Starting phenix.real_space_refine
on Tue Mar  3 18:33:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v9l_31824/03_2026/7v9l_31824.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v9l_31824/03_2026/7v9l_31824.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v9l_31824/03_2026/7v9l_31824.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v9l_31824/03_2026/7v9l_31824.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v9l_31824/03_2026/7v9l_31824.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v9l_31824/03_2026/7v9l_31824.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      45      5.16       5
     C    5108      2.51       5
     N    1404      2.21       5
     O    1490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 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: 8047
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1964
          Classifications: {'peptide': 237}
          Link IDs: {'PTRANS': 6, 'TRANS': 230}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2064
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 8, 'TRANS': 248}
          Chain breaks: 2
    Chain: "Y"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 445
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "B"
      Number of atoms: 2613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2613
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 1.94, per 1000 atoms: 0.24
  Number of scatterers: 8047
  At special positions: 0
  Unit cell: (97.185, 96.14, 118.085, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      45     16.00
     O    1490      8.00
     N    1404      7.00
     C    5108      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 138 " - pdb=" SG  CYS R 208 " 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: 0.65
  Conformation dependent library (CDL) restraints added in 276.2 milliseconds
  

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1912

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      42.8% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 39
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 233 through 241
      removed outlier: 4.301A  pdb=" N   ASP A 240 " --> pdb=" O   CYS A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
      removed outlier: 3.864A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.988A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 391
      removed outlier: 4.658A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 63 through 90
    Processing helix  chain 'R' and resid 91 through 94
    Processing helix  chain 'R' and resid 95 through 125
    Processing helix  chain 'R' and resid 134 through 169
      removed outlier: 3.679A  pdb=" N   CYS R 138 " --> pdb=" O   SER R 134 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 201
      removed outlier: 3.566A  pdb=" N   PHE R 178 " --> pdb=" O   SER R 174 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   TRP R 179 " --> pdb=" O   ARG R 175 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TRP R 180 " --> pdb=" O   ARG R 176 " (cutoff:3.500A)
      Proline residue:  R 189  - end of helix
    Processing helix  chain 'R' and resid 214 through 248
      removed outlier: 3.714A  pdb=" N   TRP R 219 " --> pdb=" O   SER R 215 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   ILE R 220 " --> pdb=" O   PRO R 216 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   ILE R 221 " --> pdb=" O   TYR R 217 " (cutoff:3.500A)
      Proline residue:  R 224  - end of helix
    Processing helix  chain 'R' and resid 257 through 275
      removed outlier: 3.677A  pdb=" N   TRP R 261 " --> pdb=" O   GLN R 257 " (cutoff:3.500A)
      Proline residue:  R 272  - end of helix
    Processing helix  chain 'R' and resid 276 through 282
      removed outlier: 3.516A  pdb=" N   ILE R 280 " --> pdb=" O   HIS R 277 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASN R 282 " --> pdb=" O   ILE R 279 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 289 through 298
      Proline residue:  R 295  - end of helix
    Processing helix  chain 'R' and resid 298 through 313
      removed outlier: 3.548A  pdb=" N   PHE R 303 " --> pdb=" O   GLY R 299 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLY R 305 " --> pdb=" O   GLY R 301 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   PHE R 306 " --> pdb=" O   SER R 302 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 327
    Processing helix  chain 'Y' and resid 7 through 24
    Processing helix  chain 'Y' and resid 29 through 45
    Processing helix  chain 'Y' and resid 46 through 48
      No H-bonds generated for 'chain 'Y' and resid 46 through 48'
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.844A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.521A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.436A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.743A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.704A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.575A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.763A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 234
      removed outlier: 6.435A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.314A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1176 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.33

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2634
        1.34 -     1.46: 1884
        1.46 -     1.58: 3640
        1.58 -     1.70: 0
        1.70 -     1.82: 61
  Bond restraints: 8219
  Sorted by residual:
  bond pdb=" CG1 ILE B  43 "
       pdb=" CD1 ILE B  43 "
    ideal  model  delta    sigma   weight residual
    1.513  1.459  0.054 3.90e-02 6.57e+02 1.92e+00
  bond pdb=" C   SER R 134 "
       pdb=" N   THR R 135 "
    ideal  model  delta    sigma   weight residual
    1.335  1.319  0.016 1.38e-02 5.25e+03 1.39e+00
  bond pdb=" CG1 ILE B 273 "
       pdb=" CD1 ILE B 273 "
    ideal  model  delta    sigma   weight residual
    1.513  1.468  0.045 3.90e-02 6.57e+02 1.32e+00
  bond pdb=" CB  MET B  61 "
       pdb=" CG  MET B  61 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" CG  ASP B 163 "
       pdb=" OD1 ASP B 163 "
    ideal  model  delta    sigma   weight residual
    1.249  1.229  0.020 1.90e-02 2.77e+03 1.07e+00
  ... (remaining 8214 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 10809
        1.75 -     3.50: 291
        3.50 -     5.25: 33
        5.25 -     7.01: 2
        7.01 -     8.76: 2
  Bond angle restraints: 11137
  Sorted by residual:
  angle pdb=" CA  TYR R  69 "
        pdb=" CB  TYR R  69 "
        pdb=" CG  TYR R  69 "
      ideal   model   delta    sigma   weight residual
     113.90  120.49   -6.59 1.80e+00 3.09e-01 1.34e+01
  angle pdb=" CB  MET B  61 "
        pdb=" CG  MET B  61 "
        pdb=" SD  MET B  61 "
      ideal   model   delta    sigma   weight residual
     112.70  103.94    8.76 3.00e+00 1.11e-01 8.52e+00
  angle pdb=" C   PHE A 238 "
        pdb=" N   ASN A 239 "
        pdb=" CA  ASN A 239 "
      ideal   model   delta    sigma   weight residual
     120.38  124.51   -4.13 1.46e+00 4.69e-01 8.00e+00
  angle pdb=" CA  TRP A 234 "
        pdb=" CB  TRP A 234 "
        pdb=" CG  TRP A 234 "
      ideal   model   delta    sigma   weight residual
     113.60  118.80   -5.20 1.90e+00 2.77e-01 7.48e+00
  angle pdb=" CA  TRP R 155 "
        pdb=" CB  TRP R 155 "
        pdb=" CG  TRP R 155 "
      ideal   model   delta    sigma   weight residual
     113.60  108.41    5.19 1.90e+00 2.77e-01 7.46e+00
  ... (remaining 11132 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 4487
       17.89 -    35.78: 315
       35.78 -    53.67: 42
       53.67 -    71.55: 9
       71.55 -    89.44: 9
  Dihedral angle restraints: 4862
    sinusoidal: 1907
      harmonic: 2955
  Sorted by residual:
  dihedral pdb=" CA  TYR A 253 "
           pdb=" C   TYR A 253 "
           pdb=" N   ARG A 265 "
           pdb=" CA  ARG A 265 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.04   27.96     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  ASP B 163 "
           pdb=" C   ASP B 163 "
           pdb=" N   THR B 164 "
           pdb=" CA  THR B 164 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.04  -27.96     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  MET B  61 "
           pdb=" C   MET B  61 "
           pdb=" N   HIS B  62 "
           pdb=" CA  HIS B  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.38   27.62     0      5.00e+00 4.00e-02 3.05e+01
  ... (remaining 4859 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 773
       0.039 -    0.078: 342
       0.078 -    0.116: 113
       0.116 -    0.155: 19
       0.155 -    0.194: 5
  Chirality restraints: 1252
  Sorted by residual:
  chirality pdb=" CA  TRP R 155 "
            pdb=" N   TRP R 155 "
            pdb=" C   TRP R 155 "
            pdb=" CB  TRP R 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.41e-01
  chirality pdb=" CA  THR A 284 "
            pdb=" N   THR A 284 "
            pdb=" C   THR A 284 "
            pdb=" CB  THR A 284 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.16 2.00e-01 2.50e+01 6.68e-01
  chirality pdb=" CB  THR A 210 "
            pdb=" CA  THR A 210 "
            pdb=" OG1 THR A 210 "
            pdb=" CG2 THR A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.63e-01
  ... (remaining 1249 not shown)

  Planarity restraints: 1416
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 314 "   -0.125 9.50e-02 1.11e+02   7.28e-02 2.87e+01
        pdb=" NE  ARG B 314 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 314 "   -0.088 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 314 "    0.031 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 314 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 342 "    0.089 9.50e-02 1.11e+02   5.29e-02 1.61e+01
        pdb=" NE  ARG A 342 "   -0.028 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 342 "    0.066 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 342 "   -0.023 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 342 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  49 "   -0.084 9.50e-02 1.11e+02   4.87e-02 1.29e+01
        pdb=" NE  ARG B  49 "    0.025 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  49 "   -0.059 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  49 "    0.021 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  49 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1413 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 137
        2.68 -     3.23: 8196
        3.23 -     3.79: 13368
        3.79 -     4.34: 18670
        4.34 -     4.90: 30293
  Nonbonded interactions: 70664
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 228 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.120 3.120
  nonbonded pdb=" OH  TYR N 117 "
            pdb=" OD1 ASP B 228 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" NH1 ARG B  22 "
            pdb=" O   ASP B 258 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" O   PHE R 269 "
            pdb=" OH  TYR R 312 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.295 3.040
  ... (remaining 70659 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.060
  Find NCS groups from input model:        0.030
  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:6.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6599
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      :  0.004   0.054   8220  Z= 0.194
  Angle     :  0.691   8.757  11139  Z= 0.409
  Chirality :  0.047   0.194   1252
  Planarity :  0.007   0.073   1416
  Dihedral  : 13.080  89.442   2947
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.26), residues: 1003
  helix:  0.49 (0.24), residues: 359
  sheet:  0.03 (0.35), residues: 207
  loop : -0.27 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.090   0.009   ARG B 314 
 TYR   0.034   0.005   TYR R  69 
 PHE   0.026   0.002   PHE R 236 
 TRP   0.036   0.003   TRP R 155 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 8219)
  covalent geometry    : angle       0.69134 (11137)
  SS BOND              : bond        0.00414 (    1)
  SS BOND              : angle       1.00801 (    2)
  hydrogen bonds       : bond        0.13775 (  423)
  hydrogen bonds       : angle       6.25772 ( 1176)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ASP cc_start: 0.6753 (m-30) cc_final: 0.6514 (m-30)
REVERT: A   53 LYS cc_start: 0.7122 (pttm) cc_final: 0.6845 (pttp)
REVERT: A  209 GLU cc_start: 0.6978 (tt0) cc_final: 0.6730 (tt0)
REVERT: A  223 ASP cc_start: 0.7041 (t0) cc_final: 0.6647 (t0)
REVERT: A  228 ARG cc_start: 0.7614 (mtp-110) cc_final: 0.7305 (mtp-110)
REVERT: A  229 ASP cc_start: 0.7191 (t0) cc_final: 0.6814 (t0)
REVERT: A  285 ILE cc_start: 0.8190 (mt) cc_final: 0.7959 (mp)
REVERT: A  356 ARG cc_start: 0.6684 (mmm-85) cc_final: 0.6482 (mmm-85)
REVERT: A  374 ARG cc_start: 0.6872 (mtt180) cc_final: 0.6584 (mtt-85)
REVERT: A  378 ASP cc_start: 0.6555 (p0) cc_final: 0.6235 (p0)
REVERT: A  381 ASP cc_start: 0.7418 (t70) cc_final: 0.7068 (t70)
REVERT: N   19 ARG cc_start: 0.7379 (ttm170) cc_final: 0.7060 (ttt-90)
REVERT: N   31 ASN cc_start: 0.7444 (m110) cc_final: 0.7139 (m110)
REVERT: B   27 ASP cc_start: 0.7135 (t0) cc_final: 0.6805 (m-30)
REVERT: B   46 ARG cc_start: 0.6951 (mtp180) cc_final: 0.6554 (mtp180)
REVERT: B   96 ARG cc_start: 0.6656 (mtm110) cc_final: 0.6182 (mtm110)
REVERT: B  101 MET cc_start: 0.8334 (mtp) cc_final: 0.8115 (mtm)
REVERT: B  179 THR cc_start: 0.7926 (t) cc_final: 0.7576 (m)
REVERT: B  181 THR cc_start: 0.7436 (p) cc_final: 0.6999 (m)
REVERT: B  186 ASP cc_start: 0.6956 (m-30) cc_final: 0.6580 (m-30)
REVERT: B  197 ARG cc_start: 0.6550 (ttt180) cc_final: 0.6323 (ttt180)
REVERT: B  214 ARG cc_start: 0.6737 (mtt180) cc_final: 0.6488 (mtt180)
REVERT: B  230 ASN cc_start: 0.8166 (m-40) cc_final: 0.7614 (m110)
REVERT: B  246 ASP cc_start: 0.7074 (m-30) cc_final: 0.6452 (m-30)
REVERT: B  251 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7774 (mtt180)
REVERT: B  254 ASP cc_start: 0.6176 (t70) cc_final: 0.5827 (t70)
REVERT: B  258 ASP cc_start: 0.6629 (t0) cc_final: 0.6353 (m-30)
REVERT: B  268 ASN cc_start: 0.7541 (m-40) cc_final: 0.7304 (m-40)
REVERT: B  295 ASN cc_start: 0.8461 (m-40) cc_final: 0.8240 (m-40)
REVERT: B  314 ARG cc_start: 0.7673 (ttt180) cc_final: 0.7220 (ttm170)
REVERT: B  322 ASP cc_start: 0.7603 (m-30) cc_final: 0.7337 (m-30)
  outliers start: 0
  outliers final: 1
  residues processed: 202
  average time/residue: 0.6136
  time to fit residues: 130.6842
Evaluate side-chains
  176 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  191 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.2980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
A 271 ASN
B 125 ASN
B 239 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.151438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.132507 restraints weight = 10422.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 1.79
r_work: 0.3630 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8220  Z= 0.192
  Angle     :  0.597   5.926  11139  Z= 0.326
  Chirality :  0.045   0.153   1252
  Planarity :  0.004   0.042   1416
  Dihedral  :  5.425  25.327   1109
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  8.73 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.26), residues: 1003
  helix:  1.77 (0.26), residues: 362
  sheet: -0.06 (0.34), residues: 205
  loop :  0.10 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 347 
 TYR   0.030   0.002   TYR R  69 
 PHE   0.022   0.002   PHE R 306 
 TRP   0.022   0.002   TRP R 155 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 8219)
  covalent geometry    : angle       0.59743 (11137)
  SS BOND              : bond        0.00385 (    1)
  SS BOND              : angle       0.64441 (    2)
  hydrogen bonds       : bond        0.04855 (  423)
  hydrogen bonds       : angle       5.00755 ( 1176)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 190
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.8025 (ttt90) cc_final: 0.7733 (ttt90)
REVERT: A   33 ASP cc_start: 0.7456 (m-30) cc_final: 0.7242 (m-30)
REVERT: A  223 ASP cc_start: 0.7753 (t0) cc_final: 0.7389 (t0)
REVERT: A  229 ASP cc_start: 0.7615 (t0) cc_final: 0.7379 (t0)
REVERT: A  231 ARG cc_start: 0.8279 (ptp-170) cc_final: 0.7987 (mtm180)
REVERT: A  343 ASP cc_start: 0.7243 (m-30) cc_final: 0.6833 (m-30)
REVERT: A  381 ASP cc_start: 0.8059 (t70) cc_final: 0.7850 (t70)
REVERT: N   25 SER cc_start: 0.8296 (t) cc_final: 0.7871 (p)
REVERT: N   31 ASN cc_start: 0.8120 (m110) cc_final: 0.7861 (m110)
REVERT: N  117 TYR cc_start: 0.8539 (m-80) cc_final: 0.8136 (m-80)
REVERT: B  150 ARG cc_start: 0.8622 (mmt180) cc_final: 0.8322 (mmt180)
REVERT: B  179 THR cc_start: 0.8197 (t) cc_final: 0.7919 (m)
REVERT: B  237 ASN cc_start: 0.7358 (t0) cc_final: 0.7132 (t0)
REVERT: B  243 THR cc_start: 0.8172 (p) cc_final: 0.7810 (p)
  outliers start: 17
  outliers final: 9
  residues processed: 193
  average time/residue: 0.6417
  time to fit residues: 130.4304
Evaluate side-chains
  188 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 179
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    0.2980
   chunk 47 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
N  35 ASN
B 155 ASN
B 230 ASN
B 239 ASN
B 268 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.151693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.132588 restraints weight = 10316.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 1.80
r_work: 0.3637 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8220  Z= 0.176
  Angle     :  0.562   5.620  11139  Z= 0.303
  Chirality :  0.043   0.147   1252
  Planarity :  0.004   0.042   1416
  Dihedral  :  5.036  24.633   1107
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 10.91 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.26), residues: 1003
  helix:  2.06 (0.26), residues: 366
  sheet: -0.31 (0.33), residues: 207
  loop :  0.03 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 347 
 TYR   0.027   0.002   TYR R  69 
 PHE   0.018   0.002   PHE A 212 
 TRP   0.019   0.002   TRP B 297 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 8219)
  covalent geometry    : angle       0.56192 (11137)
  SS BOND              : bond        0.00307 (    1)
  SS BOND              : angle       0.45502 (    2)
  hydrogen bonds       : bond        0.04514 (  423)
  hydrogen bonds       : angle       4.79813 ( 1176)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 185
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.8053 (ttt90) cc_final: 0.7767 (ttt90)
REVERT: A  223 ASP cc_start: 0.7667 (t0) cc_final: 0.7415 (t0)
REVERT: A  228 ARG cc_start: 0.8563 (mtp-110) cc_final: 0.8065 (mtp-110)
REVERT: A  229 ASP cc_start: 0.7560 (t0) cc_final: 0.7336 (t0)
REVERT: A  231 ARG cc_start: 0.8315 (ptp-170) cc_final: 0.7968 (mtm180)
REVERT: A  300 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7958 (mtpm)
REVERT: A  343 ASP cc_start: 0.7274 (m-30) cc_final: 0.6810 (m-30)
REVERT: A  356 ARG cc_start: 0.7635 (mmm-85) cc_final: 0.7398 (mmm-85)
REVERT: A  381 ASP cc_start: 0.8033 (t70) cc_final: 0.7821 (t70)
REVERT: R  178 PHE cc_start: 0.7536 (t80) cc_final: 0.7321 (t80)
REVERT: N   25 SER cc_start: 0.8265 (t) cc_final: 0.7863 (m)
REVERT: N   31 ASN cc_start: 0.8177 (m110) cc_final: 0.7912 (m110)
REVERT: B   52 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8375 (ptm160)
REVERT: B  155 ASN cc_start: 0.7810 (t0) cc_final: 0.7415 (t160)
REVERT: B  179 THR cc_start: 0.8122 (t) cc_final: 0.7862 (m)
REVERT: B  237 ASN cc_start: 0.7383 (t0) cc_final: 0.7064 (t0)
REVERT: B  239 ASN cc_start: 0.8426 (m110) cc_final: 0.8051 (m-40)
REVERT: B  243 THR cc_start: 0.8187 (p) cc_final: 0.7803 (p)
REVERT: B  254 ASP cc_start: 0.7479 (t70) cc_final: 0.7195 (t0)
  outliers start: 21
  outliers final: 9
  residues processed: 192
  average time/residue: 0.6336
  time to fit residues: 128.1539
Evaluate side-chains
  189 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 178
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 46 optimal weight:    0.5980
   chunk 97 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 93 optimal weight:    0.5980
   chunk 65 optimal weight:    4.9990
   chunk 45 optimal weight:    0.4980
   chunk 49 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
N  35 ASN
B 293 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.151715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.132432 restraints weight = 10600.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 1.84
r_work: 0.3638 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3478 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8220  Z= 0.164
  Angle     :  0.542   8.712  11139  Z= 0.290
  Chirality :  0.042   0.144   1252
  Planarity :  0.004   0.045   1416
  Dihedral  :  4.794  23.923   1107
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.17 %
    Favored  : 85.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.26), residues: 1003
  helix:  2.17 (0.26), residues: 366
  sheet: -0.34 (0.32), residues: 205
  loop : -0.13 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 347 
 TYR   0.022   0.002   TYR R  69 
 PHE   0.019   0.002   PHE A 212 
 TRP   0.017   0.002   TRP A 234 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8219)
  covalent geometry    : angle       0.54155 (11137)
  SS BOND              : bond        0.00236 (    1)
  SS BOND              : angle       0.36905 (    2)
  hydrogen bonds       : bond        0.04325 (  423)
  hydrogen bonds       : angle       4.67888 ( 1176)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.8008 (ttt90) cc_final: 0.7736 (ttt90)
REVERT: A   53 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7510 (pttp)
REVERT: A  223 ASP cc_start: 0.7644 (t0) cc_final: 0.7329 (t0)
REVERT: A  228 ARG cc_start: 0.8579 (mtp-110) cc_final: 0.8186 (mtp-110)
REVERT: A  229 ASP cc_start: 0.7531 (t0) cc_final: 0.7302 (t0)
REVERT: A  231 ARG cc_start: 0.8332 (ptp-170) cc_final: 0.7958 (mtm180)
REVERT: A  252 ASP cc_start: 0.6780 (t0) cc_final: 0.6436 (t0)
REVERT: A  343 ASP cc_start: 0.7266 (m-30) cc_final: 0.6776 (m-30)
REVERT: A  356 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7373 (mmm-85)
REVERT: A  381 ASP cc_start: 0.8053 (t70) cc_final: 0.7843 (t70)
REVERT: R  178 PHE cc_start: 0.7547 (t80) cc_final: 0.7308 (t80)
REVERT: N   25 SER cc_start: 0.8251 (t) cc_final: 0.7891 (m)
REVERT: N   28 THR cc_start: 0.8028 (p) cc_final: 0.7752 (t)
REVERT: N   31 ASN cc_start: 0.8177 (m110) cc_final: 0.7683 (m110)
REVERT: B   45 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8122 (mtt)
REVERT: B  150 ARG cc_start: 0.8616 (mmt180) cc_final: 0.8383 (mmt180)
REVERT: B  155 ASN cc_start: 0.7833 (t0) cc_final: 0.7472 (t160)
REVERT: B  237 ASN cc_start: 0.7379 (t0) cc_final: 0.7074 (t0)
REVERT: B  239 ASN cc_start: 0.8436 (m110) cc_final: 0.8026 (m-40)
REVERT: B  243 THR cc_start: 0.8175 (p) cc_final: 0.7796 (p)
REVERT: B  254 ASP cc_start: 0.7477 (t70) cc_final: 0.7195 (t0)
  outliers start: 20
  outliers final: 9
  residues processed: 193
  average time/residue: 0.6311
  time to fit residues: 128.5834
Evaluate side-chains
  197 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 186
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 85 optimal weight:    0.8980
   chunk 29 optimal weight:    7.9990
   chunk 28 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0060
   chunk 77 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
N  31 ASN
B 293 ASN
B 295 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.151847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.132598 restraints weight = 10503.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 1.82
r_work: 0.3644 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3481 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8220  Z= 0.157
  Angle     :  0.537   8.197  11139  Z= 0.286
  Chirality :  0.042   0.158   1252
  Planarity :  0.004   0.046   1416
  Dihedral  :  4.672  23.745   1107
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 13.32 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.26), residues: 1003
  helix:  2.36 (0.26), residues: 359
  sheet: -0.59 (0.32), residues: 209
  loop : -0.15 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  38 
 TYR   0.019   0.002   TYR R  69 
 PHE   0.020   0.001   PHE A 212 
 TRP   0.016   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8219)
  covalent geometry    : angle       0.53693 (11137)
  SS BOND              : bond        0.00256 (    1)
  SS BOND              : angle       0.33874 (    2)
  hydrogen bonds       : bond        0.04211 (  423)
  hydrogen bonds       : angle       4.61157 ( 1176)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 189
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.8021 (ttt90) cc_final: 0.7762 (ttt90)
REVERT: A  223 ASP cc_start: 0.7615 (t0) cc_final: 0.7315 (t0)
REVERT: A  228 ARG cc_start: 0.8549 (mtp-110) cc_final: 0.8148 (mtp-110)
REVERT: A  229 ASP cc_start: 0.7502 (t0) cc_final: 0.7256 (t0)
REVERT: A  231 ARG cc_start: 0.8329 (ptp-170) cc_final: 0.7947 (mtm180)
REVERT: A  252 ASP cc_start: 0.6581 (t0) cc_final: 0.6357 (t0)
REVERT: A  299 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7368 (mt-10)
REVERT: A  343 ASP cc_start: 0.7292 (m-30) cc_final: 0.6809 (m-30)
REVERT: A  356 ARG cc_start: 0.7653 (mmm-85) cc_final: 0.7394 (mmm-85)
REVERT: A  376 PHE cc_start: 0.8296 (t80) cc_final: 0.8052 (t80)
REVERT: A  381 ASP cc_start: 0.8039 (t70) cc_final: 0.7833 (t70)
REVERT: R  117 LEU cc_start: 0.8278 (tt) cc_final: 0.8071 (tp)
REVERT: R  178 PHE cc_start: 0.7552 (t80) cc_final: 0.7320 (t80)
REVERT: N   25 SER cc_start: 0.8224 (t) cc_final: 0.7880 (m)
REVERT: N   28 THR cc_start: 0.8032 (p) cc_final: 0.7743 (t)
REVERT: N   31 ASN cc_start: 0.8187 (m-40) cc_final: 0.7722 (m110)
REVERT: B   52 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8361 (ptm160)
REVERT: B  150 ARG cc_start: 0.8626 (mmt180) cc_final: 0.8397 (mmt180)
REVERT: B  155 ASN cc_start: 0.7895 (t0) cc_final: 0.7527 (t0)
REVERT: B  173 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.8020 (p)
REVERT: B  237 ASN cc_start: 0.7376 (t0) cc_final: 0.7078 (t0)
REVERT: B  239 ASN cc_start: 0.8443 (m110) cc_final: 0.8019 (m-40)
REVERT: B  243 THR cc_start: 0.8191 (p) cc_final: 0.7821 (p)
REVERT: B  254 ASP cc_start: 0.7453 (t70) cc_final: 0.7184 (t0)
  outliers start: 26
  outliers final: 12
  residues processed: 201
  average time/residue: 0.6217
  time to fit residues: 132.0167
Evaluate side-chains
  201 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 187
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    0.2980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 293 ASN
B 295 ASN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.151546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.132559 restraints weight = 10406.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 1.80
r_work: 0.3643 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3481 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8220  Z= 0.170
  Angle     :  0.538   7.409  11139  Z= 0.286
  Chirality :  0.042   0.149   1252
  Planarity :  0.004   0.047   1416
  Dihedral  :  4.661  24.082   1107
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.70 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.26), residues: 1003
  helix:  2.34 (0.26), residues: 360
  sheet: -0.57 (0.33), residues: 205
  loop : -0.21 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 347 
 TYR   0.017   0.002   TYR R  69 
 PHE   0.020   0.002   PHE A 212 
 TRP   0.016   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8219)
  covalent geometry    : angle       0.53849 (11137)
  SS BOND              : bond        0.00221 (    1)
  SS BOND              : angle       0.27997 (    2)
  hydrogen bonds       : bond        0.04210 (  423)
  hydrogen bonds       : angle       4.61954 ( 1176)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 188
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.8044 (ttt90) cc_final: 0.7789 (ttt90)
REVERT: A  228 ARG cc_start: 0.8533 (mtp-110) cc_final: 0.8156 (mtp-110)
REVERT: A  229 ASP cc_start: 0.7511 (t0) cc_final: 0.7236 (t0)
REVERT: A  231 ARG cc_start: 0.8328 (ptp-170) cc_final: 0.7944 (mtm180)
REVERT: A  252 ASP cc_start: 0.6553 (t0) cc_final: 0.6343 (t0)
REVERT: A  299 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7360 (mt-10)
REVERT: A  343 ASP cc_start: 0.7278 (m-30) cc_final: 0.6777 (m-30)
REVERT: A  356 ARG cc_start: 0.7629 (mmm-85) cc_final: 0.7365 (mmm-85)
REVERT: A  378 ASP cc_start: 0.7421 (p0) cc_final: 0.7203 (p0)
REVERT: A  381 ASP cc_start: 0.8047 (t70) cc_final: 0.7838 (t70)
REVERT: R  117 LEU cc_start: 0.8317 (tt) cc_final: 0.8072 (tp)
REVERT: R  178 PHE cc_start: 0.7549 (t80) cc_final: 0.7314 (t80)
REVERT: N   25 SER cc_start: 0.8214 (t) cc_final: 0.7880 (m)
REVERT: N   28 THR cc_start: 0.8066 (p) cc_final: 0.7780 (t)
REVERT: N   31 ASN cc_start: 0.8170 (m-40) cc_final: 0.7704 (m110)
REVERT: B  150 ARG cc_start: 0.8636 (mmt180) cc_final: 0.8399 (mmt180)
REVERT: B  155 ASN cc_start: 0.7867 (t0) cc_final: 0.7413 (t160)
REVERT: B  173 THR cc_start: 0.8201 (t) cc_final: 0.7999 (p)
REVERT: B  179 THR cc_start: 0.8077 (t) cc_final: 0.7822 (m)
REVERT: B  237 ASN cc_start: 0.7392 (t0) cc_final: 0.7095 (t0)
REVERT: B  239 ASN cc_start: 0.8427 (m110) cc_final: 0.7979 (m-40)
REVERT: B  243 THR cc_start: 0.8191 (p) cc_final: 0.7811 (p)
REVERT: B  254 ASP cc_start: 0.7438 (t70) cc_final: 0.7163 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 197
  average time/residue: 0.6023
  time to fit residues: 125.3862
Evaluate side-chains
  197 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 183
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  380 ARG
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 14 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 15 optimal weight:    0.3980
   chunk 91 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 295 ASN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.151494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.132349 restraints weight = 10576.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 1.82
r_work: 0.3640 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3480 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8220  Z= 0.164
  Angle     :  0.538   6.788  11139  Z= 0.285
  Chirality :  0.042   0.145   1252
  Planarity :  0.004   0.047   1416
  Dihedral  :  4.627  23.675   1107
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.04 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.26), residues: 1003
  helix:  2.34 (0.26), residues: 360
  sheet: -0.60 (0.34), residues: 189
  loop : -0.26 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 347 
 TYR   0.016   0.001   TYR R  69 
 PHE   0.020   0.001   PHE A 212 
 TRP   0.016   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 8219)
  covalent geometry    : angle       0.53804 (11137)
  SS BOND              : bond        0.00209 (    1)
  SS BOND              : angle       0.23981 (    2)
  hydrogen bonds       : bond        0.04196 (  423)
  hydrogen bonds       : angle       4.58762 ( 1176)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 186
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.8065 (ttt90) cc_final: 0.7815 (ttt90)
REVERT: A  223 ASP cc_start: 0.7618 (t0) cc_final: 0.7160 (t0)
REVERT: A  228 ARG cc_start: 0.8497 (mtp-110) cc_final: 0.7975 (mtp-110)
REVERT: A  229 ASP cc_start: 0.7463 (t0) cc_final: 0.7181 (t0)
REVERT: A  231 ARG cc_start: 0.8294 (ptp-170) cc_final: 0.7937 (mtm180)
REVERT: A  252 ASP cc_start: 0.6533 (t0) cc_final: 0.6321 (t0)
REVERT: A  280 ARG cc_start: 0.7701 (tmt-80) cc_final: 0.7284 (tmt-80)
REVERT: A  299 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7369 (mt-10)
REVERT: A  343 ASP cc_start: 0.7294 (m-30) cc_final: 0.6797 (m-30)
REVERT: A  356 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7366 (mmm-85)
REVERT: A  368 ASP cc_start: 0.7196 (t0) cc_final: 0.6948 (t0)
REVERT: A  378 ASP cc_start: 0.7415 (p0) cc_final: 0.7208 (p0)
REVERT: A  381 ASP cc_start: 0.8038 (t70) cc_final: 0.7833 (t70)
REVERT: R  117 LEU cc_start: 0.8293 (tt) cc_final: 0.8054 (tp)
REVERT: R  178 PHE cc_start: 0.7651 (t80) cc_final: 0.7399 (t80)
REVERT: N   25 SER cc_start: 0.8227 (t) cc_final: 0.7896 (m)
REVERT: N   28 THR cc_start: 0.8074 (p) cc_final: 0.7786 (t)
REVERT: N   31 ASN cc_start: 0.8108 (m-40) cc_final: 0.7727 (m110)
REVERT: B   52 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8365 (ptm160)
REVERT: B  150 ARG cc_start: 0.8627 (mmt180) cc_final: 0.8390 (mmt180)
REVERT: B  155 ASN cc_start: 0.7863 (t0) cc_final: 0.7372 (t160)
REVERT: B  179 THR cc_start: 0.8080 (t) cc_final: 0.7827 (m)
REVERT: B  237 ASN cc_start: 0.7346 (t0) cc_final: 0.7073 (t0)
REVERT: B  239 ASN cc_start: 0.8423 (m110) cc_final: 0.7984 (m-40)
REVERT: B  243 THR cc_start: 0.8192 (p) cc_final: 0.7819 (p)
REVERT: B  254 ASP cc_start: 0.7438 (t70) cc_final: 0.7175 (t0)
  outliers start: 23
  outliers final: 13
  residues processed: 197
  average time/residue: 0.6265
  time to fit residues: 130.3872
Evaluate side-chains
  199 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 185
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  380 ARG
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0970
   chunk 41 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
B 220 GLN
B 295 ASN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.151734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.132625 restraints weight = 10478.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 1.81
r_work: 0.3642 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3481 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8220  Z= 0.167
  Angle     :  0.533   6.303  11139  Z= 0.283
  Chirality :  0.042   0.179   1252
  Planarity :  0.004   0.047   1416
  Dihedral  :  4.583  23.520   1107
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 15.84 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.26), residues: 1003
  helix:  2.32 (0.26), residues: 360
  sheet: -0.65 (0.34), residues: 189
  loop : -0.29 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 347 
 TYR   0.015   0.001   TYR R  69 
 PHE   0.020   0.001   PHE A 212 
 TRP   0.016   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 8219)
  covalent geometry    : angle       0.53346 (11137)
  SS BOND              : bond        0.00211 (    1)
  SS BOND              : angle       0.24787 (    2)
  hydrogen bonds       : bond        0.04218 (  423)
  hydrogen bonds       : angle       4.62093 ( 1176)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 195
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.8075 (ttt90) cc_final: 0.7818 (ttt90)
REVERT: A  228 ARG cc_start: 0.8574 (mtp-110) cc_final: 0.8006 (mtp-110)
REVERT: A  229 ASP cc_start: 0.7480 (t0) cc_final: 0.7191 (t0)
REVERT: A  231 ARG cc_start: 0.8288 (ptp-170) cc_final: 0.7901 (mtm180)
REVERT: A  280 ARG cc_start: 0.7697 (tmt-80) cc_final: 0.7270 (tmt-80)
REVERT: A  299 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7372 (mt-10)
REVERT: A  343 ASP cc_start: 0.7302 (m-30) cc_final: 0.6786 (m-30)
REVERT: A  356 ARG cc_start: 0.7626 (mmm-85) cc_final: 0.7340 (mmm-85)
REVERT: A  368 ASP cc_start: 0.7213 (t0) cc_final: 0.6969 (t0)
REVERT: A  378 ASP cc_start: 0.7377 (p0) cc_final: 0.7127 (p0)
REVERT: R  117 LEU cc_start: 0.8300 (tt) cc_final: 0.8061 (tp)
REVERT: R  178 PHE cc_start: 0.7644 (t80) cc_final: 0.7398 (t80)
REVERT: N   25 SER cc_start: 0.8224 (t) cc_final: 0.7904 (m)
REVERT: N   28 THR cc_start: 0.8051 (p) cc_final: 0.7755 (t)
REVERT: N   31 ASN cc_start: 0.8112 (m-40) cc_final: 0.7732 (m110)
REVERT: B   52 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8340 (ptm160)
REVERT: B  150 ARG cc_start: 0.8634 (mmt180) cc_final: 0.8376 (mmt180)
REVERT: B  155 ASN cc_start: 0.7881 (t0) cc_final: 0.7499 (t160)
REVERT: B  179 THR cc_start: 0.8082 (t) cc_final: 0.7826 (m)
REVERT: B  237 ASN cc_start: 0.7378 (t0) cc_final: 0.7099 (t0)
REVERT: B  239 ASN cc_start: 0.8438 (m110) cc_final: 0.8007 (m-40)
REVERT: B  254 ASP cc_start: 0.7441 (t70) cc_final: 0.7145 (t70)
REVERT: B  259 GLN cc_start: 0.8579 (pt0) cc_final: 0.8376 (pt0)
REVERT: B  291 ASP cc_start: 0.7692 (p0) cc_final: 0.7410 (p0)
REVERT: B  333 ASP cc_start: 0.8034 (p0) cc_final: 0.7805 (p0)
  outliers start: 17
  outliers final: 13
  residues processed: 201
  average time/residue: 0.5754
  time to fit residues: 122.3267
Evaluate side-chains
  198 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 184
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  380 ARG
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 93 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0980
   chunk 40 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:    0.8980
   chunk 71 optimal weight:    0.2980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
B 293 ASN
B 295 ASN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.152581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.133823 restraints weight = 10553.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3767 rms_B_bonded: 1.81
r_work: 0.3652 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3492 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8220  Z= 0.145
  Angle     :  0.530   6.289  11139  Z= 0.281
  Chirality :  0.042   0.155   1252
  Planarity :  0.004   0.047   1416
  Dihedral  :  4.497  22.734   1107
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.07 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.27), residues: 1003
  helix:  2.36 (0.26), residues: 360
  sheet: -0.72 (0.33), residues: 195
  loop : -0.23 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 304 
 TYR   0.014   0.001   TYR R  69 
 PHE   0.018   0.001   PHE A 212 
 TRP   0.016   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8219)
  covalent geometry    : angle       0.52963 (11137)
  SS BOND              : bond        0.00218 (    1)
  SS BOND              : angle       0.22576 (    2)
  hydrogen bonds       : bond        0.04122 (  423)
  hydrogen bonds       : angle       4.56755 ( 1176)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 194
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.8060 (ttt90) cc_final: 0.7803 (ttt90)
REVERT: A  228 ARG cc_start: 0.8563 (mtp-110) cc_final: 0.8164 (mtp-110)
REVERT: A  229 ASP cc_start: 0.7448 (t0) cc_final: 0.7166 (t0)
REVERT: A  231 ARG cc_start: 0.8293 (ptp-170) cc_final: 0.7938 (mtm180)
REVERT: A  280 ARG cc_start: 0.7705 (tmt-80) cc_final: 0.7249 (tmt-80)
REVERT: A  343 ASP cc_start: 0.7304 (m-30) cc_final: 0.6802 (m-30)
REVERT: A  356 ARG cc_start: 0.7593 (mmm-85) cc_final: 0.7313 (mmm-85)
REVERT: A  368 ASP cc_start: 0.7163 (t0) cc_final: 0.6926 (t0)
REVERT: R  117 LEU cc_start: 0.8278 (tt) cc_final: 0.8050 (tp)
REVERT: R  178 PHE cc_start: 0.7647 (t80) cc_final: 0.7399 (t80)
REVERT: N   25 SER cc_start: 0.8212 (t) cc_final: 0.7887 (m)
REVERT: N   28 THR cc_start: 0.8013 (p) cc_final: 0.7736 (t)
REVERT: N   31 ASN cc_start: 0.8090 (m-40) cc_final: 0.7722 (m110)
REVERT: B   52 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8336 (ptm160)
REVERT: B  150 ARG cc_start: 0.8626 (mmt180) cc_final: 0.8365 (mmt180)
REVERT: B  155 ASN cc_start: 0.7865 (t0) cc_final: 0.7647 (t0)
REVERT: B  237 ASN cc_start: 0.7345 (t0) cc_final: 0.7051 (t0)
REVERT: B  239 ASN cc_start: 0.8418 (m110) cc_final: 0.7964 (m-40)
REVERT: B  254 ASP cc_start: 0.7571 (t70) cc_final: 0.7291 (t70)
REVERT: B  259 GLN cc_start: 0.8564 (pt0) cc_final: 0.8359 (pt0)
REVERT: B  291 ASP cc_start: 0.7689 (p0) cc_final: 0.7416 (p0)
  outliers start: 16
  outliers final: 11
  residues processed: 200
  average time/residue: 0.6089
  time to fit residues: 128.6825
Evaluate side-chains
  203 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 191
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  380 ARG
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 267 GLN
B 293 ASN
B 295 ASN
B 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.150768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.131705 restraints weight = 10450.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 1.80
r_work: 0.3628 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3466 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8220  Z= 0.207
  Angle     :  0.570   6.036  11139  Z= 0.303
  Chirality :  0.044   0.175   1252
  Planarity :  0.004   0.048   1416
  Dihedral  :  4.654  23.317   1107
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 16.65 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.26), residues: 1003
  helix:  2.26 (0.26), residues: 360
  sheet: -0.75 (0.33), residues: 197
  loop : -0.23 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 256 
 TYR   0.017   0.002   TYR N  95 
 PHE   0.019   0.002   PHE A 212 
 TRP   0.016   0.002   TRP R 155 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 8219)
  covalent geometry    : angle       0.56977 (11137)
  SS BOND              : bond        0.00170 (    1)
  SS BOND              : angle       0.21057 (    2)
  hydrogen bonds       : bond        0.04334 (  423)
  hydrogen bonds       : angle       4.66619 ( 1176)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 177
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.8089 (ttt90) cc_final: 0.7827 (ttt90)
REVERT: A  228 ARG cc_start: 0.8589 (mtp-110) cc_final: 0.8080 (mtp-110)
REVERT: A  229 ASP cc_start: 0.7448 (t0) cc_final: 0.7164 (t0)
REVERT: A  231 ARG cc_start: 0.8316 (ptp-170) cc_final: 0.7958 (mtm180)
REVERT: A  280 ARG cc_start: 0.7686 (tmt-80) cc_final: 0.7214 (tmt-80)
REVERT: A  343 ASP cc_start: 0.7295 (m-30) cc_final: 0.6787 (m-30)
REVERT: A  356 ARG cc_start: 0.7606 (mmm-85) cc_final: 0.7324 (mmm-85)
REVERT: A  368 ASP cc_start: 0.7213 (t0) cc_final: 0.6962 (t0)
REVERT: A  378 ASP cc_start: 0.7368 (p0) cc_final: 0.7119 (p0)
REVERT: R   87 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8106 (mp)
REVERT: R  117 LEU cc_start: 0.8313 (tt) cc_final: 0.8079 (tp)
REVERT: R  178 PHE cc_start: 0.7653 (t80) cc_final: 0.7389 (t80)
REVERT: N   25 SER cc_start: 0.8288 (t) cc_final: 0.7872 (p)
REVERT: N   28 THR cc_start: 0.8015 (p) cc_final: 0.7708 (t)
REVERT: N   31 ASN cc_start: 0.8182 (m-40) cc_final: 0.7797 (m110)
REVERT: B  150 ARG cc_start: 0.8645 (mmt180) cc_final: 0.8354 (mmt180)
REVERT: B  155 ASN cc_start: 0.7896 (t0) cc_final: 0.7663 (t0)
REVERT: B  179 THR cc_start: 0.8165 (t) cc_final: 0.7907 (m)
REVERT: B  237 ASN cc_start: 0.7418 (t0) cc_final: 0.7138 (t0)
REVERT: B  239 ASN cc_start: 0.8429 (m110) cc_final: 0.7874 (m-40)
REVERT: B  254 ASP cc_start: 0.7614 (t70) cc_final: 0.7332 (t0)
REVERT: B  259 GLN cc_start: 0.8584 (pt0) cc_final: 0.8379 (pt0)
  outliers start: 15
  outliers final: 14
  residues processed: 183
  average time/residue: 0.6503
  time to fit residues: 125.4498
Evaluate side-chains
  192 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 177
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  380 ARG
Chi-restraints excluded: chain R residue   87 LEU
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 76 optimal weight:    0.4980
   chunk 63 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 83 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
B 293 ASN
B 295 ASN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.150877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.131740 restraints weight = 10379.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 1.80
r_work: 0.3631 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3470 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.139   8220  Z= 0.220
  Angle     :  0.931  59.174  11139  Z= 0.534
  Chirality :  0.044   0.252   1252
  Planarity :  0.004   0.048   1416
  Dihedral  :  4.667  23.202   1107
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.99 %
    Favored  : 81.17 %
  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:  0.80 (0.26), residues: 1003
  helix:  2.27 (0.26), residues: 360
  sheet: -0.77 (0.33), residues: 197
  loop : -0.23 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 256 
 TYR   0.016   0.002   TYR N  95 
 PHE   0.018   0.002   PHE A 212 
 TRP   0.016   0.002   TRP R 155 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 8219)
  covalent geometry    : angle       0.93148 (11137)
  SS BOND              : bond        0.00172 (    1)
  SS BOND              : angle       0.21202 (    2)
  hydrogen bonds       : bond        0.04489 (  423)
  hydrogen bonds       : angle       4.66573 ( 1176)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3787.45 seconds
wall clock time: 65 minutes 4.48 seconds (3904.48 seconds total)