_start: 0.8076 (tttm) cc_final: 0.7731 (tttm)
REVERT: A  117 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7678 (mtp-110)
REVERT: A  145 LYS cc_start: 0.8422 (mttt) cc_final: 0.8163 (mttm)
REVERT: A  147 ASP cc_start: 0.8066 (p0) cc_final: 0.7741 (p0)
REVERT: A  199 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.7368 (mtm-85)
REVERT: A  223 ASN cc_start: 0.8195 (m110) cc_final: 0.7965 (m-40)
REVERT: R   51 SER cc_start: 0.8137 (m) cc_final: 0.7930 (m)
REVERT: R   84 VAL cc_start: 0.8366 (m) cc_final: 0.8021 (p)
REVERT: R   99 TYR cc_start: 0.7996 (m-80) cc_final: 0.7628 (m-80)
REVERT: R  148 VAL cc_start: 0.8308 (t) cc_final: 0.8085 (p)
REVERT: R  160 ILE cc_start: 0.8270 (mm) cc_final: 0.8020 (mm)
  outliers start: 17
  outliers final: 13
  residues processed: 212
  average time/residue: 0.5246
  time to fit residues: 118.5973
Evaluate side-chains
  219 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 204
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  181 ILE
Chi-restraints excluded: chain R residue  300 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0060
   chunk 25 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 93 optimal weight:    0.8980
   chunk 78 optimal weight:    0.5980
   chunk 94 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
A 131 ASN
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.123182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.108741 restraints weight = 11598.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 1.83
r_work: 0.3343 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8639  Z= 0.129
  Angle     :  0.498   7.093  11720  Z= 0.266
  Chirality :  0.042   0.139   1323
  Planarity :  0.004   0.045   1490
  Dihedral  :  4.134  31.998   1171
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.65 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.36 (0.27), residues: 1057
  helix:  2.39 (0.26), residues: 409
  sheet:  0.06 (0.33), residues: 223
  loop : -0.03 (0.33), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 251 
 TYR   0.014   0.001   TYR R  36 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.021   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8634)
  covalent geometry    : angle       0.49811 (11710)
  SS BOND              : bond        0.00127 (    5)
  SS BOND              : angle       0.46363 (   10)
  hydrogen bonds       : bond        0.03841 (  441)
  hydrogen bonds       : angle       4.83825 ( 1278)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3266.66 seconds
wall clock time: 56 minutes 15.58 seconds (3375.58 seconds total)