Starting phenix.real_space_refine
on Wed Mar  4 22:45:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w53_32313/03_2026/7w53_32313.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w53_32313/03_2026/7w53_32313.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w53_32313/03_2026/7w53_32313.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w53_32313/03_2026/7w53_32313.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w53_32313/03_2026/7w53_32313.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w53_32313/03_2026/7w53_32313.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    5521      2.51       5
     N    1524      2.21       5
     O    1603      1.98       5
     H    8644      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17354
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 3443
          Classifications: {'peptide': 210}
          Link IDs: {'PTRANS': 6, 'TRANS': 203}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 5109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 5109
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 136
          Classifications: {'peptide': 8}
          Link IDs: {'PTRANS': 1, 'TRANS': 6}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 3504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 3504
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "G"
      Number of atoms: 885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 885
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 4277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 4277
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 9, 'TRANS': 254}
          Chain breaks: 3
  Time building chain proxies: 2.96, per 1000 atoms: 0.17
  Number of scatterers: 17354
  At special positions: 0
  Unit cell: (117.72, 133.92, 102.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      62     16.00
     O    1603      8.00
     N    1524      7.00
     C    5521      6.00
     H    8644      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 134 " - pdb=" SG  CYS R 219 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.49
  Conformation dependent library (CDL) restraints added in 566.0 milliseconds
  

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2068

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 14 sheets defined
      38.7% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 33
      removed outlier: 3.968A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 218
      removed outlier: 3.952A  pdb=" N   ASN A 216 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   ASP A 217 " --> pdb=" O   CYS A 214 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   VAL A 218 " --> pdb=" O   PHE A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 245
    Processing helix  chain 'A' and resid 248 through 252
      removed outlier: 4.232A  pdb=" N   THR A 251 " --> pdb=" O   TRP A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 270
    Processing helix  chain 'A' and resid 298 through 319
      removed outlier: 3.572A  pdb=" N   ILE A 315 " --> pdb=" O   GLU A 311 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   SER A 319 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 358
    Processing helix  chain 'B' and resid 9 through 31
    Processing helix  chain 'B' and resid 34 through 40
    Processing helix  chain 'E' and resid 27 through 31
    Processing helix  chain 'E' and resid 52 through 55
      removed outlier: 4.089A  pdb=" N   GLY E  55 " --> pdb=" O   SER E  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 52 through 55'
    Processing helix  chain 'E' and resid 73 through 75
      No H-bonds generated for 'chain 'E' and resid 73 through 75'
    Processing helix  chain 'E' and resid 86 through 90
    Processing helix  chain 'E' and resid 220 through 224
      removed outlier: 3.682A  pdb=" N   VAL E 224 " --> pdb=" O   ALA E 221 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 60 through 86
    Processing helix  chain 'R' and resid 87 through 90
    Processing helix  chain 'R' and resid 95 through 112
      removed outlier: 4.117A  pdb=" N   LEU R  99 " --> pdb=" O   THR R  95 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 113 through 120
    Processing helix  chain 'R' and resid 131 through 165
    Processing helix  chain 'R' and resid 165 through 173
    Processing helix  chain 'R' and resid 174 through 198
      removed outlier: 4.104A  pdb=" N   ARG R 180 " --> pdb=" O   ALA R 176 " (cutoff:3.500A)
      Proline residue:  R 195  - end of helix
    Processing helix  chain 'R' and resid 227 through 263
      removed outlier: 3.641A  pdb=" N   VAL R 231 " --> pdb=" O   LEU R 227 " (cutoff:3.500A)
      Proline residue:  R 243  - end of helix
    Processing helix  chain 'R' and resid 290 through 323
      Proline residue:  R 312  - end of helix
      removed outlier: 3.704A  pdb=" N   ARG R 317 " --> pdb=" O   PHE R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 327 through 357
      Proline residue:  R 353  - end of helix
    Processing helix  chain 'R' and resid 360 through 365
      removed outlier: 4.162A  pdb=" N   GLU R 365 " --> pdb=" O   SER R 361 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.236A  pdb=" N   LEU A  34 " --> pdb=" O   HIS A 197 " (cutoff:3.500A)
      removed outlier: 7.515A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.724A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56
      removed outlier: 6.519A  pdb=" N   ILE B 343 " --> pdb=" O   ARG B  53 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   THR B  55 " --> pdb=" O   LEU B 341 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   LEU B 341 " --> pdb=" O   THR B  55 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   CYS B 322 " --> pdb=" O   GLY B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68
      removed outlier: 3.512A  pdb=" N   ALA B  65 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ASP B  88 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   LYS B  94 " --> pdb=" O   ASP B  88 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 6.312A  pdb=" N   CYS B 126 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   GLU B 143 " --> pdb=" O   CYS B 126 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ILE B 128 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 158
      removed outlier: 3.524A  pdb=" N   CYS B 153 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   GLN B 161 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE B 162 " --> pdb=" O   TRP B 174 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   ASP B 175 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   GLN B 181 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197
      removed outlier: 6.506A  pdb=" N   GLY B 207 " --> pdb=" O   MET B 193 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   LEU B 195 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   VAL B 205 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   LEU B 197 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLN B 225 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   ASP B 217 " --> pdb=" O   CYS B 223 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   CYS B 223 " --> pdb=" O   ASP B 217 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239
      removed outlier: 6.767A  pdb=" N   CYS B 255 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   THR B 268 " --> pdb=" O   CYS B 255 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LEU B 257 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLN B 264 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283
      removed outlier: 3.701A  pdb=" N   SER B 280 " --> pdb=" O   GLY B 293 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6
    Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11
      removed outlier: 5.875A  pdb=" N   GLY E   9 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   MET E  33 " --> pdb=" O   TYR E  49 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   TYR E  49 " --> pdb=" O   MET E  33 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   TRP E  35 " --> pdb=" O   VAL E  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11
      removed outlier: 5.875A  pdb=" N   GLY E   9 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   PHE E 109 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.281A  pdb=" N   VAL E 147 " --> pdb=" O   GLU E 246 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 200 through 202

    453 hydrogen bonds defined for protein.
    1266 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: 4.03

  Time building geometry restraints manager: 2.12 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 8613
        1.02 -     1.22: 45
        1.22 -     1.42: 3769
        1.42 -     1.63: 5010
        1.63 -     1.83: 93
  Bond restraints: 17530
  Sorted by residual:
  bond pdb=" SG  CYS R 219 "
       pdb=" HG  CYS R 219 "
    ideal  model  delta    sigma   weight residual
    1.200  1.344 -0.144 2.00e-02 2.50e+03 5.20e+01
  bond pdb=" SG  CYS R 134 "
       pdb=" HG  CYS R 134 "
    ideal  model  delta    sigma   weight residual
    1.200  1.343 -0.143 2.00e-02 2.50e+03 5.13e+01
  bond pdb=" SG  CYS R 241 "
       pdb=" HG  CYS R 241 "
    ideal  model  delta    sigma   weight residual
    1.200  1.340 -0.140 2.00e-02 2.50e+03 4.89e+01
  bond pdb=" SG  CYS B 299 "
       pdb=" HG  CYS B 299 "
    ideal  model  delta    sigma   weight residual
    1.200  1.338 -0.138 2.00e-02 2.50e+03 4.75e+01
  bond pdb=" ND2 ASN A 216 "
       pdb="HD22 ASN A 216 "
    ideal  model  delta    sigma   weight residual
    0.860  0.980 -0.120 2.00e-02 2.50e+03 3.63e+01
  ... (remaining 17525 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.24: 31493
        6.24 -    12.48: 15
       12.48 -    18.72: 2
       18.72 -    24.96: 0
       24.96 -    31.21: 2
  Bond angle restraints: 31512
  Sorted by residual:
  angle pdb=" N   PRO E 236 "
        pdb=" CA  PRO E 236 "
        pdb=" C   PRO E 236 "
      ideal   model   delta    sigma   weight residual
     112.36   81.15   31.21 2.06e+00 2.36e-01 2.29e+02
  angle pdb=" N   TYR E 235 "
        pdb=" CA  TYR E 235 "
        pdb=" C   TYR E 235 "
      ideal   model   delta    sigma   weight residual
     108.66  135.51  -26.85 2.16e+00 2.14e-01 1.55e+02
  angle pdb=" N   ASP B 296 "
        pdb=" CA  ASP B 296 "
        pdb=" C   ASP B 296 "
      ideal   model   delta    sigma   weight residual
     110.50   96.45   14.05 1.41e+00 5.03e-01 9.93e+01
  angle pdb=" N   PHE B 240 "
        pdb=" CA  PHE B 240 "
        pdb=" C   PHE B 240 "
      ideal   model   delta    sigma   weight residual
     110.08  102.09    7.99 1.38e+00 5.25e-01 3.36e+01
  angle pdb=" N   ILE A 184 "
        pdb=" CA  ILE A 184 "
        pdb=" C   ILE A 184 "
      ideal   model   delta    sigma   weight residual
     109.34  121.29  -11.95 2.08e+00 2.31e-01 3.30e+01
  ... (remaining 31507 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 7517
       17.86 -    35.72: 495
       35.72 -    53.58: 180
       53.58 -    71.44: 61
       71.44 -    89.31: 9
  Dihedral angle restraints: 8262
    sinusoidal: 4452
      harmonic: 3810
  Sorted by residual:
  dihedral pdb=" C   TYR E 235 "
           pdb=" N   TYR E 235 "
           pdb=" CA  TYR E 235 "
           pdb=" CB  TYR E 235 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.26   14.66     0      2.50e+00 1.60e-01 3.44e+01
  dihedral pdb=" N   TYR E 235 "
           pdb=" C   TYR E 235 "
           pdb=" CA  TYR E 235 "
           pdb=" CB  TYR E 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.08  -14.28     0      2.50e+00 1.60e-01 3.26e+01
  dihedral pdb=" N   PRO E 236 "
           pdb=" C   PRO E 236 "
           pdb=" CA  PRO E 236 "
           pdb=" CB  PRO E 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10  102.07   13.03     0      2.50e+00 1.60e-01 2.72e+01
  ... (remaining 8259 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.202: 1355
       0.202 -    0.404: 4
       0.404 -    0.605: 0
       0.605 -    0.807: 0
       0.807 -    1.009: 1
  Chirality restraints: 1360
  Sorted by residual:
  chirality pdb=" CA  TYR E 235 "
            pdb=" N   TYR E 235 "
            pdb=" C   TYR E 235 "
            pdb=" CB  TYR E 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.50    1.01 2.00e-01 2.50e+01 2.54e+01
  chirality pdb=" CA  PRO E 236 "
            pdb=" N   PRO E 236 "
            pdb=" C   PRO E 236 "
            pdb=" CB  PRO E 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.95   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  ILE A 184 "
            pdb=" N   ILE A 184 "
            pdb=" C   ILE A 184 "
            pdb=" CB  ILE A 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.21    0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 1357 not shown)

  Planarity restraints: 2589
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 216 "   -0.308 2.00e-02 2.50e+03   3.57e-01 1.91e+03
        pdb=" CG  ASN A 216 "    0.028 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 216 "    0.300 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 216 "   -0.003 2.00e-02 2.50e+03
        pdb="HD21 ASN A 216 "    0.529 2.00e-02 2.50e+03
        pdb="HD22 ASN A 216 "   -0.547 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 259 "   -0.250 2.00e-02 2.50e+03   2.64e-01 1.05e+03
        pdb=" CG  ASN A 259 "    0.003 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 259 "    0.245 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 259 "   -0.005 2.00e-02 2.50e+03
        pdb="HD21 ASN A 259 "    0.388 2.00e-02 2.50e+03
        pdb="HD22 ASN A 259 "   -0.382 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 298 "    0.139 2.00e-02 2.50e+03   1.38e-01 2.86e+02
        pdb=" CG  ASN B 298 "   -0.010 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 298 "   -0.133 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 298 "    0.001 2.00e-02 2.50e+03
        pdb="HD21 ASN B 298 "   -0.195 2.00e-02 2.50e+03
        pdb="HD22 ASN B 298 "    0.198 2.00e-02 2.50e+03
  ... (remaining 2586 not shown)

  Histogram of nonbonded interaction distances:
        1.42 -     2.05: 316
        2.05 -     2.69: 27725
        2.69 -     3.33: 52097
        3.33 -     3.96: 66630
        3.96 -     4.60: 105385
  Nonbonded interactions: 252153
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  63 "
            pdb=" HG  SER B 321 "
     model   vdw
     1.415 2.450
  nonbonded pdb=" OE2 GLU E   5 "
            pdb=" H   CYS E  95 "
     model   vdw
     1.462 2.450
  nonbonded pdb="HH12 ARG A  15 "
            pdb=" O   VAL B  95 "
     model   vdw
     1.478 2.450
  nonbonded pdb=" OD1 ASN C   9 "
            pdb="HD22 ASN R 196 "
     model   vdw
     1.487 2.450
  nonbonded pdb=" O   ASP B  71 "
            pdb=" H   ARG B  73 "
     model   vdw
     1.510 2.450
  ... (remaining 252148 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             0.490
  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:             0.100
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     16.780
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
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      :  0.007   0.053   8887  Z= 0.334
  Angle     :  0.861  31.205  12031  Z= 0.503
  Chirality :  0.055   1.009   1360
  Planarity :  0.004   0.051   1528
  Dihedral  : 12.622  89.306   3210
  Min Nonbonded Distance : 1.769

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  6.33 %
    Favored  : 93.04 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.24), residues: 1082
  helix:  0.03 (0.24), residues: 377
  sheet: -0.54 (0.30), residues: 272
  loop : -0.60 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 292 
 TYR   0.027   0.002   TYR E 235 
 PHE   0.015   0.002   PHE B 240 
 TRP   0.012   0.002   TRP R 310 
 HIS   0.006   0.002   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00687 ( 8886)
  covalent geometry    : angle       0.86023 (12029)
  SS BOND              : bond        0.00812 (    1)
  SS BOND              : angle       1.91119 (    2)
  hydrogen bonds       : bond        0.17727 (  449)
  hydrogen bonds       : angle       7.29365 ( 1266)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Evaluate side-chains
  232 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 226
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7150 (mt0)
REVERT: A  319 SER cc_start: 0.5546 (t) cc_final: 0.5313 (m)
REVERT: B  228 THR cc_start: 0.7805 (p) cc_final: 0.7433 (t)
REVERT: B  306 LYS cc_start: 0.8223 (mmmm) cc_final: 0.7985 (mmmt)
REVERT: R  158 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6784 (mm-30)
REVERT: R  293 ARG cc_start: 0.6913 (ptt-90) cc_final: 0.6388 (ptm160)
  outliers start: 6
  outliers final: 3
  residues processed: 230
  average time/residue: 0.3467
  time to fit residues: 98.6539
Evaluate side-chains
  174 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 171
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain R residue  240 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    9.9990
   chunk 106 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 216 ASN
B 300 ASN
** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 331 HIS
R 335 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.156167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.120442 restraints weight = 34160.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.20
r_work: 0.3343 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8887  Z= 0.182
  Angle     :  0.605   7.999  12031  Z= 0.328
  Chirality :  0.041   0.152   1360
  Planarity :  0.005   0.099   1528
  Dihedral  :  6.260  56.848   1216
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 10.76 %
    Favored  : 87.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.24), residues: 1082
  helix:  1.03 (0.25), residues: 385
  sheet: -0.64 (0.31), residues: 258
  loop : -0.70 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 202 
 TYR   0.019   0.002   TYR E 235 
 PHE   0.012   0.001   PHE R 334 
 TRP   0.016   0.001   TRP B  87 
 HIS   0.006   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 8886)
  covalent geometry    : angle       0.60499 (12029)
  SS BOND              : bond        0.00753 (    1)
  SS BOND              : angle       1.53502 (    2)
  hydrogen bonds       : bond        0.05030 (  449)
  hydrogen bonds       : angle       5.39827 ( 1266)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Evaluate side-chains
  199 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 186
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7363 (mt0)
REVERT: E  160 ARG cc_start: 0.7799 (tpp80) cc_final: 0.7544 (mmm-85)
REVERT: G   11 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7241 (tt0)
REVERT: G   22 GLU cc_start: 0.6865 (tp30) cc_final: 0.6562 (tp30)
REVERT: R  158 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7395 (mm-30)
REVERT: R  223 ARG cc_start: 0.7820 (mmt-90) cc_final: 0.7132 (mmm160)
REVERT: R  293 ARG cc_start: 0.6889 (ptt-90) cc_final: 0.6209 (ptm160)
  outliers start: 13
  outliers final: 10
  residues processed: 193
  average time/residue: 0.3040
  time to fit residues: 75.0110
Evaluate side-chains
  176 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 166
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  231 GLU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain E residue    2 GLN
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain R residue   64 CYS
Chi-restraints excluded: chain R residue  240 PHE
Chi-restraints excluded: chain R residue  304 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 96 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   chunk 94 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 100 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B 115 ASN
** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 335 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.157044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.121572 restraints weight = 34134.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.19
r_work: 0.3364 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8887  Z= 0.147
  Angle     :  0.555   7.570  12031  Z= 0.297
  Chirality :  0.040   0.139   1360
  Planarity :  0.004   0.069   1528
  Dihedral  :  5.779  58.327   1216
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.92 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.25), residues: 1082
  helix:  1.63 (0.26), residues: 386
  sheet: -0.67 (0.31), residues: 258
  loop : -0.56 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 218 
 TYR   0.020   0.002   TYR R 135 
 PHE   0.010   0.001   PHE R 334 
 TRP   0.016   0.001   TRP B  87 
 HIS   0.006   0.001   HIS R 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8886)
  covalent geometry    : angle       0.55476 (12029)
  SS BOND              : bond        0.00842 (    1)
  SS BOND              : angle       1.48645 (    2)
  hydrogen bonds       : bond        0.04335 (  449)
  hydrogen bonds       : angle       4.97972 ( 1266)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Evaluate side-chains
  190 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 178
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7388 (mt0)
REVERT: A  319 SER cc_start: 0.5874 (t) cc_final: 0.5530 (m)
REVERT: B   21 ASN cc_start: 0.7458 (m-40) cc_final: 0.6824 (m-40)
REVERT: B  263 ASP cc_start: 0.7847 (t0) cc_final: 0.7542 (t0)
REVERT: E   41 GLU cc_start: 0.7407 (tp30) cc_final: 0.7109 (tp30)
REVERT: E  160 ARG cc_start: 0.7749 (tpp80) cc_final: 0.7546 (mmm-85)
REVERT: G   11 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7159 (tt0)
REVERT: R   61 MET cc_start: 0.5560 (tpt) cc_final: 0.5105 (tpp)
REVERT: R   64 CYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6692 (p)
REVERT: R  158 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7326 (mm-30)
REVERT: R  223 ARG cc_start: 0.7747 (mmt-90) cc_final: 0.7123 (mmm160)
REVERT: R  228 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.6239 (m-80)
REVERT: R  293 ARG cc_start: 0.6792 (ptt-90) cc_final: 0.6086 (ptm160)
  outliers start: 12
  outliers final: 7
  residues processed: 184
  average time/residue: 0.3022
  time to fit residues: 71.4956
Evaluate side-chains
  172 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain E residue    2 GLN
Chi-restraints excluded: chain R residue   64 CYS
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  228 TYR
Chi-restraints excluded: chain R residue  240 PHE
Chi-restraints excluded: chain R residue  304 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 99 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 97 optimal weight:    9.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 331 HIS
R 335 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.157294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.121988 restraints weight = 33891.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.19
r_work: 0.3374 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8887  Z= 0.135
  Angle     :  0.526   7.169  12031  Z= 0.281
  Chirality :  0.040   0.134   1360
  Planarity :  0.004   0.060   1528
  Dihedral  :  5.556  59.567   1215
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 12.24 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.25), residues: 1082
  helix:  1.93 (0.26), residues: 385
  sheet: -0.69 (0.31), residues: 257
  loop : -0.58 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 202 
 TYR   0.024   0.001   TYR R 135 
 PHE   0.010   0.001   PHE B 204 
 TRP   0.014   0.001   TRP B  87 
 HIS   0.009   0.001   HIS R 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8886)
  covalent geometry    : angle       0.52548 (12029)
  SS BOND              : bond        0.00544 (    1)
  SS BOND              : angle       1.46208 (    2)
  hydrogen bonds       : bond        0.04002 (  449)
  hydrogen bonds       : angle       4.79085 ( 1266)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Evaluate side-chains
  182 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 171
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7452 (mt0)
REVERT: B   21 ASN cc_start: 0.7387 (m-40) cc_final: 0.6852 (m-40)
REVERT: B   24 ARG cc_start: 0.7698 (ttp80) cc_final: 0.7373 (ttp80)
REVERT: B  202 ARG cc_start: 0.7485 (mtp-110) cc_final: 0.7092 (mtm110)
REVERT: B  239 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.8637 (t80)
REVERT: B  263 ASP cc_start: 0.7972 (t0) cc_final: 0.7459 (t0)
REVERT: E   41 GLU cc_start: 0.7360 (tp30) cc_final: 0.7043 (tp30)
REVERT: E   54 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8441 (p)
REVERT: E  160 ARG cc_start: 0.7815 (tpp80) cc_final: 0.7595 (mmm-85)
REVERT: R   61 MET cc_start: 0.5519 (tpt) cc_final: 0.5003 (tpp)
REVERT: R   64 CYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6702 (p)
REVERT: R  223 ARG cc_start: 0.7746 (mmt-90) cc_final: 0.7148 (mmm160)
REVERT: R  228 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.6223 (m-80)
REVERT: R  240 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.6545 (t80)
REVERT: R  293 ARG cc_start: 0.6485 (ptt-90) cc_final: 0.5765 (ptm160)
  outliers start: 11
  outliers final: 5
  residues processed: 178
  average time/residue: 0.3059
  time to fit residues: 69.6212
Evaluate side-chains
  170 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 160
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain E residue   54 SER
Chi-restraints excluded: chain R residue   64 CYS
Chi-restraints excluded: chain R residue  228 TYR
Chi-restraints excluded: chain R residue  240 PHE
Chi-restraints excluded: chain R residue  304 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 80 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 12 optimal weight:    0.2980
   chunk 75 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   chunk 84 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 331 HIS
R 335 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.157356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.122141 restraints weight = 33808.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.17
r_work: 0.3372 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8887  Z= 0.138
  Angle     :  0.522   6.860  12031  Z= 0.279
  Chirality :  0.040   0.135   1360
  Planarity :  0.004   0.052   1528
  Dihedral  :  5.452  59.501   1215
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 12.45 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.25), residues: 1082
  helix:  2.15 (0.26), residues: 379
  sheet: -0.68 (0.31), residues: 267
  loop : -0.47 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 134 
 TYR   0.025   0.001   TYR R 135 
 PHE   0.010   0.001   PHE B 204 
 TRP   0.013   0.001   TRP B  87 
 HIS   0.008   0.001   HIS R 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8886)
  covalent geometry    : angle       0.52169 (12029)
  SS BOND              : bond        0.00536 (    1)
  SS BOND              : angle       1.53604 (    2)
  hydrogen bonds       : bond        0.03925 (  449)
  hydrogen bonds       : angle       4.70363 ( 1266)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Evaluate side-chains
  187 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 174
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7457 (mt0)
REVERT: A  261 GLN cc_start: 0.5610 (pt0) cc_final: 0.5356 (pt0)
REVERT: B  202 ARG cc_start: 0.7487 (mtp-110) cc_final: 0.7076 (mtm110)
REVERT: B  239 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8704 (t80)
REVERT: B  263 ASP cc_start: 0.7942 (t0) cc_final: 0.7695 (t0)
REVERT: E   41 GLU cc_start: 0.7455 (tp30) cc_final: 0.7071 (tp30)
REVERT: E   54 SER cc_start: 0.8802 (OUTLIER) cc_final: 0.8430 (p)
REVERT: E  171 ASN cc_start: 0.8339 (p0) cc_final: 0.8096 (p0)
REVERT: G   11 GLN cc_start: 0.7480 (tm-30) cc_final: 0.6830 (tt0)
REVERT: R   61 MET cc_start: 0.5502 (tpt) cc_final: 0.4994 (tpp)
REVERT: R   64 CYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6693 (p)
REVERT: R  223 ARG cc_start: 0.7748 (mmt-90) cc_final: 0.7050 (mmm160)
REVERT: R  240 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.6455 (t80)
REVERT: R  293 ARG cc_start: 0.6460 (ptt-90) cc_final: 0.5729 (ptm160)
  outliers start: 13
  outliers final: 7
  residues processed: 183
  average time/residue: 0.2993
  time to fit residues: 70.2202
Evaluate side-chains
  176 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 165
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain E residue   54 SER
Chi-restraints excluded: chain R residue   64 CYS
Chi-restraints excluded: chain R residue  156 SER
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  240 PHE
Chi-restraints excluded: chain R residue  304 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 88 optimal weight:   20.0000
   chunk 68 optimal weight:   10.0000
   chunk 55 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0270
   chunk 37 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    2.6046

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 331 HIS
R 335 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.154769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.119177 restraints weight = 34093.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.18
r_work: 0.3323 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.3393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8887  Z= 0.188
  Angle     :  0.552   7.220  12031  Z= 0.298
  Chirality :  0.040   0.135   1360
  Planarity :  0.004   0.051   1528
  Dihedral  :  5.584  57.892   1215
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.76 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.25), residues: 1082
  helix:  2.07 (0.26), residues: 379
  sheet: -0.78 (0.31), residues: 262
  loop : -0.60 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 134 
 TYR   0.023   0.002   TYR R 135 
 PHE   0.014   0.002   PHE B 204 
 TRP   0.012   0.001   TRP B  87 
 HIS   0.008   0.001   HIS R 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 8886)
  covalent geometry    : angle       0.55206 (12029)
  SS BOND              : bond        0.00590 (    1)
  SS BOND              : angle       1.57523 (    2)
  hydrogen bonds       : bond        0.04107 (  449)
  hydrogen bonds       : angle       4.80901 ( 1266)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Evaluate side-chains
  173 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8861 (mttt) cc_final: 0.8191 (mmtt)
REVERT: A   24 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7567 (mt0)
REVERT: B  128 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8389 (mp)
REVERT: B  202 ARG cc_start: 0.7469 (mtp-110) cc_final: 0.7060 (mtm110)
REVERT: B  239 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.8911 (t80)
REVERT: B  263 ASP cc_start: 0.7966 (t0) cc_final: 0.7641 (t0)
REVERT: B  298 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7960 (p0)
REVERT: E   41 GLU cc_start: 0.7455 (tp30) cc_final: 0.7054 (tp30)
REVERT: E   54 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8560 (p)
REVERT: G   11 GLN cc_start: 0.7425 (tm-30) cc_final: 0.6932 (tt0)
REVERT: R  223 ARG cc_start: 0.7755 (mmt-90) cc_final: 0.7044 (mmm160)
REVERT: R  240 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.6494 (t80)
REVERT: R  293 ARG cc_start: 0.6694 (ptt-90) cc_final: 0.5878 (ptm160)
REVERT: R  325 GLN cc_start: 0.7527 (pp30) cc_final: 0.7155 (pp30)
  outliers start: 17
  outliers final: 9
  residues processed: 168
  average time/residue: 0.3116
  time to fit residues: 66.5854
Evaluate side-chains
  169 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 155
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  298 ASN
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain E residue   54 SER
Chi-restraints excluded: chain R residue   64 CYS
Chi-restraints excluded: chain R residue  156 SER
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  240 PHE
Chi-restraints excluded: chain R residue  304 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0270
   chunk 7 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 105 optimal weight:    7.9990
   chunk 66 optimal weight:    7.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    1.9644

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 331 HIS
R 335 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.155971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.120437 restraints weight = 34193.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.19
r_work: 0.3347 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8887  Z= 0.151
  Angle     :  0.529   6.703  12031  Z= 0.283
  Chirality :  0.039   0.132   1360
  Planarity :  0.004   0.058   1528
  Dihedral  :  5.402  56.331   1215
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.92 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.26), residues: 1082
  helix:  2.24 (0.26), residues: 379
  sheet: -0.84 (0.31), residues: 269
  loop : -0.56 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG E 218 
 TYR   0.023   0.001   TYR R 135 
 PHE   0.010   0.001   PHE A 189 
 TRP   0.013   0.001   TRP B  87 
 HIS   0.007   0.001   HIS R 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8886)
  covalent geometry    : angle       0.52914 (12029)
  SS BOND              : bond        0.00480 (    1)
  SS BOND              : angle       1.57157 (    2)
  hydrogen bonds       : bond        0.03894 (  449)
  hydrogen bonds       : angle       4.69881 ( 1266)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Evaluate side-chains
  181 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 169
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8787 (mttt) cc_final: 0.8102 (mmtt)
REVERT: A   24 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7490 (mt0)
REVERT: B  202 ARG cc_start: 0.7619 (mtp-110) cc_final: 0.7220 (mtm110)
REVERT: B  239 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8847 (t80)
REVERT: B  263 ASP cc_start: 0.7989 (t0) cc_final: 0.7714 (t0)
REVERT: E   41 GLU cc_start: 0.7513 (tp30) cc_final: 0.7064 (tp30)
REVERT: E   54 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8582 (p)
REVERT: E  171 ASN cc_start: 0.8377 (p0) cc_final: 0.8144 (p0)
REVERT: G   11 GLN cc_start: 0.7439 (tm-30) cc_final: 0.6983 (tt0)
REVERT: R  223 ARG cc_start: 0.7754 (mmt-90) cc_final: 0.7033 (mmm160)
REVERT: R  240 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.6500 (t80)
REVERT: R  293 ARG cc_start: 0.6736 (ptt-90) cc_final: 0.5954 (ptm160)
REVERT: R  294 GLN cc_start: 0.7411 (tm-30) cc_final: 0.7150 (tm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 178
  average time/residue: 0.2886
  time to fit residues: 65.8037
Evaluate side-chains
  177 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 167
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain E residue   54 SER
Chi-restraints excluded: chain R residue  156 SER
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  240 PHE
Chi-restraints excluded: chain R residue  304 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 17 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 102 optimal weight:    5.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 331 HIS
R 335 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.155978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.120381 restraints weight = 34176.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.22
r_work: 0.3353 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8887  Z= 0.145
  Angle     :  0.522   6.518  12031  Z= 0.279
  Chirality :  0.039   0.131   1360
  Planarity :  0.004   0.061   1528
  Dihedral  :  5.323  55.358   1215
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 13.92 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.26), residues: 1082
  helix:  2.35 (0.26), residues: 379
  sheet: -0.83 (0.31), residues: 269
  loop : -0.54 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG E 218 
 TYR   0.023   0.001   TYR R 135 
 PHE   0.010   0.001   PHE B 204 
 TRP   0.013   0.001   TRP B  87 
 HIS   0.008   0.001   HIS R 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8886)
  covalent geometry    : angle       0.52205 (12029)
  SS BOND              : bond        0.00397 (    1)
  SS BOND              : angle       1.46616 (    2)
  hydrogen bonds       : bond        0.03833 (  449)
  hydrogen bonds       : angle       4.63184 ( 1266)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Evaluate side-chains
  189 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 176
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8807 (mttt) cc_final: 0.8122 (mmtt)
REVERT: A   24 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7453 (mt0)
REVERT: A  300 ARG cc_start: 0.7528 (mtm180) cc_final: 0.7107 (mtm110)
REVERT: B  128 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8366 (mp)
REVERT: B  202 ARG cc_start: 0.7625 (mtp-110) cc_final: 0.7210 (mtm110)
REVERT: B  239 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.8799 (t80)
REVERT: B  263 ASP cc_start: 0.8009 (t0) cc_final: 0.7712 (t0)
REVERT: E   41 GLU cc_start: 0.7503 (tp30) cc_final: 0.7042 (tp30)
REVERT: E   54 SER cc_start: 0.8928 (OUTLIER) cc_final: 0.8580 (p)
REVERT: E  171 ASN cc_start: 0.8345 (p0) cc_final: 0.8128 (p0)
REVERT: E  234 GLU cc_start: 0.7261 (tt0) cc_final: 0.7019 (tt0)
REVERT: G   11 GLN cc_start: 0.7443 (tm-30) cc_final: 0.6890 (tt0)
REVERT: R  135 TYR cc_start: 0.4595 (m-80) cc_final: 0.4376 (m-10)
REVERT: R  223 ARG cc_start: 0.7796 (mmt-90) cc_final: 0.7124 (mmm160)
REVERT: R  240 PHE cc_start: 0.6622 (OUTLIER) cc_final: 0.6268 (t80)
REVERT: R  293 ARG cc_start: 0.6767 (ptt-90) cc_final: 0.5950 (ptm160)
  outliers start: 13
  outliers final: 7
  residues processed: 186
  average time/residue: 0.3083
  time to fit residues: 73.1531
Evaluate side-chains
  179 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 168
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  298 ASN
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain E residue   54 SER
Chi-restraints excluded: chain R residue  156 SER
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  240 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 106 optimal weight:    6.9990
   chunk 98 optimal weight:    4.9990
   chunk 84 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
R 331 HIS
R 335 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.159090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.125165 restraints weight = 34077.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 2.09
r_work: 0.3393 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.3871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8887  Z= 0.116
  Angle     :  0.507   6.021  12031  Z= 0.270
  Chirality :  0.039   0.134   1360
  Planarity :  0.004   0.063   1528
  Dihedral  :  5.120  54.466   1215
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 14.77 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.26), residues: 1082
  helix:  2.51 (0.26), residues: 380
  sheet: -0.71 (0.31), residues: 269
  loop : -0.47 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E 218 
 TYR   0.019   0.001   TYR R 135 
 PHE   0.009   0.001   PHE A 189 
 TRP   0.014   0.001   TRP B  87 
 HIS   0.008   0.001   HIS R 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 8886)
  covalent geometry    : angle       0.50722 (12029)
  SS BOND              : bond        0.00290 (    1)
  SS BOND              : angle       1.40080 (    2)
  hydrogen bonds       : bond        0.03635 (  449)
  hydrogen bonds       : angle       4.46769 ( 1266)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Evaluate side-chains
  186 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 177
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8696 (mttt) cc_final: 0.8048 (mmtt)
REVERT: A   24 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7538 (mt0)
REVERT: A  300 ARG cc_start: 0.7522 (mtm180) cc_final: 0.7073 (mtm110)
REVERT: B  202 ARG cc_start: 0.7654 (mtp-110) cc_final: 0.7263 (mtm110)
REVERT: B  239 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8651 (t80)
REVERT: B  263 ASP cc_start: 0.7925 (t0) cc_final: 0.7683 (t0)
REVERT: E   41 GLU cc_start: 0.7452 (tp30) cc_final: 0.6969 (tp30)
REVERT: E   42 LYS cc_start: 0.8671 (mmmm) cc_final: 0.8180 (mmtm)
REVERT: E  171 ASN cc_start: 0.8293 (p0) cc_final: 0.8089 (p0)
REVERT: G   11 GLN cc_start: 0.7469 (tm-30) cc_final: 0.6753 (tt0)
REVERT: R  143 MET cc_start: 0.6903 (ttt) cc_final: 0.6662 (tpt)
REVERT: R  220 MET cc_start: 0.5950 (ttt) cc_final: 0.5689 (ttp)
REVERT: R  223 ARG cc_start: 0.7674 (mmt-90) cc_final: 0.7107 (mmm160)
REVERT: R  293 ARG cc_start: 0.6814 (ptt-90) cc_final: 0.6009 (ptm160)
REVERT: R  294 GLN cc_start: 0.7226 (tm-30) cc_final: 0.6993 (tm-30)
  outliers start: 9
  outliers final: 6
  residues processed: 184
  average time/residue: 0.3013
  time to fit residues: 70.9560
Evaluate side-chains
  182 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 175
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain R residue  156 SER
Chi-restraints excluded: chain R residue  197 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
R 331 HIS
R 335 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.158163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.123305 restraints weight = 33709.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.17
r_work: 0.3389 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.3945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8887  Z= 0.121
  Angle     :  0.506   6.329  12031  Z= 0.268
  Chirality :  0.039   0.134   1360
  Planarity :  0.004   0.068   1528
  Dihedral  :  4.922  53.555   1213
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 14.66 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.26), residues: 1082
  helix:  2.56 (0.26), residues: 379
  sheet: -0.64 (0.32), residues: 259
  loop : -0.46 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG E 218 
 TYR   0.023   0.001   TYR R 135 
 PHE   0.009   0.001   PHE B 204 
 TRP   0.014   0.001   TRP B  87 
 HIS   0.010   0.001   HIS R 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8886)
  covalent geometry    : angle       0.50550 (12029)
  SS BOND              : bond        0.00333 (    1)
  SS BOND              : angle       1.52075 (    2)
  hydrogen bonds       : bond        0.03612 (  449)
  hydrogen bonds       : angle       4.43819 ( 1266)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Evaluate side-chains
  186 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 176
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8753 (mttt) cc_final: 0.8045 (mmtt)
REVERT: A   24 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7463 (mt0)
REVERT: B   28 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8294 (mtpp)
REVERT: B  128 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8336 (mp)
REVERT: B  202 ARG cc_start: 0.7660 (mtp-110) cc_final: 0.7216 (mtm110)
REVERT: B  239 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8672 (t80)
REVERT: B  263 ASP cc_start: 0.7989 (t0) cc_final: 0.7724 (t0)
REVERT: E   41 GLU cc_start: 0.7452 (tp30) cc_final: 0.6922 (tp30)
REVERT: E   42 LYS cc_start: 0.8637 (mmmm) cc_final: 0.8167 (mmtm)
REVERT: E  171 ASN cc_start: 0.8270 (p0) cc_final: 0.8044 (p0)
REVERT: G   11 GLN cc_start: 0.7497 (tm-30) cc_final: 0.6826 (tt0)
REVERT: R   64 CYS cc_start: 0.7113 (t) cc_final: 0.6659 (p)
REVERT: R  143 MET cc_start: 0.6872 (ttt) cc_final: 0.6630 (tpt)
REVERT: R  220 MET cc_start: 0.5911 (ttt) cc_final: 0.5672 (ttp)
REVERT: R  223 ARG cc_start: 0.7717 (mmt-90) cc_final: 0.7072 (mmm160)
REVERT: R  293 ARG cc_start: 0.6806 (ptt-90) cc_final: 0.5977 (ptm160)
REVERT: R  294 GLN cc_start: 0.7328 (tm-30) cc_final: 0.7108 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 184
  average time/residue: 0.3027
  time to fit residues: 71.4383
Evaluate side-chains
  180 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 172
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain R residue  156 SER
Chi-restraints excluded: chain R residue  197 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 80 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 101 optimal weight:    7.9990
   chunk 17 optimal weight:   10.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 331 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.153757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.118258 restraints weight = 34132.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.17
r_work: 0.3309 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   8887  Z= 0.254
  Angle     :  0.614   8.166  12031  Z= 0.330
  Chirality :  0.042   0.145   1360
  Planarity :  0.005   0.073   1528
  Dihedral  :  5.483  54.385   1213
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 14.56 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.25), residues: 1082
  helix:  2.04 (0.26), residues: 378
  sheet: -0.93 (0.31), residues: 272
  loop : -0.64 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 218 
 TYR   0.024   0.002   TYR E 235 
 PHE   0.017   0.002   PHE R 334 
 TRP   0.012   0.002   TRP R 326 
 HIS   0.010   0.001   HIS R 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 8886)
  covalent geometry    : angle       0.61351 (12029)
  SS BOND              : bond        0.00604 (    1)
  SS BOND              : angle       1.49035 (    2)
  hydrogen bonds       : bond        0.04256 (  449)
  hydrogen bonds       : angle       4.92614 ( 1266)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5466.21 seconds
wall clock time: 93 minutes 23.14 seconds (5603.14 seconds total)