Starting phenix.real_space_refine
on Thu Mar 13 21:55:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ts0_26104/03_2025/7ts0_26104.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ts0_26104/03_2025/7ts0_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ts0_26104/03_2025/7ts0_26104.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ts0_26104/03_2025/7ts0_26104.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ts0_26104/03_2025/7ts0_26104.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ts0_26104/03_2025/7ts0_26104.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'TYR:plan': 1, 'GLU:plan': 2, '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: 6.24, per 1000 atoms: 0.67
  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: 2.07
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.03
  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: 2.58

  Time building geometry restraints manager: 2.49 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:             0.730
  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:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     23.670
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  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:12.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.420
-------------------------------------------------------------------------------
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   9588  Z= 0.232
  Angle     :  0.787   8.784  12987  Z= 0.456
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.023   0.002   TRP H 111 
 HIS   0.016   0.001   HIS H  35 
 PHE   0.025   0.003   PHE A 190 
 TYR   0.020   0.002   TYR H 175 
 ARG   0.006   0.000   ARG P 223 

*********************** 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  : 0.945 
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: 0.7949 (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: 1.1400
  time to fit residues: 365.8771
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  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 87 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0050
   chunk 30 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 90 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   overall best weight:    1.8000

-------------------------------------------------------------------------------
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 259 GLN
H 194 ASN
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.153291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.109723 restraints weight = 16262.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 2.68
r_work: 0.3153 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9588  Z= 0.295
  Angle     :  0.621   8.467  12987  Z= 0.328
  Chirality :  0.044   0.189   1457
  Planarity :  0.005   0.047   1649
  Dihedral  :  4.202  23.227   1290
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 12.13 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.24), residues: 1167
  helix:  2.00 (0.24), residues: 424
  sheet: -0.11 (0.28), residues: 291
  loop : -0.63 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP H 111 
 HIS   0.007   0.002   HIS B 142 
 PHE   0.020   0.002   PHE A 190 
 TYR   0.022   0.002   TYR A 231 
 ARG   0.006   0.001   ARG B  68 

*********************** 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
  245 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 197
  time to evaluate  : 0.951 
Fit side-chains
REVERT: P  205 GLU cc_start: 0.7858 (tp30) cc_final: 0.7604 (tt0)
REVERT: P  215 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6451 (tpt)
REVERT: P  365 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7463 (mt-10)
REVERT: P  372 LYS cc_start: 0.7788 (mtpt) cc_final: 0.6955 (mmtt)
REVERT: U   24 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7484 (tp40)
REVERT: A   44 SER cc_start: 0.8347 (t) cc_final: 0.7755 (m)
REVERT: A  229 SER cc_start: 0.8151 (t) cc_final: 0.7923 (m)
REVERT: A  298 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7514 (tp30)
REVERT: A  314 SER cc_start: 0.8458 (m) cc_final: 0.8128 (t)
REVERT: A  341 ASP cc_start: 0.8147 (m-30) cc_final: 0.7930 (m-30)
REVERT: B  150 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8451 (mmt90)
REVERT: G   20 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7874 (mtmm)
REVERT: H    6 GLU cc_start: 0.8053 (mp0) cc_final: 0.7789 (mp0)
REVERT: H   80 PHE cc_start: 0.8642 (m-80) cc_final: 0.8172 (m-80)
REVERT: H   85 SER cc_start: 0.8445 (m) cc_final: 0.8098 (t)
REVERT: H  160 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7579 (ttm-80)
REVERT: H  208 SER cc_start: 0.7606 (t) cc_final: 0.7376 (m)
  outliers start: 48
  outliers final: 16
  residues processed: 225
  average time/residue: 1.3088
  time to fit residues: 314.5530
Evaluate side-chains
  183 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 165
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
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  215 MET
Chi-restraints excluded: chain P residue  219 THR
Chi-restraints excluded: chain P residue  244 ILE
Chi-restraints excluded: chain P residue  303 ILE
Chi-restraints excluded: chain U residue    6 SER
Chi-restraints excluded: chain U residue   23 THR
Chi-restraints excluded: chain A residue  244 MET
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  250 CYS
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  210 THR
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 1 optimal weight:   20.0000
   chunk 33 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 109 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 89 optimal weight:    4.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.144575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.101275 restraints weight = 11815.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.31
r_work: 0.3037 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.4382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9588  Z= 0.339
  Angle     :  0.611   8.699  12987  Z= 0.322
  Chirality :  0.044   0.190   1457
  Planarity :  0.005   0.048   1649
  Dihedral  :  4.255  18.249   1290
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 14.29 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.24), residues: 1167
  helix:  2.35 (0.25), residues: 421
  sheet: -0.01 (0.28), residues: 284
  loop : -0.45 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP H 111 
 HIS   0.006   0.002   HIS B 183 
 PHE   0.016   0.002   PHE H 110 
 TYR   0.031   0.002   TYR H  94 
 ARG   0.003   0.001   ARG B 314 

*********************** 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
  212 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 163
  time to evaluate  : 0.995 
Fit side-chains
REVERT: P  175 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7719 (mm-30)
REVERT: P  178 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7419 (mm-30)
REVERT: P  215 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.6878 (tpt)
REVERT: P  372 LYS cc_start: 0.7632 (mtpt) cc_final: 0.6803 (mmtt)
REVERT: A  298 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7416 (tp30)
REVERT: B   46 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8104 (mtp-110)
REVERT: B  130 GLU cc_start: 0.8449 (mp0) cc_final: 0.8027 (mp0)
REVERT: B  150 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8375 (mmt90)
REVERT: G   46 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8342 (tppt)
REVERT: H   85 SER cc_start: 0.8737 (m) cc_final: 0.8322 (t)
REVERT: H  160 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7511 (ttm-80)
REVERT: H  201 ASP cc_start: 0.8342 (p0) cc_final: 0.7993 (t0)
  outliers start: 49
  outliers final: 23
  residues processed: 189
  average time/residue: 1.6142
  time to fit residues: 325.4251
Evaluate side-chains
  168 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 140
  time to evaluate  : 2.241 
-------------------------------------------------------------------------------
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  197 THR
Chi-restraints excluded: chain P residue  215 MET
Chi-restraints excluded: chain P residue  219 THR
Chi-restraints excluded: chain P residue  240 VAL
Chi-restraints excluded: chain P residue  244 ILE
Chi-restraints excluded: chain P residue  287 VAL
Chi-restraints excluded: chain U residue    6 SER
Chi-restraints excluded: chain U residue   10 THR
Chi-restraints excluded: chain U residue   23 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 B residue   46 ARG
Chi-restraints excluded: chain B residue   50 THR
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  213 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 79 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 8 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 114 optimal weight:    5.9990
   chunk 78 optimal weight:    4.9990
   chunk 111 optimal weight:    0.0020
   chunk 60 optimal weight:    0.8980
   chunk 101 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.8390

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.147074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.101671 restraints weight = 20610.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.98
r_work: 0.3048 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.4459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9588  Z= 0.161
  Angle     :  0.491   7.954  12987  Z= 0.261
  Chirality :  0.040   0.156   1457
  Planarity :  0.004   0.043   1649
  Dihedral  :  3.851  16.525   1290
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 16.83 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.25), residues: 1167
  helix:  2.97 (0.25), residues: 414
  sheet:  0.26 (0.29), residues: 280
  loop : -0.42 (0.29), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.004   0.001   HIS P 174 
 PHE   0.015   0.001   PHE P 256 
 TYR   0.022   0.001   TYR A 231 
 ARG   0.003   0.000   ARG B  42 

*********************** 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
  193 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 156
  time to evaluate  : 0.947 
Fit side-chains
REVERT: P  175 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7701 (mm-30)
REVERT: P  215 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.6640 (tpt)
REVERT: P  372 LYS cc_start: 0.7445 (mtpt) cc_final: 0.6562 (mmmt)
REVERT: A   44 SER cc_start: 0.8525 (t) cc_final: 0.8123 (p)
REVERT: A  277 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7011 (mt-10)
REVERT: A  278 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7894 (ptmt)
REVERT: A  298 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7281 (tp30)
REVERT: B   52 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8385 (ptp-170)
REVERT: B  101 MET cc_start: 0.9295 (mtp) cc_final: 0.9038 (mtm)
REVERT: B  130 GLU cc_start: 0.8193 (mp0) cc_final: 0.7686 (mp0)
REVERT: B  150 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8394 (mmt90)
REVERT: B  197 ARG cc_start: 0.8089 (mmt180) cc_final: 0.7770 (mmm160)
REVERT: B  234 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8860 (t80)
REVERT: G   46 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8280 (tppt)
REVERT: H   80 PHE cc_start: 0.8464 (m-80) cc_final: 0.7952 (m-80)
REVERT: H   85 SER cc_start: 0.8736 (m) cc_final: 0.8308 (t)
REVERT: H  160 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7215 (ttm-80)
REVERT: H  192 MET cc_start: 0.8598 (ptm) cc_final: 0.8295 (ppp)
REVERT: H  201 ASP cc_start: 0.8274 (p0) cc_final: 0.7899 (t0)
  outliers start: 37
  outliers final: 16
  residues processed: 179
  average time/residue: 1.2710
  time to fit residues: 243.4970
Evaluate side-chains
  168 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  165 MET
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  215 MET
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 A residue  278 LYS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  150 ARG
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  115 THR
Chi-restraints excluded: chain H residue  146 SER
Chi-restraints excluded: chain H residue  206 SER
Chi-restraints excluded: chain H residue  208 SER
Chi-restraints excluded: chain H residue  213 THR
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 22 optimal weight:    2.9990
   chunk 104 optimal weight:    8.9990
   chunk 46 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9980
   chunk 28 optimal weight:    8.9990
   chunk 111 optimal weight:    0.7980
   chunk 13 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0170
   overall best weight:    1.5622

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

Flipped N/Q/H residues before XYZ refinement:
P 120 ASN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 295 ASN
B  44 GLN
H 171 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.144327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.100897 restraints weight = 13430.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.44
r_work: 0.3027 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2873
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    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 = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2873
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.4721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9588  Z= 0.245
  Angle     :  0.537   8.315  12987  Z= 0.282
  Chirality :  0.041   0.153   1457
  Planarity :  0.004   0.042   1649
  Dihedral  :  3.970  17.734   1290
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 16.24 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.25), residues: 1167
  helix:  2.93 (0.25), residues: 415
  sheet:  0.30 (0.29), residues: 282
  loop : -0.38 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP H 111 
 HIS   0.004   0.001   HIS P 174 
 PHE   0.014   0.002   PHE P 256 
 TYR   0.021   0.002   TYR A 231 
 ARG   0.004   0.000   ARG B  42 

*********************** 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
  193 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 150
  time to evaluate  : 1.092 
Fit side-chains
REVERT: P  175 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7808 (mm-30)
REVERT: P  178 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7407 (mm-30)
REVERT: P  215 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.6968 (tpt)
REVERT: P  372 LYS cc_start: 0.7753 (mtpt) cc_final: 0.6849 (mmmt)
REVERT: A   44 SER cc_start: 0.8605 (t) cc_final: 0.8195 (p)
REVERT: A  261 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8589 (pp)
REVERT: A  273 ASP cc_start: 0.7763 (p0) cc_final: 0.7470 (p0)
REVERT: A  277 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7093 (mt-10)
REVERT: A  278 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7924 (ptmt)
REVERT: A  298 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7394 (tp30)
REVERT: A  332 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7871 (mt)
REVERT: B  130 GLU cc_start: 0.8435 (mp0) cc_final: 0.8015 (mp0)
REVERT: B  132 ASN cc_start: 0.7741 (t0) cc_final: 0.7009 (p0)
REVERT: B  150 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8412 (mmt90)
REVERT: B  280 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8681 (tmtm)
REVERT: G   46 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8334 (tppt)
REVERT: H   85 SER cc_start: 0.8784 (m) cc_final: 0.8342 (t)
REVERT: H  145 SER cc_start: 0.7334 (OUTLIER) cc_final: 0.7016 (t)
REVERT: H  160 ARG cc_start: 0.7793 (ttp80) cc_final: 0.7322 (ttm-80)
REVERT: H  192 MET cc_start: 0.8738 (ptm) cc_final: 0.8452 (ppp)
REVERT: H  201 ASP cc_start: 0.8314 (p0) cc_final: 0.7945 (t0)
REVERT: H  206 SER cc_start: 0.8197 (OUTLIER) cc_final: 0.7753 (t)
  outliers start: 43
  outliers final: 21
  residues processed: 180
  average time/residue: 1.3024
  time to fit residues: 250.4996
Evaluate side-chains
  172 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 141
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  165 MET
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  215 MET
Chi-restraints excluded: chain P residue  219 THR
Chi-restraints excluded: chain P residue  240 VAL
Chi-restraints excluded: chain P residue  263 LEU
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  332 ILE
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   54 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  116 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 91 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   chunk 76 optimal weight:    6.9990
   chunk 98 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
P 152 HIS
P 170 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 189 HIS
A 242 ASN
A 295 ASN
B   6 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.145372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.100533 restraints weight = 20295.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.93
r_work: 0.3021 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2883
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    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 = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.4807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9588  Z= 0.190
  Angle     :  0.507   8.560  12987  Z= 0.264
  Chirality :  0.040   0.151   1457
  Planarity :  0.004   0.040   1649
  Dihedral  :  3.843  17.516   1290
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 17.12 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.25), residues: 1167
  helix:  3.09 (0.25), residues: 414
  sheet:  0.33 (0.29), residues: 281
  loop : -0.40 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS P 174 
 PHE   0.015   0.001   PHE P 256 
 TYR   0.021   0.001   TYR A 231 
 ARG   0.003   0.000   ARG B 197 

*********************** 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
  187 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 148
  time to evaluate  : 1.014 
Fit side-chains
REVERT: P  175 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7773 (mm-30)
REVERT: P  215 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.6927 (tpt)
REVERT: P  250 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7497 (pt0)
REVERT: P  372 LYS cc_start: 0.7683 (mtpt) cc_final: 0.6777 (mmmt)
REVERT: A   44 SER cc_start: 0.8541 (t) cc_final: 0.8082 (p)
REVERT: A  195 LEU cc_start: 0.8156 (mt) cc_final: 0.7952 (mt)
REVERT: A  261 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8501 (pp)
REVERT: A  273 ASP cc_start: 0.7740 (p0) cc_final: 0.7441 (p0)
REVERT: A  277 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7098 (mt-10)
REVERT: A  278 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7846 (ptmt)
REVERT: A  295 ASN cc_start: 0.7534 (OUTLIER) cc_final: 0.7259 (t0)
REVERT: A  298 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7299 (tp30)
REVERT: A  332 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7793 (mt)
REVERT: B   46 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8056 (mtp180)
REVERT: B   52 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8556 (ptp-170)
REVERT: B  101 MET cc_start: 0.9403 (mtp) cc_final: 0.9135 (mtm)
REVERT: B  130 GLU cc_start: 0.8407 (mp0) cc_final: 0.8025 (mp0)
REVERT: B  132 ASN cc_start: 0.7717 (t0) cc_final: 0.6901 (p0)
REVERT: B  150 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8459 (mmt90)
REVERT: B  197 ARG cc_start: 0.8153 (mmt180) cc_final: 0.7701 (mmm160)
REVERT: B  280 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8602 (tmtm)
REVERT: G   46 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8296 (tppt)
REVERT: H   85 SER cc_start: 0.8782 (m) cc_final: 0.8339 (t)
REVERT: H  145 SER cc_start: 0.7156 (OUTLIER) cc_final: 0.6834 (t)
REVERT: H  160 ARG cc_start: 0.7757 (ttp80) cc_final: 0.7210 (ttm-80)
REVERT: H  192 MET cc_start: 0.8711 (ptm) cc_final: 0.8433 (ppp)
REVERT: H  201 ASP cc_start: 0.8262 (p0) cc_final: 0.7862 (t0)
REVERT: H  206 SER cc_start: 0.8285 (OUTLIER) cc_final: 0.7813 (t)
  outliers start: 39
  outliers final: 19
  residues processed: 172
  average time/residue: 1.2402
  time to fit residues: 227.5759
Evaluate side-chains
  175 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 143
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  165 MET
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  215 MET
Chi-restraints excluded: chain P residue  219 THR
Chi-restraints excluded: chain P residue  240 VAL
Chi-restraints excluded: chain P residue  250 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   46 ARG
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  280 LYS
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  116 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 107 optimal weight:    6.9990
   chunk 37 optimal weight:    0.0670
   chunk 8 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 109 optimal weight:    0.2980
   chunk 2 optimal weight:    4.9990
   chunk 92 optimal weight:    0.6980
   overall best weight:    0.5920

-------------------------------------------------------------------------------
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
B  44 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.146958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.102324 restraints weight = 20589.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.92
r_work: 0.3029 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    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 = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.4806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9588  Z= 0.134
  Angle     :  0.477   8.222  12987  Z= 0.249
  Chirality :  0.039   0.151   1457
  Planarity :  0.003   0.040   1649
  Dihedral  :  3.677  16.765   1290
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.30 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.25), residues: 1167
  helix:  3.15 (0.25), residues: 417
  sheet:  0.31 (0.29), residues: 280
  loop : -0.34 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.003   0.001   HIS P 174 
 PHE   0.016   0.001   PHE P 256 
 TYR   0.022   0.001   TYR A 231 
 ARG   0.003   0.000   ARG B  42 

*********************** 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
  186 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 155
  time to evaluate  : 1.031 
Fit side-chains
REVERT: P  175 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7700 (mm-30)
REVERT: P  215 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.6873 (tpt)
REVERT: P  250 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7263 (pt0)
REVERT: P  372 LYS cc_start: 0.7563 (mtpt) cc_final: 0.6658 (mmmt)
REVERT: A   44 SER cc_start: 0.8409 (t) cc_final: 0.8034 (p)
REVERT: A  273 ASP cc_start: 0.7730 (p0) cc_final: 0.7422 (p0)
REVERT: A  277 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7033 (mt-10)
REVERT: A  278 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7863 (ptmt)
REVERT: A  295 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.7251 (t0)
REVERT: A  298 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7285 (tp30)
REVERT: A  332 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7674 (mt)
REVERT: B   46 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7819 (mtp180)
REVERT: B  130 GLU cc_start: 0.8301 (mp0) cc_final: 0.8030 (mp0)
REVERT: B  132 ASN cc_start: 0.7615 (t0) cc_final: 0.6967 (p0)
REVERT: B  197 ARG cc_start: 0.8095 (mmt180) cc_final: 0.7701 (mmm160)
REVERT: B  280 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8582 (tmtm)
REVERT: G   46 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8252 (tppt)
REVERT: H   80 PHE cc_start: 0.8533 (m-80) cc_final: 0.8067 (m-80)
REVERT: H   85 SER cc_start: 0.8720 (m) cc_final: 0.8330 (t)
REVERT: H  145 SER cc_start: 0.7257 (t) cc_final: 0.6948 (t)
REVERT: H  160 ARG cc_start: 0.7822 (ttp80) cc_final: 0.7228 (ttm-80)
REVERT: H  186 GLN cc_start: 0.8351 (tt0) cc_final: 0.7990 (pt0)
REVERT: H  192 MET cc_start: 0.8638 (ptm) cc_final: 0.8355 (ppp)
REVERT: H  201 ASP cc_start: 0.8141 (p0) cc_final: 0.7815 (t0)
  outliers start: 31
  outliers final: 15
  residues processed: 175
  average time/residue: 1.3010
  time to fit residues: 242.5299
Evaluate side-chains
  171 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  165 MET
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  215 MET
Chi-restraints excluded: chain P residue  240 VAL
Chi-restraints excluded: chain P residue  250 GLU
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   46 ARG
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   46 LYS
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  116 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 16 optimal weight:    0.6980
   chunk 86 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 113 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 93 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
P 177 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 = 0.3713 r_free = 0.3713 target = 0.144275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.100877 restraints weight = 13673.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 2.44
r_work: 0.3041 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.4985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   9588  Z= 0.235
  Angle     :  0.528   8.349  12987  Z= 0.275
  Chirality :  0.041   0.159   1457
  Planarity :  0.004   0.042   1649
  Dihedral  :  3.886  18.136   1290
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 18.20 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.25), residues: 1167
  helix:  3.09 (0.25), residues: 415
  sheet:  0.27 (0.29), residues: 283
  loop : -0.31 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.016   0.001   PHE P 256 
 TYR   0.022   0.002   TYR A 231 
 ARG   0.003   0.000   ARG B 197 

*********************** 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
  188 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 152
  time to evaluate  : 0.941 
Fit side-chains
REVERT: P  109 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.4860 (p90)
REVERT: P  175 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7747 (mm-30)
REVERT: P  178 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7410 (mm-30)
REVERT: P  215 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7053 (tpt)
REVERT: P  250 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7486 (pt0)
REVERT: P  372 LYS cc_start: 0.7651 (mtpt) cc_final: 0.6755 (mmmt)
REVERT: A  198 ARG cc_start: 0.8655 (mtp180) cc_final: 0.8326 (mtm-85)
REVERT: A  246 GLU cc_start: 0.8107 (tt0) cc_final: 0.7402 (tp30)
REVERT: A  261 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8498 (pp)
REVERT: A  277 GLU cc_start: 0.7771 (mt-10) cc_final: 0.6989 (mt-10)
REVERT: A  278 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7846 (ptmt)
REVERT: A  298 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7289 (tp30)
REVERT: A  332 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7837 (mt)
REVERT: B   46 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8000 (mtp180)
REVERT: B  124 TYR cc_start: 0.9133 (m-80) cc_final: 0.8923 (m-80)
REVERT: B  130 GLU cc_start: 0.8392 (mp0) cc_final: 0.8153 (mp0)
REVERT: B  132 ASN cc_start: 0.7673 (t0) cc_final: 0.6990 (p0)
REVERT: B  150 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8374 (mmt90)
REVERT: B  197 ARG cc_start: 0.8172 (mmt180) cc_final: 0.7704 (mmm160)
REVERT: G   46 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8243 (tppt)
REVERT: H   85 SER cc_start: 0.8639 (m) cc_final: 0.8253 (t)
REVERT: H  145 SER cc_start: 0.7236 (OUTLIER) cc_final: 0.6924 (t)
REVERT: H  160 ARG cc_start: 0.7786 (ttp80) cc_final: 0.7240 (ttm-80)
REVERT: H  186 GLN cc_start: 0.8439 (tt0) cc_final: 0.8155 (pt0)
REVERT: H  192 MET cc_start: 0.8781 (ptm) cc_final: 0.8420 (ppp)
REVERT: H  201 ASP cc_start: 0.8230 (p0) cc_final: 0.7823 (t0)
  outliers start: 36
  outliers final: 19
  residues processed: 174
  average time/residue: 1.5240
  time to fit residues: 282.0679
Evaluate side-chains
  173 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 143
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  109 TYR
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  215 MET
Chi-restraints excluded: chain P residue  240 VAL
Chi-restraints excluded: chain P residue  250 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  332 ILE
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   42 GLU
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  116 THR
Chi-restraints excluded: chain H residue  145 SER
Chi-restraints excluded: chain H residue  146 SER
Chi-restraints excluded: chain H residue  158 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 107 optimal weight:    8.9990
   chunk 95 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.9588

-------------------------------------------------------------------------------
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 ** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.145760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.101202 restraints weight = 18983.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.83
r_work: 0.3017 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2903
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2903
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.4986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9588  Z= 0.169
  Angle     :  0.497   8.387  12987  Z= 0.258
  Chirality :  0.040   0.155   1457
  Planarity :  0.003   0.040   1649
  Dihedral  :  3.742  17.737   1290
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.20 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.25), residues: 1167
  helix:  3.20 (0.25), residues: 417
  sheet:  0.28 (0.29), residues: 280
  loop : -0.30 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS P 174 
 PHE   0.016   0.001   PHE P 256 
 TYR   0.011   0.001   TYR H  59 
 ARG   0.002   0.000   ARG B  42 

*********************** 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
  186 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 152
  time to evaluate  : 0.981 
Fit side-chains
REVERT: P  215 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7040 (tpt)
REVERT: P  250 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7520 (pt0)
REVERT: P  372 LYS cc_start: 0.7772 (mtpt) cc_final: 0.6867 (mmmt)
REVERT: U   27 ARG cc_start: 0.8127 (tmm-80) cc_final: 0.7909 (tmm-80)
REVERT: A   44 SER cc_start: 0.8537 (t) cc_final: 0.8086 (p)
REVERT: A  198 ARG cc_start: 0.8703 (mtp180) cc_final: 0.8385 (mtm-85)
REVERT: A  261 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8526 (pp)
REVERT: A  277 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7514 (mt-10)
REVERT: A  278 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7866 (ptmt)
REVERT: A  295 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7382 (t0)
REVERT: A  298 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7255 (tp30)
REVERT: A  332 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7795 (mt)
REVERT: B   46 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8106 (mtp180)
REVERT: B  124 TYR cc_start: 0.9179 (m-80) cc_final: 0.8954 (m-80)
REVERT: B  130 GLU cc_start: 0.8481 (mp0) cc_final: 0.8279 (mp0)
REVERT: B  132 ASN cc_start: 0.7737 (t0) cc_final: 0.7101 (p0)
REVERT: B  150 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8431 (mmt90)
REVERT: B  197 ARG cc_start: 0.8195 (mmt180) cc_final: 0.7732 (mmm160)
REVERT: G   46 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8255 (tppt)
REVERT: H   80 PHE cc_start: 0.8625 (m-80) cc_final: 0.8187 (m-80)
REVERT: H   85 SER cc_start: 0.8609 (m) cc_final: 0.8246 (t)
REVERT: H  145 SER cc_start: 0.7236 (OUTLIER) cc_final: 0.6915 (t)
REVERT: H  160 ARG cc_start: 0.7814 (ttp80) cc_final: 0.7282 (ttm-80)
REVERT: H  186 GLN cc_start: 0.8497 (tt0) cc_final: 0.8263 (pt0)
REVERT: H  192 MET cc_start: 0.8741 (ptm) cc_final: 0.8433 (ppp)
  outliers start: 34
  outliers final: 20
  residues processed: 171
  average time/residue: 1.3090
  time to fit residues: 240.9355
Evaluate side-chains
  179 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 149
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
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  215 MET
Chi-restraints excluded: chain P residue  219 THR
Chi-restraints excluded: chain P residue  240 VAL
Chi-restraints excluded: chain P residue  250 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   46 ARG
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   46 LYS
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  116 THR
Chi-restraints excluded: chain H residue  145 SER
Chi-restraints excluded: chain H residue  146 SER
Chi-restraints excluded: chain H residue  158 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 45 optimal weight:    0.1980
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0980
   chunk 12 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 27 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 101 optimal weight:    0.0980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 194 ASN
A 242 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 171 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.146140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.102919 restraints weight = 14194.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.46
r_work: 0.3038 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2920
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2920 r_free = 0.2920    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2920 r_free = 0.2920    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2920
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.4999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   9588  Z= 0.155
  Angle     :  0.496   8.344  12987  Z= 0.256
  Chirality :  0.040   0.153   1457
  Planarity :  0.003   0.040   1649
  Dihedral  :  3.706  17.537   1290
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.59 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.25), residues: 1167
  helix:  3.28 (0.24), residues: 415
  sheet:  0.28 (0.29), residues: 283
  loop : -0.26 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.005   0.001   HIS P 174 
 PHE   0.016   0.001   PHE P 256 
 TYR   0.011   0.001   TYR H  59 
 ARG   0.002   0.000   ARG B  42 

********************** 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
  183 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 152
  time to evaluate  : 1.044 
Fit side-chains
REVERT: P  215 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.6994 (tpt)
REVERT: P  250 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7418 (pt0)
REVERT: P  372 LYS cc_start: 0.7713 (mtpt) cc_final: 0.6808 (mmmt)
REVERT: U   27 ARG cc_start: 0.8140 (tmm-80) cc_final: 0.7923 (tmm-80)
REVERT: A  198 ARG cc_start: 0.8663 (mtp180) cc_final: 0.8341 (mtm-85)
REVERT: A  261 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8563 (pp)
REVERT: A  277 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7496 (mt-10)
REVERT: A  278 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7915 (ptmt)
REVERT: A  298 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7255 (tp30)
REVERT: A  332 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7749 (mt)
REVERT: B   46 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8041 (mtp180)
REVERT: B  124 TYR cc_start: 0.9153 (m-80) cc_final: 0.8924 (m-80)
REVERT: B  130 GLU cc_start: 0.8435 (mp0) cc_final: 0.8227 (mp0)
REVERT: B  132 ASN cc_start: 0.7701 (t0) cc_final: 0.7080 (p0)
REVERT: B  150 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8401 (mmt90)
REVERT: B  197 ARG cc_start: 0.8160 (mmt180) cc_final: 0.7684 (mmm160)
REVERT: G   46 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8238 (tppt)
REVERT: H   80 PHE cc_start: 0.8600 (m-80) cc_final: 0.8111 (m-80)
REVERT: H   85 SER cc_start: 0.8621 (m) cc_final: 0.8266 (t)
REVERT: H  145 SER cc_start: 0.7192 (OUTLIER) cc_final: 0.6864 (t)
REVERT: H  160 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7256 (ttm-80)
REVERT: H  186 GLN cc_start: 0.8459 (tt0) cc_final: 0.8199 (pt0)
REVERT: H  192 MET cc_start: 0.8709 (ptm) cc_final: 0.8408 (ppp)
REVERT: H  201 ASP cc_start: 0.8216 (p0) cc_final: 0.7816 (t0)
  outliers start: 31
  outliers final: 20
  residues processed: 171
  average time/residue: 1.2629
  time to fit residues: 230.4919
Evaluate side-chains
  179 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
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  215 MET
Chi-restraints excluded: chain P residue  219 THR
Chi-restraints excluded: chain P residue  240 VAL
Chi-restraints excluded: chain P residue  250 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  332 ILE
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   42 GLU
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  116 THR
Chi-restraints excluded: chain H residue  145 SER
Chi-restraints excluded: chain H residue  146 SER
Chi-restraints excluded: chain H residue  158 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 57 optimal weight:    0.4980
   chunk 6 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0270
   chunk 32 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   chunk 109 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.6640

-------------------------------------------------------------------------------
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 242 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 171 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.147178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.104497 restraints weight = 13723.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 2.40
r_work: 0.3083 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2943
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2943
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.5004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9588  Z= 0.143
  Angle     :  0.481   8.276  12987  Z= 0.252
  Chirality :  0.039   0.151   1457
  Planarity :  0.003   0.040   1649
  Dihedral  :  3.618  17.162   1290
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.08 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.25), residues: 1167
  helix:  3.34 (0.24), residues: 415
  sheet:  0.31 (0.29), residues: 280
  loop : -0.24 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.008   0.001   HIS P 174 
 PHE   0.016   0.001   PHE P 256 
 TYR   0.010   0.001   TYR H  59 
 ARG   0.003   0.000   ARG B  42 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10743.26 seconds
wall clock time: 187 minutes 27.58 seconds (11247.58 seconds total)