Starting phenix.real_space_refine
on Sat Aug 23 01:06:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xqt_38588/08_2025/8xqt_38588.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xqt_38588/08_2025/8xqt_38588.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xqt_38588/08_2025/8xqt_38588.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xqt_38588/08_2025/8xqt_38588.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xqt_38588/08_2025/8xqt_38588.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xqt_38588/08_2025/8xqt_38588.cif"
  }
  resolution = 2.94
  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=   0.001 sd=   0.021
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      59      5.16       5
     C    5707      2.51       5
     N    1494      2.21       5
     O    1637      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8897
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1813
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    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: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2216
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2216
          Classifications: {'peptide': 274}
          Link IDs: {'PTRANS': 3, 'TRANS': 270}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.74, per 1000 atoms: 0.20
  Number of scatterers: 8897
  At special positions: 0
  Unit cell: (90.48, 119.6, 122.72, 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      59     16.00
     O    1637      8.00
     N    1494      7.00
     C    5707      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " 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: 0.81
  Conformation dependent library (CDL) restraints added in 242.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2106

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 12 sheets defined
      41.1% alpha, 21.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.657A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 3.809A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.859A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 8 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.288A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.846A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 3.615A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 3 through 37
    Processing helix  chain 'R' and resid 42 through 72
    Processing helix  chain 'R' and resid 72 through 77
      removed outlier: 3.561A  pdb=" N   PHE R  76 " --> pdb=" O   PHE R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 78 through 112
    Processing helix  chain 'R' and resid 116 through 125
      removed outlier: 3.731A  pdb=" N   LEU R 120 " --> pdb=" O   ASN R 116 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   TYR R 121 " --> pdb=" O   SER R 117 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 125 through 157
    Processing helix  chain 'R' and resid 173 through 216
      removed outlier: 4.067A  pdb=" N   ILE R 189 " --> pdb=" O   VAL R 185 " (cutoff:3.500A)
      Proline residue:  R 190  - end of helix
    Processing helix  chain 'R' and resid 229 through 252
      removed outlier: 3.534A  pdb=" N   ILE R 234 " --> pdb=" O   VAL R 230 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   LEU R 239 " --> pdb=" O   THR R 235 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   ILE R 249 " --> pdb=" O   LEU R 245 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   SER R 250 " --> pdb=" O   SER R 246 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   TRP R 252 " --> pdb=" O   PHE R 248 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 257 through 284
      removed outlier: 3.831A  pdb=" N   ILE R 263 " --> pdb=" O   GLU R 259 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   TYR R 272 " --> pdb=" O   MET R 268 " (cutoff:3.500A)
      Proline residue:  R 273  - end of helix
      removed outlier: 3.966A  pdb=" N   SER R 277 " --> pdb=" O   PRO R 273 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   CYS R 278 " --> pdb=" O   SER R 274 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 284 through 299
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190
      removed outlier: 3.591A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.422A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.730A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.179A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.192A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.545A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.698A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.252A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.241A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 17 through 23
    Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129
      removed outlier: 3.545A  pdb=" N   VAL S 143 " --> pdb=" O   ILE S 204 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136
      removed outlier: 6.756A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    474 hydrogen bonds defined for protein.
    1362 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: 1.19

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2822
        1.34 -     1.46: 1932
        1.46 -     1.58: 4244
        1.58 -     1.69: 0
        1.69 -     1.81: 87
  Bond restraints: 9085
  Sorted by residual:
  bond pdb=" CB  MET R 212 "
       pdb=" CG  MET R 212 "
    ideal  model  delta    sigma   weight residual
    1.520  1.469  0.051 3.00e-02 1.11e+03 2.84e+00
  bond pdb=" CB  GLU A 245 "
       pdb=" CG  GLU A 245 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.14e+00
  bond pdb=" C   TYR A 287 "
       pdb=" O   TYR A 287 "
    ideal  model  delta    sigma   weight residual
    1.249  1.238  0.011 8.50e-03 1.38e+04 1.75e+00
  bond pdb=" CB  GLN B  44 "
       pdb=" CG  GLN B  44 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 3.00e-02 1.11e+03 1.66e+00
  bond pdb=" C3  CLR R 501 "
       pdb=" O1  CLR R 501 "
    ideal  model  delta    sigma   weight residual
    1.413  1.433 -0.020 2.00e-02 2.50e+03 9.78e-01
  ... (remaining 9080 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.05: 12238
        3.05 -     6.11: 50
        6.11 -     9.16: 10
        9.16 -    12.21: 0
       12.21 -    15.27: 1
  Bond angle restraints: 12299
  Sorted by residual:
  angle pdb=" CB  MET R 212 "
        pdb=" CG  MET R 212 "
        pdb=" SD  MET R 212 "
      ideal   model   delta    sigma   weight residual
     112.70   97.43   15.27 3.00e+00 1.11e-01 2.59e+01
  angle pdb=" N   THR B 196 "
        pdb=" CA  THR B 196 "
        pdb=" CB  THR B 196 "
      ideal   model   delta    sigma   weight residual
     114.17  109.27    4.90 1.14e+00 7.69e-01 1.85e+01
  angle pdb=" CA  GLU A 245 "
        pdb=" CB  GLU A 245 "
        pdb=" CG  GLU A 245 "
      ideal   model   delta    sigma   weight residual
     114.10  121.63   -7.53 2.00e+00 2.50e-01 1.42e+01
  angle pdb=" C   LYS R 211 "
        pdb=" N   MET R 212 "
        pdb=" CA  MET R 212 "
      ideal   model   delta    sigma   weight residual
     122.38  116.07    6.31 1.81e+00 3.05e-01 1.22e+01
  angle pdb=" CA  GLN B  44 "
        pdb=" CB  GLN B  44 "
        pdb=" CG  GLN B  44 "
      ideal   model   delta    sigma   weight residual
     114.10  120.91   -6.81 2.00e+00 2.50e-01 1.16e+01
  ... (remaining 12294 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 4823
       17.73 -    35.47: 484
       35.47 -    53.20: 128
       53.20 -    70.93: 24
       70.93 -    88.66: 6
  Dihedral angle restraints: 5465
    sinusoidal: 2210
      harmonic: 3255
  Sorted by residual:
  dihedral pdb=" CA  GLU S 222 "
           pdb=" C   GLU S 222 "
           pdb=" N   TYR S 223 "
           pdb=" CA  TYR S 223 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.36  -19.64     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  MET R 212 "
           pdb=" C   MET R 212 "
           pdb=" N   GLN R 213 "
           pdb=" CA  GLN R 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.06   18.94     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  PHE S  32 "
           pdb=" C   PHE S  32 "
           pdb=" N   GLY S  33 "
           pdb=" CA  GLY S  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.73   18.27     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 5462 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1036
       0.040 -    0.081: 290
       0.081 -    0.121: 74
       0.121 -    0.161: 6
       0.161 -    0.202: 4
  Chirality restraints: 1410
  Sorted by residual:
  chirality pdb=" C9  CLR R 502 "
            pdb=" C10 CLR R 502 "
            pdb=" C11 CLR R 502 "
            pdb=" C8  CLR R 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.25   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  MET R 212 "
            pdb=" N   MET R 212 "
            pdb=" C   MET R 212 "
            pdb=" CB  MET R 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.66e-01
  chirality pdb=" CA  ASP A 341 "
            pdb=" N   ASP A 341 "
            pdb=" C   ASP A 341 "
            pdb=" CB  ASP A 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.67e-01
  ... (remaining 1407 not shown)

  Planarity restraints: 1525
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR S 223 "    0.036 5.00e-02 4.00e+02   5.39e-02 4.65e+00
        pdb=" N   PRO S 224 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO S 224 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO S 224 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 259 "    0.011 2.00e-02 2.50e+03   1.36e-02 3.24e+00
        pdb=" CG  PHE A 259 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 259 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 259 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 259 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 259 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 259 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR S 223 "    0.019 2.00e-02 2.50e+03   1.18e-02 2.77e+00
        pdb=" CG  TYR S 223 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR S 223 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR S 223 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR S 223 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR S 223 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR S 223 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR S 223 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1522 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 345
        2.71 -     3.26: 9147
        3.26 -     3.81: 15297
        3.81 -     4.35: 18945
        4.35 -     4.90: 31925
  Nonbonded interactions: 75659
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" OG  SER R 250 "
            pdb=" O   SER R 254 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OH  TYR B 289 "
            pdb=" NE1 TRP B 297 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   THR R  86 "
            pdb=" OG1 THR R  90 "
     model   vdw
     2.249 3.040
  ... (remaining 75654 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:             1.090
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.250
  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:7.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
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   0.051   9087  Z= 0.140
  Angle     :  0.595  15.265  12303  Z= 0.311
  Chirality :  0.040   0.202   1410
  Planarity :  0.004   0.054   1525
  Dihedral  : 15.339  88.665   3353
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 24.46 %
    Favored  : 75.33 %
  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 aren not related in a simple way.
  whole:  0.33 (0.25), residues: 1107
  helix:  1.64 (0.25), residues: 417
  sheet: -0.55 (0.33), residues: 253
  loop : -0.62 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 197 
 TYR   0.027   0.001   TYR S 223 
 PHE   0.031   0.002   PHE A 259 
 TRP   0.013   0.001   TRP R  98 
 HIS   0.004   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9085)
  covalent geometry    : angle       0.59495 (12299)
  SS BOND              : bond        0.00130 (    2)
  SS BOND              : angle       0.36009 (    4)
  hydrogen bonds       : bond        0.16409 (  474)
  hydrogen bonds       : angle       6.95143 ( 1362)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 202
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 LYS cc_start: 0.7935 (mttm) cc_final: 0.7700 (mttm)
REVERT: B   10 GLU cc_start: 0.7620 (tp30) cc_final: 0.7246 (tp30)
REVERT: S   38 ARG cc_start: 0.8272 (ptt-90) cc_final: 0.7972 (ptt180)
REVERT: S   69 THR cc_start: 0.8065 (p) cc_final: 0.7819 (t)
REVERT: S  119 VAL cc_start: 0.8430 (t) cc_final: 0.8102 (m)
  outliers start: 2
  outliers final: 2
  residues processed: 204
  average time/residue: 0.4966
  time to fit residues: 108.6313
Evaluate side-chains
  190 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 188
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain S residue   87 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0670
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
** R  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 151 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.150599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.130717 restraints weight = 13294.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.01
r_work: 0.3625 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3470 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.1013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9087  Z= 0.181
  Angle     :  0.573   8.515  12303  Z= 0.303
  Chirality :  0.042   0.219   1410
  Planarity :  0.004   0.058   1525
  Dihedral  :  5.978  56.858   1340
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 19.73 %
    Favored  : 74.92 %
  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 aren not related in a simple way.
  whole:  0.40 (0.25), residues: 1107
  helix:  1.83 (0.25), residues: 413
  sheet: -0.61 (0.30), residues: 265
  loop : -0.63 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 129 
 TYR   0.021   0.002   TYR S 223 
 PHE   0.026   0.002   PHE R  82 
 TRP   0.017   0.002   TRP B 169 
 HIS   0.005   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 9085)
  covalent geometry    : angle       0.57306 (12299)
  SS BOND              : bond        0.00300 (    2)
  SS BOND              : angle       0.74319 (    4)
  hydrogen bonds       : bond        0.04749 (  474)
  hydrogen bonds       : angle       5.31035 ( 1362)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 214
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  245 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7161 (tm-30)
REVERT: A  271 LYS cc_start: 0.7995 (ptpp) cc_final: 0.7763 (ptpp)
REVERT: A  315 ASP cc_start: 0.7411 (p0) cc_final: 0.7125 (p0)
REVERT: B  137 ARG cc_start: 0.7629 (tpp-160) cc_final: 0.7245 (tpp80)
REVERT: B  219 ARG cc_start: 0.8078 (mtt90) cc_final: 0.7820 (mpt90)
REVERT: C   48 ASP cc_start: 0.7652 (t0) cc_final: 0.7449 (t0)
REVERT: S   67 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7889 (mtp180)
REVERT: S  218 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7971 (ttp)
REVERT: R   81 MET cc_start: 0.5553 (OUTLIER) cc_final: 0.5259 (tmm)
  outliers start: 52
  outliers final: 23
  residues processed: 240
  average time/residue: 0.3998
  time to fit residues: 104.0006
Evaluate side-chains
  230 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 204
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  210 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  138 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  218 MET
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  149 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 102 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 6 optimal weight:    0.2980
   chunk 1 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B 110 ASN
B 119 ASN
B 230 ASN
B 239 ASN
S  77 ASN
** R  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.150538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.129821 restraints weight = 13104.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 2.09
r_work: 0.3603 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9087  Z= 0.199
  Angle     :  0.586   7.839  12303  Z= 0.307
  Chirality :  0.042   0.229   1410
  Planarity :  0.004   0.055   1525
  Dihedral  :  5.726  57.278   1334
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 20.66 %
    Favored  : 73.38 %
  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 aren not related in a simple way.
  whole:  0.24 (0.25), residues: 1107
  helix:  1.72 (0.25), residues: 414
  sheet: -0.80 (0.29), residues: 274
  loop : -0.65 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  52 
 TYR   0.022   0.002   TYR S 223 
 PHE   0.024   0.002   PHE R  82 
 TRP   0.015   0.002   TRP B 169 
 HIS   0.005   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 9085)
  covalent geometry    : angle       0.58632 (12299)
  SS BOND              : bond        0.00245 (    2)
  SS BOND              : angle       0.80249 (    4)
  hydrogen bonds       : bond        0.04555 (  474)
  hydrogen bonds       : angle       5.13098 ( 1362)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 217
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  245 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7054 (tm-30)
REVERT: A  271 LYS cc_start: 0.8079 (ptpp) cc_final: 0.7777 (ptpp)
REVERT: A  315 ASP cc_start: 0.7457 (p0) cc_final: 0.7148 (p0)
REVERT: B  133 VAL cc_start: 0.8264 (t) cc_final: 0.8042 (p)
REVERT: B  227 SER cc_start: 0.8818 (m) cc_final: 0.8590 (t)
REVERT: B  234 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8612 (m-80)
REVERT: C   48 ASP cc_start: 0.7713 (t0) cc_final: 0.7490 (t0)
REVERT: S  216 TYR cc_start: 0.8241 (m-80) cc_final: 0.7931 (m-80)
REVERT: R   81 MET cc_start: 0.5466 (OUTLIER) cc_final: 0.5192 (tmm)
  outliers start: 58
  outliers final: 27
  residues processed: 244
  average time/residue: 0.3983
  time to fit residues: 105.2571
Evaluate side-chains
  235 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 206
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  138 THR
Chi-restraints excluded: chain S residue  150 SER
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue  132 VAL
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  149 ASN
Chi-restraints excluded: chain R residue  178 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 89 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0370
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
B 119 ASN
B 230 ASN
B 239 ASN
B 340 ASN
S  77 ASN
** R  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.151784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.131074 restraints weight = 13254.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 2.09
r_work: 0.3615 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3458 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9087  Z= 0.161
  Angle     :  0.557   8.644  12303  Z= 0.292
  Chirality :  0.041   0.214   1410
  Planarity :  0.004   0.057   1525
  Dihedral  :  5.608  57.331   1334
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 21.79 %
    Favored  : 72.87 %
  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 aren not related in a simple way.
  whole:  0.29 (0.25), residues: 1107
  helix:  1.81 (0.25), residues: 414
  sheet: -0.84 (0.29), residues: 275
  loop : -0.62 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  52 
 TYR   0.019   0.001   TYR S 223 
 PHE   0.026   0.002   PHE R  82 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9085)
  covalent geometry    : angle       0.55691 (12299)
  SS BOND              : bond        0.00226 (    2)
  SS BOND              : angle       0.65667 (    4)
  hydrogen bonds       : bond        0.04184 (  474)
  hydrogen bonds       : angle       4.99085 ( 1362)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 217
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  188 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.7092 (m-70)
REVERT: A  245 GLU cc_start: 0.7494 (tm-30) cc_final: 0.6991 (tm-30)
REVERT: A  271 LYS cc_start: 0.8083 (ptpp) cc_final: 0.7780 (ptpp)
REVERT: A  315 ASP cc_start: 0.7425 (p0) cc_final: 0.7122 (p0)
REVERT: B  137 ARG cc_start: 0.7578 (tpp-160) cc_final: 0.7349 (tpp-160)
REVERT: B  227 SER cc_start: 0.8805 (m) cc_final: 0.8565 (t)
REVERT: B  234 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8598 (m-80)
REVERT: C   48 ASP cc_start: 0.7721 (t0) cc_final: 0.7484 (t0)
REVERT: S  216 TYR cc_start: 0.8236 (m-80) cc_final: 0.7957 (m-80)
REVERT: R   81 MET cc_start: 0.5471 (OUTLIER) cc_final: 0.5155 (tmm)
REVERT: R  126 VAL cc_start: 0.5001 (OUTLIER) cc_final: 0.4783 (t)
  outliers start: 52
  outliers final: 24
  residues processed: 242
  average time/residue: 0.3911
  time to fit residues: 102.6294
Evaluate side-chains
  234 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 206
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  188 HIS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  138 THR
Chi-restraints excluded: chain S residue  150 SER
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue  126 VAL
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  149 ASN
Chi-restraints excluded: chain R residue  178 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0020
   chunk 108 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 94 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0060
   overall best weight:    0.5604

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
S  77 ASN
** R  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.151242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.130975 restraints weight = 13430.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.03
r_work: 0.3627 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9087  Z= 0.154
  Angle     :  0.552   8.676  12303  Z= 0.288
  Chirality :  0.041   0.200   1410
  Planarity :  0.004   0.057   1525
  Dihedral  :  5.478  56.525   1334
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 21.79 %
    Favored  : 72.87 %
  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 aren not related in a simple way.
  whole:  0.34 (0.25), residues: 1107
  helix:  1.89 (0.25), residues: 415
  sheet: -0.85 (0.30), residues: 275
  loop : -0.62 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  52 
 TYR   0.021   0.001   TYR S 223 
 PHE   0.031   0.002   PHE R  72 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 9085)
  covalent geometry    : angle       0.55174 (12299)
  SS BOND              : bond        0.00243 (    2)
  SS BOND              : angle       0.60374 (    4)
  hydrogen bonds       : bond        0.04069 (  474)
  hydrogen bonds       : angle       4.86437 ( 1362)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 218
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A  188 HIS cc_start: 0.7336 (OUTLIER) cc_final: 0.7059 (m-70)
REVERT: A  245 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7074 (tm-30)
REVERT: A  271 LYS cc_start: 0.8122 (ptpp) cc_final: 0.7821 (ptpp)
REVERT: A  315 ASP cc_start: 0.7442 (p0) cc_final: 0.7058 (p0)
REVERT: B  137 ARG cc_start: 0.7493 (tpp-160) cc_final: 0.7164 (tpp-160)
REVERT: B  234 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8632 (m-80)
REVERT: C   48 ASP cc_start: 0.7623 (t0) cc_final: 0.7405 (t0)
REVERT: S  216 TYR cc_start: 0.8244 (m-80) cc_final: 0.7925 (m-80)
REVERT: R    6 LYS cc_start: 0.7524 (mmmm) cc_final: 0.7042 (mmmt)
REVERT: R   81 MET cc_start: 0.5642 (OUTLIER) cc_final: 0.5319 (tmm)
REVERT: R  126 VAL cc_start: 0.5010 (OUTLIER) cc_final: 0.4781 (t)
REVERT: R  197 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6713 (ttp)
REVERT: R  212 MET cc_start: 0.5682 (mmm) cc_final: 0.4836 (mtt)
  outliers start: 52
  outliers final: 25
  residues processed: 246
  average time/residue: 0.4595
  time to fit residues: 121.9501
Evaluate side-chains
  238 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 208
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  188 HIS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  150 SER
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue  126 VAL
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  149 ASN
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  197 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 4 optimal weight:    8.9990
   chunk 2 optimal weight:    0.8980
   chunk 104 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
S  77 ASN
** R  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.150484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.130202 restraints weight = 13372.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 2.04
r_work: 0.3618 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9087  Z= 0.186
  Angle     :  0.575   9.236  12303  Z= 0.301
  Chirality :  0.042   0.212   1410
  Planarity :  0.004   0.057   1525
  Dihedral  :  5.510  56.431   1334
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 22.10 %
    Favored  : 72.15 %
  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 aren not related in a simple way.
  whole:  0.25 (0.25), residues: 1107
  helix:  1.80 (0.24), residues: 415
  sheet: -0.85 (0.30), residues: 275
  loop : -0.69 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG S 168 
 TYR   0.022   0.002   TYR S 223 
 PHE   0.033   0.002   PHE R  72 
 TRP   0.013   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 9085)
  covalent geometry    : angle       0.57486 (12299)
  SS BOND              : bond        0.00255 (    2)
  SS BOND              : angle       0.55967 (    4)
  hydrogen bonds       : bond        0.04150 (  474)
  hydrogen bonds       : angle       4.86668 ( 1362)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 213
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  188 HIS cc_start: 0.7346 (OUTLIER) cc_final: 0.7060 (m-70)
REVERT: A  245 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7039 (tm-30)
REVERT: A  271 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7829 (ptpp)
REVERT: A  315 ASP cc_start: 0.7420 (p0) cc_final: 0.7035 (p0)
REVERT: B  137 ARG cc_start: 0.7499 (tpp-160) cc_final: 0.7197 (tpp-160)
REVERT: B  234 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8582 (m-80)
REVERT: C   48 ASP cc_start: 0.7666 (t0) cc_final: 0.7443 (t0)
REVERT: S   69 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7876 (t)
REVERT: S  216 TYR cc_start: 0.8292 (m-80) cc_final: 0.7920 (m-80)
REVERT: R    6 LYS cc_start: 0.7492 (mmmm) cc_final: 0.7043 (mmmt)
REVERT: R   81 MET cc_start: 0.5623 (OUTLIER) cc_final: 0.5294 (tmm)
  outliers start: 56
  outliers final: 33
  residues processed: 238
  average time/residue: 0.4370
  time to fit residues: 112.5107
Evaluate side-chains
  254 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 216
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  188 HIS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue   93 MET
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  150 SER
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  149 ASN
Chi-restraints excluded: chain R residue  178 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0670
   chunk 43 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
S  77 ASN
** R  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.150685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.130286 restraints weight = 13539.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 2.05
r_work: 0.3619 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3467 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9087  Z= 0.177
  Angle     :  0.586  12.101  12303  Z= 0.305
  Chirality :  0.042   0.208   1410
  Planarity :  0.004   0.057   1525
  Dihedral  :  5.526  56.817   1334
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 23.54 %
    Favored  : 71.84 %
  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 aren not related in a simple way.
  whole:  0.22 (0.25), residues: 1107
  helix:  1.78 (0.24), residues: 415
  sheet: -0.87 (0.30), residues: 275
  loop : -0.71 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 283 
 TYR   0.021   0.002   TYR S 223 
 PHE   0.031   0.002   PHE R  72 
 TRP   0.015   0.002   TRP S 164 
 HIS   0.004   0.001   HIS R 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 9085)
  covalent geometry    : angle       0.58631 (12299)
  SS BOND              : bond        0.00228 (    2)
  SS BOND              : angle       0.48977 (    4)
  hydrogen bonds       : bond        0.04092 (  474)
  hydrogen bonds       : angle       4.87042 ( 1362)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 216
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6777 (mp0)
REVERT: A  188 HIS cc_start: 0.7362 (OUTLIER) cc_final: 0.7025 (m-70)
REVERT: A  245 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7080 (tm-30)
REVERT: A  271 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7818 (ptpp)
REVERT: A  315 ASP cc_start: 0.7427 (p0) cc_final: 0.7046 (p0)
REVERT: A  341 ASP cc_start: 0.7531 (m-30) cc_final: 0.7205 (m-30)
REVERT: B   52 ARG cc_start: 0.8134 (ptp90) cc_final: 0.7878 (ptp-170)
REVERT: B  137 ARG cc_start: 0.7483 (tpp-160) cc_final: 0.7204 (tpp-160)
REVERT: B  234 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8593 (m-80)
REVERT: B  289 TYR cc_start: 0.8449 (m-80) cc_final: 0.7894 (m-80)
REVERT: C   48 ASP cc_start: 0.7672 (t0) cc_final: 0.7450 (t0)
REVERT: S   69 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7878 (t)
REVERT: S  216 TYR cc_start: 0.8314 (m-80) cc_final: 0.7995 (m-80)
REVERT: R    6 LYS cc_start: 0.7571 (mmmm) cc_final: 0.7103 (mmmt)
REVERT: R   81 MET cc_start: 0.5652 (OUTLIER) cc_final: 0.5328 (tmm)
  outliers start: 45
  outliers final: 29
  residues processed: 236
  average time/residue: 0.4719
  time to fit residues: 120.2700
Evaluate side-chains
  248 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 214
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  188 HIS
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue   93 MET
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  149 ASN
Chi-restraints excluded: chain R residue  178 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 92 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   chunk 68 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
S  77 ASN
** R  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.150915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.130465 restraints weight = 13377.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.05
r_work: 0.3622 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3471 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9087  Z= 0.172
  Angle     :  0.577  10.054  12303  Z= 0.302
  Chirality :  0.041   0.195   1410
  Planarity :  0.004   0.059   1525
  Dihedral  :  5.512  56.503   1334
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 23.84 %
    Favored  : 71.63 %
  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 aren not related in a simple way.
  whole:  0.22 (0.25), residues: 1107
  helix:  1.76 (0.24), residues: 415
  sheet: -0.81 (0.30), residues: 272
  loop : -0.74 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 134 
 TYR   0.023   0.002   TYR S 223 
 PHE   0.032   0.002   PHE R  72 
 TRP   0.018   0.002   TRP S 164 
 HIS   0.004   0.001   HIS R 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 9085)
  covalent geometry    : angle       0.57697 (12299)
  SS BOND              : bond        0.00237 (    2)
  SS BOND              : angle       0.47290 (    4)
  hydrogen bonds       : bond        0.04081 (  474)
  hydrogen bonds       : angle       4.85563 ( 1362)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 215
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  188 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.7059 (m-70)
REVERT: A  245 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7108 (tm-30)
REVERT: A  271 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7824 (ptpp)
REVERT: A  315 ASP cc_start: 0.7433 (p0) cc_final: 0.7045 (p0)
REVERT: A  341 ASP cc_start: 0.7504 (m-30) cc_final: 0.7215 (m-30)
REVERT: B   48 ARG cc_start: 0.7996 (mmt-90) cc_final: 0.7771 (mmt-90)
REVERT: B   52 ARG cc_start: 0.8138 (ptp90) cc_final: 0.7890 (ptp-170)
REVERT: B  137 ARG cc_start: 0.7462 (tpp-160) cc_final: 0.7191 (tpp-160)
REVERT: B  234 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8573 (m-80)
REVERT: B  289 TYR cc_start: 0.8437 (m-80) cc_final: 0.7909 (m-80)
REVERT: C   48 ASP cc_start: 0.7656 (t0) cc_final: 0.7433 (t0)
REVERT: S   69 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7870 (t)
REVERT: S  145 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7994 (mt)
REVERT: S  216 TYR cc_start: 0.8321 (m-80) cc_final: 0.7893 (m-80)
REVERT: R    6 LYS cc_start: 0.7563 (mmmm) cc_final: 0.7101 (mmmt)
REVERT: R   81 MET cc_start: 0.5662 (OUTLIER) cc_final: 0.5339 (tmm)
  outliers start: 44
  outliers final: 27
  residues processed: 237
  average time/residue: 0.4649
  time to fit residues: 119.4326
Evaluate side-chains
  246 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 213
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  188 HIS
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue   93 MET
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  145 ILE
Chi-restraints excluded: chain S residue  150 SER
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  149 ASN
Chi-restraints excluded: chain R residue  178 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 29 optimal weight:    0.1980
   chunk 45 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
S  77 ASN
** R  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.151022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.130726 restraints weight = 13417.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.04
r_work: 0.3623 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3471 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9087  Z= 0.170
  Angle     :  0.588  10.353  12303  Z= 0.307
  Chirality :  0.042   0.189   1410
  Planarity :  0.004   0.061   1525
  Dihedral  :  5.496  56.718   1334
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 24.36 %
    Favored  : 71.12 %
  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 aren not related in a simple way.
  whole:  0.24 (0.25), residues: 1107
  helix:  1.80 (0.24), residues: 412
  sheet: -0.87 (0.30), residues: 274
  loop : -0.68 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 134 
 TYR   0.024   0.002   TYR S 223 
 PHE   0.032   0.002   PHE R  72 
 TRP   0.020   0.002   TRP S 164 
 HIS   0.005   0.001   HIS R 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 9085)
  covalent geometry    : angle       0.58802 (12299)
  SS BOND              : bond        0.00235 (    2)
  SS BOND              : angle       0.49565 (    4)
  hydrogen bonds       : bond        0.04087 (  474)
  hydrogen bonds       : angle       4.87775 ( 1362)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 216
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6764 (mp0)
REVERT: A  188 HIS cc_start: 0.7349 (OUTLIER) cc_final: 0.6967 (m-70)
REVERT: A  245 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7101 (tm-30)
REVERT: A  271 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7818 (ptpp)
REVERT: A  315 ASP cc_start: 0.7416 (p0) cc_final: 0.7034 (p0)
REVERT: A  341 ASP cc_start: 0.7510 (m-30) cc_final: 0.7197 (m-30)
REVERT: B   48 ARG cc_start: 0.8020 (mmt-90) cc_final: 0.7792 (mmt-90)
REVERT: B   52 ARG cc_start: 0.8131 (ptp90) cc_final: 0.7838 (ptp-170)
REVERT: B   61 MET cc_start: 0.8102 (tmm) cc_final: 0.7886 (ppp)
REVERT: B   78 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7581 (mttp)
REVERT: B  111 TYR cc_start: 0.8645 (m-80) cc_final: 0.8416 (m-80)
REVERT: B  137 ARG cc_start: 0.7445 (tpp-160) cc_final: 0.7189 (tpp-160)
REVERT: B  234 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8561 (m-80)
REVERT: B  289 TYR cc_start: 0.8446 (m-80) cc_final: 0.7949 (m-80)
REVERT: C   48 ASP cc_start: 0.7674 (t0) cc_final: 0.7446 (t0)
REVERT: S   69 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7833 (t)
REVERT: S  145 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7993 (mt)
REVERT: S  216 TYR cc_start: 0.8326 (m-80) cc_final: 0.7914 (m-80)
REVERT: R   81 MET cc_start: 0.5665 (OUTLIER) cc_final: 0.5350 (tmm)
  outliers start: 44
  outliers final: 27
  residues processed: 239
  average time/residue: 0.4909
  time to fit residues: 126.5251
Evaluate side-chains
  248 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 214
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  188 HIS
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  145 ILE
Chi-restraints excluded: chain S residue  150 SER
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  149 ASN
Chi-restraints excluded: chain R residue  178 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0770
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 98 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
B 230 ASN
S  77 ASN
** R  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.151139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.130696 restraints weight = 13411.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.05
r_work: 0.3623 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3471 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
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      :  0.004   0.049   9087  Z= 0.170
  Angle     :  0.599  10.429  12303  Z= 0.312
  Chirality :  0.041   0.170   1410
  Planarity :  0.004   0.063   1525
  Dihedral  :  5.492  55.934   1334
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 25.59 %
    Favored  : 70.71 %
  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 aren not related in a simple way.
  whole:  0.20 (0.25), residues: 1107
  helix:  1.73 (0.24), residues: 415
  sheet: -0.85 (0.30), residues: 274
  loop : -0.71 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 134 
 TYR   0.026   0.002   TYR S 223 
 PHE   0.033   0.002   PHE R  72 
 TRP   0.023   0.002   TRP S 164 
 HIS   0.004   0.001   HIS R 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 9085)
  covalent geometry    : angle       0.59873 (12299)
  SS BOND              : bond        0.00258 (    2)
  SS BOND              : angle       0.49802 (    4)
  hydrogen bonds       : bond        0.04069 (  474)
  hydrogen bonds       : angle       4.84248 ( 1362)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 203
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6760 (mp0)
REVERT: A  188 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.7025 (m-70)
REVERT: A  245 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7104 (tm-30)
REVERT: A  271 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7824 (ptpp)
REVERT: A  315 ASP cc_start: 0.7430 (p0) cc_final: 0.7053 (p0)
REVERT: A  341 ASP cc_start: 0.7541 (m-30) cc_final: 0.7227 (m-30)
REVERT: B   48 ARG cc_start: 0.8000 (mmt-90) cc_final: 0.7779 (mmt-90)
REVERT: B   52 ARG cc_start: 0.8112 (ptp90) cc_final: 0.7831 (ptp-170)
REVERT: B   61 MET cc_start: 0.8114 (tmm) cc_final: 0.7901 (ppp)
REVERT: B   78 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7578 (mttp)
REVERT: B  111 TYR cc_start: 0.8638 (m-80) cc_final: 0.8424 (m-80)
REVERT: B  137 ARG cc_start: 0.7443 (tpp-160) cc_final: 0.7191 (tpp-160)
REVERT: B  234 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8579 (m-80)
REVERT: B  289 TYR cc_start: 0.8419 (m-80) cc_final: 0.7876 (m-80)
REVERT: C   48 ASP cc_start: 0.7677 (t0) cc_final: 0.7451 (t0)
REVERT: S   69 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7818 (t)
REVERT: S  145 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7948 (mt)
REVERT: S  216 TYR cc_start: 0.8329 (m-80) cc_final: 0.7932 (m-80)
REVERT: R   81 MET cc_start: 0.5687 (OUTLIER) cc_final: 0.5378 (tmm)
REVERT: R  268 MET cc_start: 0.7000 (mmm) cc_final: 0.6658 (mmm)
  outliers start: 36
  outliers final: 26
  residues processed: 219
  average time/residue: 0.5255
  time to fit residues: 123.7868
Evaluate side-chains
  237 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 204
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  188 HIS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  145 ILE
Chi-restraints excluded: chain S residue  150 SER
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  149 ASN
Chi-restraints excluded: chain R residue  178 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    0.3980
   chunk 76 optimal weight:    0.9980
   chunk 92 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   chunk 94 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
B 230 ASN
S  77 ASN
** R  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.151279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.130820 restraints weight = 13301.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 2.04
r_work: 0.3627 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3474 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9087  Z= 0.168
  Angle     :  0.602  10.524  12303  Z= 0.312
  Chirality :  0.041   0.176   1410
  Planarity :  0.004   0.063   1525
  Dihedral  :  5.443  55.070   1334
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 25.59 %
    Favored  : 70.50 %
  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 aren not related in a simple way.
  whole:  0.17 (0.25), residues: 1107
  helix:  1.71 (0.24), residues: 415
  sheet: -0.88 (0.30), residues: 274
  loop : -0.72 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 134 
 TYR   0.024   0.002   TYR S 223 
 PHE   0.033   0.002   PHE R  72 
 TRP   0.026   0.002   TRP S 164 
 HIS   0.005   0.001   HIS R 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 9085)
  covalent geometry    : angle       0.60245 (12299)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       0.50321 (    4)
  hydrogen bonds       : bond        0.04058 (  474)
  hydrogen bonds       : angle       4.81430 ( 1362)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3570.77 seconds
wall clock time: 61 minutes 45.58 seconds (3705.58 seconds total)