Starting phenix.real_space_refine
on Tue Mar  3 23:29:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ts0_26104/03_2026/7ts0_26104.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ts0_26104/03_2026/7ts0_26104.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ts0_26104/03_2026/7ts0_26104.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ts0_26104/03_2026/7ts0_26104.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ts0_26104/03_2026/7ts0_26104.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ts0_26104/03_2026/7ts0_26104.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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      63      5.16       5
     C    5979      2.51       5
     N    1607      2.21       5
     O    1734      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 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: 9383
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "P"
      Number of atoms: 2459
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2459
          Classifications: {'peptide': 296}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 8, 'TRANS': 287}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 21
    Chain: "U"
      Number of atoms: 301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 301
          Classifications: {'peptide': 36}
          Link IDs: {'PTRANS': 1, 'TRANS': 34}
    Chain: "A"
      Number of atoms: 1788
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1788
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 219}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2616
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "H"
      Number of atoms: 1783
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 232, 1780
          Classifications: {'peptide': 232}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 232, 1780
          Classifications: {'peptide': 232}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 1820
  Time building chain proxies: 2.74, per 1000 atoms: 0.29
  Number of scatterers: 9383
  At special positions: 0
  Unit cell: (108.498, 132.834, 128.778, 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      63     16.00
     O    1734      8.00
     N    1607      7.00
     C    5979      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS P  64 " - pdb=" SG  CYS P  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P 184 " - pdb=" SG  CYS P 254 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " 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: 0.67
  Conformation dependent library (CDL) restraints added in 365.0 milliseconds
  

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2222

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 14 sheets defined
      40.0% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'P' and resid 102 through 106
      removed outlier: 4.115A  pdb=" N   LYS P 105 " --> pdb=" O   LEU P 102 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 110 through 138
      removed outlier: 4.100A  pdb=" N   ALA P 133 " --> pdb=" O   ALA P 129 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 146 through 171
      removed outlier: 4.094A  pdb=" N   LEU P 171 " --> pdb=" O   PHE P 167 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 173 through 179
    Processing helix  chain 'P' and resid 181 through 214
      removed outlier: 3.709A  pdb=" N   ARG P 185 " --> pdb=" O   GLU P 181 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 219 through 233
    Processing helix  chain 'P' and resid 234 through 250
      removed outlier: 4.087A  pdb=" N   ILE P 238 " --> pdb=" O   ILE P 234 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 252 through 256
    Processing helix  chain 'P' and resid 265 through 298
      removed outlier: 3.919A  pdb=" N   GLN P 269 " --> pdb=" O   ASP P 265 " (cutoff:3.500A)
      Proline residue:  P 271  - end of helix
      removed outlier: 3.511A  pdb=" N   LEU P 274 " --> pdb=" O   GLY P 270 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU P 277 " --> pdb=" O   ILE P 273 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   MET P 291 " --> pdb=" O   VAL P 287 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   ALA P 296 " --> pdb=" O   THR P 292 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   SER P 297 " --> pdb=" O   LYS P 293 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   THR P 298 " --> pdb=" O   LEU P 294 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 300 through 320
      removed outlier: 3.617A  pdb=" N   VAL P 314 " --> pdb=" O   LYS P 310 " (cutoff:3.500A)
      Proline residue:  P 317  - end of helix
    Processing helix  chain 'P' and resid 321 through 326
      removed outlier: 4.028A  pdb=" N   PHE P 326 " --> pdb=" O   THR P 322 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 334 through 362
      removed outlier: 3.514A  pdb=" N   PHE P 350 " --> pdb=" O   PHE P 346 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   GLY P 352 " --> pdb=" O   GLN P 348 " (cutoff:3.500A)
      removed outlier: 4.941A  pdb=" N   PHE P 353 " --> pdb=" O   SER P 349 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 363 through 383
      removed outlier: 3.635A  pdb=" N   ARG P 367 " --> pdb=" O   ASN P 363 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 8 through 37
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 4.189A  pdb=" N   LYS A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.525A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 218
      removed outlier: 4.362A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU A 217 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   ASP A 218 " --> pdb=" O   CYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 232
      removed outlier: 4.070A  pdb=" N   ASP A 232 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 229 through 232'
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 4.179A  pdb=" N   LYS A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   LYS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 31 through 35
      removed outlier: 3.704A  pdb=" N   THR B  34 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASN B  35 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 31 through 35'
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.554A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.608A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 220 through 224
      removed outlier: 3.589A  pdb=" N   VAL H 224 " --> pdb=" O   ALA H 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'P' and resid 67 through 68
      removed outlier: 3.711A  pdb=" N   PHE P  68 " --> pdb=" O   VAL P  71 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191
      removed outlier: 3.514A  pdb=" N   VAL A  34 " --> pdb=" O   HIS A 196 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.522A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 9.698A  pdb=" N   ALA A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   ILE A 265 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   LEU A 267 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51
      removed outlier: 6.846A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.977A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.195A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.035A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.667A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.546A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.904A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 5.748A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.585A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.821A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.649A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.906A  pdb=" N   ARG H  98 " --> pdb=" O   PHE H 110 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141
    Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148
      removed outlier: 7.045A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASN H 194 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)

    475 hydrogen bonds defined for protein.
    1337 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: 1.50

  Time building geometry restraints manager: 0.91 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: 3013
        1.34 -     1.46: 2216
        1.46 -     1.58: 4271
        1.58 -     1.70: 0
        1.70 -     1.82: 88
  Bond restraints: 9588
  Sorted by residual:
  bond pdb=" C   ASN U   2 "
       pdb=" N   PRO U   3 "
    ideal  model  delta    sigma   weight residual
    1.334  1.385 -0.051 2.34e-02 1.83e+03 4.70e+00
  bond pdb=" C   ASP H  74 "
       pdb=" N   PRO H  75 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.023 1.28e-02 6.10e+03 3.26e+00
  bond pdb=" C   PHE P 236 "
       pdb=" N   PRO P 237 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.36e-02 5.41e+03 3.08e+00
  bond pdb=" C   LEU P 316 "
       pdb=" N   PRO P 317 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.021 1.19e-02 7.06e+03 3.02e+00
  bond pdb=" CA  ASN U   2 "
       pdb=" C   ASN U   2 "
    ideal  model  delta    sigma   weight residual
    1.525  1.557 -0.032 2.10e-02 2.27e+03 2.32e+00
  ... (remaining 9583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 12490
        1.76 -     3.51: 410
        3.51 -     5.27: 63
        5.27 -     7.03: 13
        7.03 -     8.78: 11
  Bond angle restraints: 12987
  Sorted by residual:
  angle pdb=" CA  ARG H 218 "
        pdb=" CB  ARG H 218 "
        pdb=" CG  ARG H 218 "
      ideal   model   delta    sigma   weight residual
     114.10  122.59   -8.49 2.00e+00 2.50e-01 1.80e+01
  angle pdb=" C   ARG H 191 "
        pdb=" N   MET H 192 "
        pdb=" CA  MET H 192 "
      ideal   model   delta    sigma   weight residual
     124.31  131.01   -6.70 1.67e+00 3.59e-01 1.61e+01
  angle pdb=" CA  ARG A 210 "
        pdb=" CB  ARG A 210 "
        pdb=" CG  ARG A 210 "
      ideal   model   delta    sigma   weight residual
     114.10  120.98   -6.88 2.00e+00 2.50e-01 1.18e+01
  angle pdb=" C   ARG A 209 "
        pdb=" N   ARG A 210 "
        pdb=" CA  ARG A 210 "
      ideal   model   delta    sigma   weight residual
     122.68  127.54   -4.86 1.47e+00 4.63e-01 1.09e+01
  angle pdb=" C   GLU A 237 "
        pdb=" N   ASP A 238 "
        pdb=" CA  ASP A 238 "
      ideal   model   delta    sigma   weight residual
     123.47  128.46   -4.99 1.53e+00 4.27e-01 1.06e+01
  ... (remaining 12982 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.03: 5462
       15.03 -    30.06: 154
       30.06 -    45.08: 47
       45.08 -    60.11: 1
       60.11 -    75.14: 3
  Dihedral angle restraints: 5667
    sinusoidal: 2223
      harmonic: 3444
  Sorted by residual:
  dihedral pdb=" CB  CYS P 184 "
           pdb=" SG  CYS P 184 "
           pdb=" SG  CYS P 254 "
           pdb=" CB  CYS P 254 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  124.78  -31.78     1      1.00e+01 1.00e-02 1.44e+01
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.54   18.46     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  SER A 310 "
           pdb=" C   SER A 310 "
           pdb=" N   LYS A 311 "
           pdb=" CA  LYS A 311 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.80  -18.20     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 5664 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1045
       0.047 -    0.095: 300
       0.095 -    0.142: 85
       0.142 -    0.189: 23
       0.189 -    0.236: 4
  Chirality restraints: 1457
  Sorted by residual:
  chirality pdb=" CG  LEU H 174 "
            pdb=" CB  LEU H 174 "
            pdb=" CD1 LEU H 174 "
            pdb=" CD2 LEU H 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CB  THR B 223 "
            pdb=" CA  THR B 223 "
            pdb=" OG1 THR B 223 "
            pdb=" CG2 THR B 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CB  ILE A 185 "
            pdb=" CA  ILE A 185 "
            pdb=" CG1 ILE A 185 "
            pdb=" CG2 ILE A 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1454 not shown)

  Planarity restraints: 1649
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL P 314 "    0.015 2.00e-02 2.50e+03   2.96e-02 8.75e+00
        pdb=" C   VAL P 314 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   VAL P 314 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LEU P 315 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG H 191 "   -0.013 2.00e-02 2.50e+03   2.67e-02 7.11e+00
        pdb=" C   ARG H 191 "    0.046 2.00e-02 2.50e+03
        pdb=" O   ARG H 191 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   MET H 192 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.037 5.00e-02 4.00e+02   5.63e-02 5.07e+00
        pdb=" N   PRO B 236 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1646 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2077
        2.80 -     3.32: 8259
        3.32 -     3.85: 14810
        3.85 -     4.37: 16991
        4.37 -     4.90: 30308
  Nonbonded interactions: 72445
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OD1 ASN A 270 "
            pdb=" OG1 THR A 324 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" OD1 ASN P 120 "
            pdb=" OG  SER P 349 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" O   THR P 298 "
            pdb=" NE2 GLN P 304 "
     model   vdw
     2.344 3.120
  ... (remaining 72440 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.020
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
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   0.056   9592  Z= 0.201
  Angle     :  0.790   8.784  12995  Z= 0.457
  Chirality :  0.051   0.236   1457
  Planarity :  0.006   0.056   1649
  Dihedral  :  8.381  75.139   3433
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.98 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.22), residues: 1167
  helix: -0.11 (0.22), residues: 419
  sheet: -0.62 (0.29), residues: 287
  loop : -1.51 (0.25), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG P 223 
 TYR   0.020   0.002   TYR H 175 
 PHE   0.025   0.003   PHE A 190 
 TRP   0.023   0.002   TRP H 111 
 HIS   0.016   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9588)
  covalent geometry    : angle       0.78700 (12987)
  SS BOND              : bond        0.00461 (    4)
  SS BOND              : angle       2.67120 (    8)
  hydrogen bonds       : bond        0.13452 (  468)
  hydrogen bonds       : angle       6.13878 ( 1337)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 298
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  265 ASP cc_start: 0.8104 (t70) cc_final: 0.7902 (t70)
REVERT: P  305 TYR cc_start: 0.5611 (m-80) cc_final: 0.5388 (m-80)
REVERT: P  372 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7507 (mmtt)
REVERT: P  379 ASP cc_start: 0.8018 (t0) cc_final: 0.7813 (t0)
REVERT: A   44 SER cc_start: 0.7860 (t) cc_final: 0.7650 (m)
REVERT: A  232 ASP cc_start: 0.8365 (m-30) cc_final: 0.7942 (m-30)
REVERT: A  298 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8053 (mp0)
REVERT: B  205 ASP cc_start: 0.7717 (p0) cc_final: 0.7465 (p0)
REVERT: H   80 PHE cc_start: 0.8193 (m-80) cc_final: 0.7931 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 299
  average time/residue: 0.5602
  time to fit residues: 179.1753
Evaluate side-chains
  187 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.0050
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.3980
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
P  69 ASN
P 106 GLN
P 198 ASN
P 251 ASN
U  24 GLN
A 189 HIS
B  44 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
H 179 GLN
H 231 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.164594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.122569 restraints weight = 20958.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 3.02
r_work: 0.3341 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9592  Z= 0.115
  Angle     :  0.525   7.936  12995  Z= 0.278
  Chirality :  0.041   0.158   1457
  Planarity :  0.004   0.040   1649
  Dihedral  :  3.844  22.440   1290
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 13.31 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.64 (0.24), residues: 1167
  helix:  2.17 (0.24), residues: 419
  sheet: -0.16 (0.29), residues: 281
  loop : -0.80 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 198 
 TYR   0.026   0.001   TYR A 231 
 PHE   0.016   0.001   PHE A 190 
 TRP   0.017   0.001   TRP H 111 
 HIS   0.004   0.001   HIS P 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9588)
  covalent geometry    : angle       0.52496 (12987)
  SS BOND              : bond        0.00368 (    4)
  SS BOND              : angle       0.80732 (    8)
  hydrogen bonds       : bond        0.03576 (  468)
  hydrogen bonds       : angle       4.36239 ( 1337)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 193
  time to evaluate  : 0.358 
Fit side-chains
REVERT: P  236 PHE cc_start: 0.6950 (m-80) cc_final: 0.6672 (t80)
REVERT: P  305 TYR cc_start: 0.5085 (m-80) cc_final: 0.4785 (m-80)
REVERT: P  310 LYS cc_start: 0.8069 (tmtt) cc_final: 0.7843 (tmtt)
REVERT: P  372 LYS cc_start: 0.7536 (mtpt) cc_final: 0.6748 (mmtt)
REVERT: U   24 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7436 (tp40)
REVERT: A   44 SER cc_start: 0.8118 (t) cc_final: 0.7522 (m)
REVERT: A  231 TYR cc_start: 0.6729 (p90) cc_final: 0.6373 (p90)
REVERT: G   20 LYS cc_start: 0.7967 (mtmt) cc_final: 0.7750 (mtmm)
REVERT: H   80 PHE cc_start: 0.8095 (m-80) cc_final: 0.7596 (m-80)
REVERT: H   83 MET cc_start: 0.8886 (mtm) cc_final: 0.8640 (mtp)
REVERT: H   85 SER cc_start: 0.8107 (m) cc_final: 0.7769 (t)
REVERT: H  160 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7482 (ttm-80)
REVERT: H  230 MET cc_start: 0.8546 (ttp) cc_final: 0.8315 (ttm)
  outliers start: 36
  outliers final: 8
  residues processed: 212
  average time/residue: 0.5812
  time to fit residues: 131.5144
Evaluate side-chains
  172 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 164
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  169 LEU
Chi-restraints excluded: chain P residue  219 THR
Chi-restraints excluded: chain P residue  303 ILE
Chi-restraints excluded: chain U residue   23 THR
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  179 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 71 optimal weight:    7.9990
   chunk 107 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
P 251 ASN
P 285 ASN
A 270 ASN
B 220 GLN
H 171 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.146216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.102162 restraints weight = 12719.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.42
r_work: 0.3059 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9592  Z= 0.224
  Angle     :  0.655   8.960  12995  Z= 0.344
  Chirality :  0.045   0.235   1457
  Planarity :  0.005   0.062   1649
  Dihedral  :  4.287  18.577   1290
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 13.80 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.25), residues: 1167
  helix:  2.36 (0.25), residues: 421
  sheet:  0.10 (0.29), residues: 279
  loop : -0.51 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  46 
 TYR   0.024   0.003   TYR A 231 
 PHE   0.019   0.002   PHE H 110 
 TRP   0.043   0.003   TRP H 111 
 HIS   0.009   0.002   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 ( 9588)
  covalent geometry    : angle       0.65495 (12987)
  SS BOND              : bond        0.00961 (    4)
  SS BOND              : angle       1.14084 (    8)
  hydrogen bonds       : bond        0.05122 (  468)
  hydrogen bonds       : angle       4.56105 ( 1337)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 177
  time to evaluate  : 0.354 
Fit side-chains
REVERT: P  178 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7405 (mm-30)
REVERT: P  310 LYS cc_start: 0.8030 (tmtt) cc_final: 0.7801 (tmtt)
REVERT: P  372 LYS cc_start: 0.7498 (mtpt) cc_final: 0.6627 (mmtt)
REVERT: A  277 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7180 (mt-10)
REVERT: B   46 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.8304 (mtp-110)
REVERT: B  150 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8304 (mmt90)
REVERT: B  234 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8969 (t80)
REVERT: G   46 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8328 (tppt)
REVERT: H    6 GLU cc_start: 0.8081 (mp0) cc_final: 0.7523 (mp0)
REVERT: H   85 SER cc_start: 0.8702 (m) cc_final: 0.8273 (t)
REVERT: H  160 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7377 (ttm110)
REVERT: H  179 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8698 (tt0)
REVERT: H  201 ASP cc_start: 0.8423 (p0) cc_final: 0.8076 (t0)
  outliers start: 42
  outliers final: 15
  residues processed: 203
  average time/residue: 0.6392
  time to fit residues: 137.8292
Evaluate side-chains
  170 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  169 LEU
Chi-restraints excluded: chain P residue  178 GLU
Chi-restraints excluded: chain P residue  219 THR
Chi-restraints excluded: chain P residue  244 ILE
Chi-restraints excluded: chain P residue  287 VAL
Chi-restraints excluded: chain U residue   23 THR
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  146 SER
Chi-restraints excluded: chain H residue  179 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 75 optimal weight:    0.4980
   chunk 21 optimal weight:    9.9990
   chunk 101 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 115 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
P 198 ASN
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 295 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
H 194 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.146440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.103364 restraints weight = 11889.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 2.31
r_work: 0.3077 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.4406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9592  Z= 0.134
  Angle     :  0.517   8.006  12995  Z= 0.274
  Chirality :  0.041   0.142   1457
  Planarity :  0.004   0.043   1649
  Dihedral  :  3.920  17.214   1290
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 16.83 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.25), residues: 1167
  helix:  2.84 (0.25), residues: 420
  sheet:  0.17 (0.29), residues: 284
  loop : -0.40 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  42 
 TYR   0.025   0.002   TYR A 231 
 PHE   0.013   0.001   PHE P 256 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.009   0.001   HIS P 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9588)
  covalent geometry    : angle       0.51715 (12987)
  SS BOND              : bond        0.00533 (    4)
  SS BOND              : angle       0.69413 (    8)
  hydrogen bonds       : bond        0.03930 (  468)
  hydrogen bonds       : angle       4.17621 ( 1337)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 164
  time to evaluate  : 0.384 
Fit side-chains
REVERT: P  372 LYS cc_start: 0.7596 (mtpt) cc_final: 0.6694 (mmmt)
REVERT: A   44 SER cc_start: 0.8584 (t) cc_final: 0.8188 (p)
REVERT: A  298 GLU cc_start: 0.7740 (mp0) cc_final: 0.6858 (tp30)
REVERT: B  101 MET cc_start: 0.9362 (mtp) cc_final: 0.9139 (mtm)
REVERT: B  130 GLU cc_start: 0.8419 (mp0) cc_final: 0.8164 (mp0)
REVERT: B  150 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8426 (mmt90)
REVERT: B  197 ARG cc_start: 0.8021 (mmt180) cc_final: 0.7690 (mmm160)
REVERT: B  217 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8027 (pmt)
REVERT: B  333 ASP cc_start: 0.8759 (p0) cc_final: 0.8514 (p0)
REVERT: G   46 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8349 (tppt)
REVERT: H   85 SER cc_start: 0.8709 (m) cc_final: 0.8328 (t)
REVERT: H  160 ARG cc_start: 0.7777 (ttp80) cc_final: 0.7370 (ttm-80)
REVERT: H  201 ASP cc_start: 0.8336 (p0) cc_final: 0.7985 (t0)
  outliers start: 34
  outliers final: 14
  residues processed: 187
  average time/residue: 0.6656
  time to fit residues: 132.3285
Evaluate side-chains
  165 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  169 LEU
Chi-restraints excluded: chain P residue  182 VAL
Chi-restraints excluded: chain P residue  197 THR
Chi-restraints excluded: chain P residue  219 THR
Chi-restraints excluded: chain U residue   10 THR
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  146 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 189 HIS
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 295 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.145098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.099714 restraints weight = 19104.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 2.87
r_work: 0.3009 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.4651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9592  Z= 0.154
  Angle     :  0.531   8.234  12995  Z= 0.280
  Chirality :  0.041   0.160   1457
  Planarity :  0.004   0.042   1649
  Dihedral  :  3.948  17.541   1290
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.03 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.25), residues: 1167
  helix:  2.96 (0.25), residues: 415
  sheet:  0.24 (0.29), residues: 285
  loop : -0.38 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  42 
 TYR   0.023   0.002   TYR A 231 
 PHE   0.013   0.001   PHE P 256 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.008   0.001   HIS P 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9588)
  covalent geometry    : angle       0.53056 (12987)
  SS BOND              : bond        0.00637 (    4)
  SS BOND              : angle       0.65548 (    8)
  hydrogen bonds       : bond        0.04084 (  468)
  hydrogen bonds       : angle       4.21496 ( 1337)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 159
  time to evaluate  : 0.354 
Fit side-chains
REVERT: P  178 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7364 (mm-30)
REVERT: P  372 LYS cc_start: 0.7616 (mtpt) cc_final: 0.6725 (mmmt)
REVERT: A   44 SER cc_start: 0.8562 (t) cc_final: 0.8142 (p)
REVERT: A  261 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8484 (pp)
REVERT: A  277 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7355 (mt-10)
REVERT: A  278 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7874 (ptmt)
REVERT: A  316 ASN cc_start: 0.6547 (m110) cc_final: 0.6264 (m-40)
REVERT: B  130 GLU cc_start: 0.8458 (mp0) cc_final: 0.8193 (mp0)
REVERT: B  132 ASN cc_start: 0.7658 (t0) cc_final: 0.6988 (p0)
REVERT: B  150 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8461 (mmt90)
REVERT: B  197 ARG cc_start: 0.8033 (mmt180) cc_final: 0.7728 (mmm160)
REVERT: B  217 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8011 (pmt)
REVERT: B  333 ASP cc_start: 0.8769 (p0) cc_final: 0.8564 (p0)
REVERT: G   46 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8325 (tppt)
REVERT: H    7 SER cc_start: 0.8513 (p) cc_final: 0.8258 (m)
REVERT: H   85 SER cc_start: 0.8775 (m) cc_final: 0.8320 (t)
REVERT: H  160 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7444 (ttm-80)
REVERT: H  201 ASP cc_start: 0.8383 (p0) cc_final: 0.7923 (t0)
  outliers start: 35
  outliers final: 21
  residues processed: 182
  average time/residue: 0.5870
  time to fit residues: 113.6920
Evaluate side-chains
  178 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  169 LEU
Chi-restraints excluded: chain P residue  178 GLU
Chi-restraints excluded: chain P residue  182 VAL
Chi-restraints excluded: chain P residue  197 THR
Chi-restraints excluded: chain P residue  219 THR
Chi-restraints excluded: chain U residue   10 THR
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  145 SER
Chi-restraints excluded: chain H residue  146 SER
Chi-restraints excluded: chain H residue  208 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 115 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 110 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
P 152 HIS
A  52 GLN
** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 242 ASN
A 295 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 171 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.146778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.101463 restraints weight = 20326.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.94
r_work: 0.3033 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.4686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9592  Z= 0.109
  Angle     :  0.492   8.175  12995  Z= 0.257
  Chirality :  0.040   0.159   1457
  Planarity :  0.003   0.040   1649
  Dihedral  :  3.743  16.886   1290
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 16.93 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.25), residues: 1167
  helix:  3.11 (0.25), residues: 419
  sheet:  0.35 (0.30), residues: 277
  loop : -0.40 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  42 
 TYR   0.025   0.001   TYR A 231 
 PHE   0.015   0.001   PHE P 256 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.008   0.001   HIS P 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 9588)
  covalent geometry    : angle       0.49155 (12987)
  SS BOND              : bond        0.00436 (    4)
  SS BOND              : angle       0.54210 (    8)
  hydrogen bonds       : bond        0.03536 (  468)
  hydrogen bonds       : angle       4.07493 ( 1337)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 167
  time to evaluate  : 0.298 
Fit side-chains
REVERT: P  252 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8295 (pt0)
REVERT: P  372 LYS cc_start: 0.7419 (mtpt) cc_final: 0.6516 (mmmt)
REVERT: A   44 SER cc_start: 0.8394 (t) cc_final: 0.8046 (p)
REVERT: A  278 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7903 (ptmt)
REVERT: A  316 ASN cc_start: 0.6498 (m110) cc_final: 0.6177 (m-40)
REVERT: A  332 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7721 (mt)
REVERT: B  130 GLU cc_start: 0.8361 (mp0) cc_final: 0.8102 (mp0)
REVERT: B  132 ASN cc_start: 0.7531 (t0) cc_final: 0.6957 (p0)
REVERT: B  150 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8364 (mmt90)
REVERT: B  197 ARG cc_start: 0.7957 (mmt180) cc_final: 0.7649 (mmm160)
REVERT: B  217 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7841 (pmt)
REVERT: B  280 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8636 (tmtm)
REVERT: H    6 GLU cc_start: 0.8511 (mp0) cc_final: 0.8219 (mp0)
REVERT: H    7 SER cc_start: 0.8489 (p) cc_final: 0.8277 (m)
REVERT: H   80 PHE cc_start: 0.8547 (m-80) cc_final: 0.8059 (m-80)
REVERT: H   85 SER cc_start: 0.8756 (m) cc_final: 0.8309 (t)
REVERT: H  145 SER cc_start: 0.7288 (OUTLIER) cc_final: 0.6859 (p)
REVERT: H  160 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7376 (ttm-80)
REVERT: H  201 ASP cc_start: 0.8223 (p0) cc_final: 0.7895 (t0)
  outliers start: 36
  outliers final: 17
  residues processed: 193
  average time/residue: 0.6183
  time to fit residues: 127.2543
Evaluate side-chains
  184 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 160
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  169 LEU
Chi-restraints excluded: chain P residue  182 VAL
Chi-restraints excluded: chain P residue  197 THR
Chi-restraints excluded: chain P residue  219 THR
Chi-restraints excluded: chain P residue  252 GLU
Chi-restraints excluded: chain U residue   10 THR
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  145 SER
Chi-restraints excluded: chain H residue  206 SER
Chi-restraints excluded: chain H residue  208 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 107 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   chunk 56 optimal weight:    0.4980
   chunk 61 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 89 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
P 120 ASN
P 170 GLN
A 189 HIS
A 214 HIS
A 242 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 171 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.147601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.101929 restraints weight = 24167.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 3.17
r_work: 0.3035 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.4739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9592  Z= 0.103
  Angle     :  0.481   8.137  12995  Z= 0.255
  Chirality :  0.040   0.161   1457
  Planarity :  0.003   0.040   1649
  Dihedral  :  3.671  16.545   1290
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.40 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.25), residues: 1167
  helix:  3.18 (0.25), residues: 419
  sheet:  0.35 (0.29), residues: 283
  loop : -0.30 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  42 
 TYR   0.028   0.001   TYR A 231 
 PHE   0.015   0.001   PHE P 256 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.008   0.001   HIS P 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 9588)
  covalent geometry    : angle       0.48141 (12987)
  SS BOND              : bond        0.00417 (    4)
  SS BOND              : angle       0.50604 (    8)
  hydrogen bonds       : bond        0.03364 (  468)
  hydrogen bonds       : angle       4.00110 ( 1337)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 168
  time to evaluate  : 0.391 
Fit side-chains
REVERT: P  252 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8323 (pt0)
REVERT: P  372 LYS cc_start: 0.7441 (mtpt) cc_final: 0.6540 (mmmt)
REVERT: A   44 SER cc_start: 0.8365 (t) cc_final: 0.8003 (p)
REVERT: A  277 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7496 (mt-10)
REVERT: A  278 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7874 (ptmt)
REVERT: A  295 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7350 (t0)
REVERT: A  332 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7718 (mt)
REVERT: B   52 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8077 (ptp90)
REVERT: B  130 GLU cc_start: 0.8348 (mp0) cc_final: 0.8088 (mp0)
REVERT: B  132 ASN cc_start: 0.7530 (t0) cc_final: 0.6950 (p0)
REVERT: B  197 ARG cc_start: 0.7955 (mmt180) cc_final: 0.7645 (mmm160)
REVERT: B  217 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7887 (pmt)
REVERT: B  280 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8629 (tmtm)
REVERT: H    6 GLU cc_start: 0.8487 (mp0) cc_final: 0.8219 (mt-10)
REVERT: H    7 SER cc_start: 0.8498 (p) cc_final: 0.8229 (m)
REVERT: H   80 PHE cc_start: 0.8538 (m-80) cc_final: 0.8043 (m-80)
REVERT: H   85 SER cc_start: 0.8704 (m) cc_final: 0.8284 (t)
REVERT: H  145 SER cc_start: 0.7331 (t) cc_final: 0.6889 (p)
REVERT: H  160 ARG cc_start: 0.7783 (ttp80) cc_final: 0.7358 (ttm-80)
REVERT: H  186 GLN cc_start: 0.8398 (tt0) cc_final: 0.8126 (pt0)
REVERT: H  201 ASP cc_start: 0.8227 (p0) cc_final: 0.7898 (t0)
  outliers start: 24
  outliers final: 15
  residues processed: 184
  average time/residue: 0.6256
  time to fit residues: 122.6592
Evaluate side-chains
  175 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  169 LEU
Chi-restraints excluded: chain P residue  182 VAL
Chi-restraints excluded: chain P residue  252 GLU
Chi-restraints excluded: chain U residue   10 THR
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  295 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  146 SER
Chi-restraints excluded: chain H residue  208 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 107 optimal weight:    0.3980
   chunk 89 optimal weight:    5.9990
   chunk 42 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 60 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 93 optimal weight:    8.9990
   chunk 57 optimal weight:    0.0870
   chunk 69 optimal weight:    3.9990
   overall best weight:    1.0560

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

Flipped N/Q/H residues before XYZ refinement:
P 198 ASN
A  52 GLN
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 242 ASN
A 295 ASN
B   6 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 171 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.146414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.102630 restraints weight = 15819.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.61
r_work: 0.3017 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.4868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9592  Z= 0.119
  Angle     :  0.502   8.319  12995  Z= 0.262
  Chirality :  0.040   0.165   1457
  Planarity :  0.003   0.041   1649
  Dihedral  :  3.724  17.061   1290
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.51 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.25), residues: 1167
  helix:  3.16 (0.25), residues: 419
  sheet:  0.31 (0.29), residues: 283
  loop : -0.28 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  42 
 TYR   0.011   0.001   TYR H  59 
 PHE   0.015   0.001   PHE P 256 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.008   0.001   HIS P 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9588)
  covalent geometry    : angle       0.50204 (12987)
  SS BOND              : bond        0.00459 (    4)
  SS BOND              : angle       0.56742 (    8)
  hydrogen bonds       : bond        0.03566 (  468)
  hydrogen bonds       : angle       4.06210 ( 1337)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 161
  time to evaluate  : 0.379 
Fit side-chains
REVERT: P  178 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7354 (mm-30)
REVERT: P  252 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8417 (pt0)
REVERT: P  372 LYS cc_start: 0.7536 (mtpt) cc_final: 0.6638 (mmmt)
REVERT: A   44 SER cc_start: 0.8424 (t) cc_final: 0.8026 (p)
REVERT: A  261 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8590 (pp)
REVERT: A  277 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7375 (mt-10)
REVERT: A  278 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7883 (ptmt)
REVERT: A  295 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.7326 (t0)
REVERT: A  332 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7788 (mt)
REVERT: B  101 MET cc_start: 0.9378 (mtp) cc_final: 0.9130 (mtm)
REVERT: B  124 TYR cc_start: 0.9176 (m-80) cc_final: 0.8976 (m-80)
REVERT: B  130 GLU cc_start: 0.8457 (mp0) cc_final: 0.8214 (mp0)
REVERT: B  132 ASN cc_start: 0.7645 (t0) cc_final: 0.6999 (p0)
REVERT: B  150 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8418 (mmt90)
REVERT: B  197 ARG cc_start: 0.8047 (mmt180) cc_final: 0.7518 (mmm160)
REVERT: B  217 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7979 (pmt)
REVERT: B  280 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8645 (tmtm)
REVERT: H    6 GLU cc_start: 0.8524 (mp0) cc_final: 0.8284 (mt-10)
REVERT: H   80 PHE cc_start: 0.8576 (m-80) cc_final: 0.8079 (m-80)
REVERT: H   85 SER cc_start: 0.8646 (m) cc_final: 0.8216 (t)
REVERT: H  145 SER cc_start: 0.7313 (OUTLIER) cc_final: 0.6871 (p)
REVERT: H  160 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7402 (ttm-80)
REVERT: H  186 GLN cc_start: 0.8522 (tt0) cc_final: 0.8267 (pt0)
REVERT: H  201 ASP cc_start: 0.8242 (p0) cc_final: 0.7839 (t0)
  outliers start: 34
  outliers final: 20
  residues processed: 183
  average time/residue: 0.6158
  time to fit residues: 119.5740
Evaluate side-chains
  187 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 157
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  169 LEU
Chi-restraints excluded: chain P residue  178 GLU
Chi-restraints excluded: chain P residue  182 VAL
Chi-restraints excluded: chain P residue  197 THR
Chi-restraints excluded: chain P residue  219 THR
Chi-restraints excluded: chain P residue  252 GLU
Chi-restraints excluded: chain U residue    7 ILE
Chi-restraints excluded: chain U residue   10 THR
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  295 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  145 SER
Chi-restraints excluded: chain H residue  146 SER
Chi-restraints excluded: chain H residue  208 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 115 optimal weight:    0.0980
   chunk 57 optimal weight:    0.0000
   chunk 112 optimal weight:    2.9990
   chunk 108 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.7186

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

Flipped N/Q/H residues before XYZ refinement:
P 177 HIS
A  52 GLN
A 242 ASN
A 295 ASN
B  75 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 171 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.147279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.102819 restraints weight = 20454.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.91
r_work: 0.3026 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.4893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9592  Z= 0.101
  Angle     :  0.491  10.599  12995  Z= 0.254
  Chirality :  0.040   0.163   1457
  Planarity :  0.003   0.040   1649
  Dihedral  :  3.644  16.616   1290
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.10 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.25), residues: 1167
  helix:  3.21 (0.24), residues: 420
  sheet:  0.30 (0.29), residues: 281
  loop : -0.25 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  42 
 TYR   0.011   0.001   TYR B  59 
 PHE   0.015   0.001   PHE P 256 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.008   0.001   HIS P 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 9588)
  covalent geometry    : angle       0.49130 (12987)
  SS BOND              : bond        0.00389 (    4)
  SS BOND              : angle       0.47298 (    8)
  hydrogen bonds       : bond        0.03304 (  468)
  hydrogen bonds       : angle       4.00324 ( 1337)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 164
  time to evaluate  : 0.368 
Fit side-chains
REVERT: P  178 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7326 (mm-30)
REVERT: P  252 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8229 (pt0)
REVERT: P  372 LYS cc_start: 0.7461 (mtpt) cc_final: 0.6558 (mmmt)
REVERT: U   27 ARG cc_start: 0.8171 (tmm-80) cc_final: 0.7952 (tmm-80)
REVERT: A   44 SER cc_start: 0.8376 (t) cc_final: 0.8011 (p)
REVERT: A  261 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8572 (pp)
REVERT: A  277 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7357 (mt-10)
REVERT: A  278 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7885 (ptmt)
REVERT: A  295 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7480 (t0)
REVERT: A  332 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7710 (mt)
REVERT: B  101 MET cc_start: 0.9323 (mtp) cc_final: 0.9083 (mtm)
REVERT: B  124 TYR cc_start: 0.9089 (m-80) cc_final: 0.8877 (m-80)
REVERT: B  130 GLU cc_start: 0.8354 (mp0) cc_final: 0.8127 (mp0)
REVERT: B  132 ASN cc_start: 0.7551 (t0) cc_final: 0.7025 (p0)
REVERT: B  150 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8348 (mmt90)
REVERT: B  197 ARG cc_start: 0.7970 (mmt180) cc_final: 0.7465 (mmm160)
REVERT: B  217 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7854 (pmt)
REVERT: B  280 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8605 (tmtm)
REVERT: H    6 GLU cc_start: 0.8465 (mp0) cc_final: 0.8200 (mt-10)
REVERT: H   80 PHE cc_start: 0.8561 (m-80) cc_final: 0.8073 (m-80)
REVERT: H   85 SER cc_start: 0.8718 (m) cc_final: 0.8290 (t)
REVERT: H  145 SER cc_start: 0.7424 (OUTLIER) cc_final: 0.6988 (p)
REVERT: H  160 ARG cc_start: 0.7756 (ttp80) cc_final: 0.7372 (ttm-80)
REVERT: H  186 GLN cc_start: 0.8413 (tt0) cc_final: 0.8156 (pt0)
REVERT: H  201 ASP cc_start: 0.8161 (p0) cc_final: 0.7828 (t0)
  outliers start: 31
  outliers final: 19
  residues processed: 182
  average time/residue: 0.6364
  time to fit residues: 122.9558
Evaluate side-chains
  194 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  138 PHE
Chi-restraints excluded: chain P residue  169 LEU
Chi-restraints excluded: chain P residue  178 GLU
Chi-restraints excluded: chain P residue  182 VAL
Chi-restraints excluded: chain P residue  197 THR
Chi-restraints excluded: chain P residue  219 THR
Chi-restraints excluded: chain P residue  252 GLU
Chi-restraints excluded: chain U residue   10 THR
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  295 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  145 SER
Chi-restraints excluded: chain H residue  146 SER
Chi-restraints excluded: chain H residue  208 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 97 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 98 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0670
   chunk 95 optimal weight:    6.9990
   overall best weight:    2.4126

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

Flipped N/Q/H residues before XYZ refinement:
A 214 HIS
A 242 ASN
A 295 ASN
B  75 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 171 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.142998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.097979 restraints weight = 19387.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 2.86
r_work: 0.2992 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.5076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9592  Z= 0.210
  Angle     :  0.593  10.146  12995  Z= 0.306
  Chirality :  0.043   0.172   1457
  Planarity :  0.004   0.043   1649
  Dihedral  :  3.980  17.897   1290
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 18.59 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.25), residues: 1167
  helix:  2.93 (0.25), residues: 419
  sheet:  0.20 (0.29), residues: 288
  loop : -0.33 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 314 
 TYR   0.016   0.002   TYR H 175 
 PHE   0.029   0.002   PHE P 138 
 TRP   0.015   0.002   TRP H 111 
 HIS   0.008   0.002   HIS P 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 ( 9588)
  covalent geometry    : angle       0.59295 (12987)
  SS BOND              : bond        0.00740 (    4)
  SS BOND              : angle       0.81842 (    8)
  hydrogen bonds       : bond        0.04406 (  468)
  hydrogen bonds       : angle       4.26837 ( 1337)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 159
  time to evaluate  : 0.371 
Fit side-chains
REVERT: P  178 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7404 (mm-30)
REVERT: P  252 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8381 (pt0)
REVERT: P  372 LYS cc_start: 0.7591 (mtpt) cc_final: 0.6726 (mmmt)
REVERT: A   44 SER cc_start: 0.8548 (t) cc_final: 0.8121 (p)
REVERT: A  246 GLU cc_start: 0.8157 (tt0) cc_final: 0.7439 (tp30)
REVERT: A  261 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8591 (pp)
REVERT: A  278 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7870 (ptmt)
REVERT: A  295 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7396 (t0)
REVERT: B  130 GLU cc_start: 0.8511 (mp0) cc_final: 0.8161 (mp0)
REVERT: B  132 ASN cc_start: 0.7608 (t0) cc_final: 0.7086 (p0)
REVERT: B  150 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8442 (mmt90)
REVERT: B  217 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8033 (pmt)
REVERT: H    6 GLU cc_start: 0.8596 (mp0) cc_final: 0.8337 (mt-10)
REVERT: H   85 SER cc_start: 0.8660 (m) cc_final: 0.8232 (t)
REVERT: H  145 SER cc_start: 0.7373 (OUTLIER) cc_final: 0.6936 (p)
REVERT: H  160 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7444 (ttm-80)
REVERT: H  201 ASP cc_start: 0.8256 (p0) cc_final: 0.7836 (t0)
REVERT: H  206 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.7736 (t)
  outliers start: 30
  outliers final: 19
  residues processed: 178
  average time/residue: 0.5912
  time to fit residues: 112.0692
Evaluate side-chains
  185 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  169 LEU
Chi-restraints excluded: chain P residue  178 GLU
Chi-restraints excluded: chain P residue  182 VAL
Chi-restraints excluded: chain P residue  197 THR
Chi-restraints excluded: chain P residue  219 THR
Chi-restraints excluded: chain P residue  252 GLU
Chi-restraints excluded: chain U residue   10 THR
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  295 ASN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  145 SER
Chi-restraints excluded: chain H residue  146 SER
Chi-restraints excluded: chain H residue  206 SER
Chi-restraints excluded: chain H residue  208 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 101 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 HIS
A 242 ASN
A 295 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 171 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.145334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.100838 restraints weight = 20249.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.89
r_work: 0.3037 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2924
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2924
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.5061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9592  Z= 0.120
  Angle     :  0.518   9.802  12995  Z= 0.268
  Chirality :  0.040   0.164   1457
  Planarity :  0.003   0.041   1649
  Dihedral  :  3.812  17.487   1290
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 18.69 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.25), residues: 1167
  helix:  3.09 (0.24), residues: 419
  sheet:  0.26 (0.29), residues: 281
  loop : -0.35 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 197 
 TYR   0.012   0.001   TYR H  59 
 PHE   0.015   0.001   PHE P 256 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.008   0.001   HIS P 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9588)
  covalent geometry    : angle       0.51754 (12987)
  SS BOND              : bond        0.00437 (    4)
  SS BOND              : angle       0.48667 (    8)
  hydrogen bonds       : bond        0.03656 (  468)
  hydrogen bonds       : angle       4.16457 ( 1337)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5041.15 seconds
wall clock time: 86 minutes 9.20 seconds (5169.20 seconds total)