Starting phenix.real_space_refine
on Thu Feb 13 18:45:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ts0_26104/02_2025/7ts0_26104.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ts0_26104/02_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_26104/02_2025/7ts0_26104.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ts0_26104/02_2025/7ts0_26104.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ts0_26104/02_2025/7ts0_26104.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ts0_26104/02_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-5592/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: 6.36, per 1000 atoms: 0.68
  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: 2.42
  Conformation dependent library (CDL) restraints added in 1.3 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: 1.13
  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: 2.91

  Time building geometry restraints manager: 2.80 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:             0.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.210
  Find NCS groups from input model:        0.110
  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:14.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.340
-------------------------------------------------------------------------------
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  : 1.036 
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: 1.1026
  time to fit residues: 353.8683
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  : 1.030 
-------------------------------------------------------------------------------
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 = 0.153292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.109692 restraints weight = 16263.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.70
r_work: 0.3151 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    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 = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9588  Z= 0.295
  Angle     :  0.620   8.463  12987  Z= 0.328
  Chirality :  0.044   0.189   1457
  Planarity :  0.005   0.047   1649
  Dihedral  :  4.202  23.229   1290
  Min Nonbonded Distance : 2.567

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 : -0.64 (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  : 1.013 
Fit side-chains
REVERT: P  205 GLU cc_start: 0.7871 (tp30) cc_final: 0.7618 (tt0)
REVERT: P  215 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6483 (tpt)
REVERT: P  365 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7492 (mt-10)
REVERT: P  372 LYS cc_start: 0.7845 (mtpt) cc_final: 0.7019 (mmtt)
REVERT: U   24 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7511 (tp40)
REVERT: A   44 SER cc_start: 0.8347 (t) cc_final: 0.7767 (m)
REVERT: A  229 SER cc_start: 0.8159 (t) cc_final: 0.7944 (m)
REVERT: A  298 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7542 (tp30)
REVERT: A  314 SER cc_start: 0.8476 (m) cc_final: 0.8156 (t)
REVERT: A  341 ASP cc_start: 0.8164 (m-30) cc_final: 0.7952 (m-30)
REVERT: B  150 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8457 (mmt90)
REVERT: G   20 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7910 (mtmm)
REVERT: H    6 GLU cc_start: 0.8057 (mp0) cc_final: 0.7799 (mp0)
REVERT: H   80 PHE cc_start: 0.8663 (m-80) cc_final: 0.8197 (m-80)
REVERT: H   85 SER cc_start: 0.8446 (m) cc_final: 0.8108 (t)
REVERT: H  160 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7611 (ttm-80)
REVERT: H  208 SER cc_start: 0.7624 (t) cc_final: 0.7398 (m)
  outliers start: 48
  outliers final: 16
  residues processed: 225
  average time/residue: 1.2711
  time to fit residues: 304.7679
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  : 0.964 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0060
   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:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 89 optimal weight:    5.9990
   overall best weight:    1.1200

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

Flipped N/Q/H residues before XYZ refinement:
P 198 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.149684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.106635 restraints weight = 11798.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.34
r_work: 0.3098 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2996
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2996
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9588  Z= 0.193
  Angle     :  0.525   8.302  12987  Z= 0.276
  Chirality :  0.041   0.151   1457
  Planarity :  0.004   0.043   1649
  Dihedral  :  3.868  16.570   1290
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 15.66 %
    Favored  : 80.72 %
  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:  1.22 (0.25), residues: 1167
  helix:  2.63 (0.25), residues: 424
  sheet:  0.11 (0.29), residues: 277
  loop : -0.43 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP H 111 
 HIS   0.004   0.001   HIS P 174 
 PHE   0.012   0.001   PHE P 343 
 TYR   0.026   0.002   TYR A 231 
 ARG   0.004   0.000   ARG B  42 

*********************** 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
  196 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 159
  time to evaluate  : 1.007 
Fit side-chains
REVERT: P  175 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7706 (mm-30)
REVERT: P  215 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.6623 (tpt)
REVERT: P  372 LYS cc_start: 0.7616 (mtpt) cc_final: 0.6747 (mmtt)
REVERT: U   24 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7440 (tp40)
REVERT: A   44 SER cc_start: 0.8498 (t) cc_final: 0.8058 (p)
REVERT: A  298 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7490 (tp30)
REVERT: B  130 GLU cc_start: 0.8500 (mp0) cc_final: 0.7976 (mp0)
REVERT: B  150 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8413 (mmt90)
REVERT: B  333 ASP cc_start: 0.8664 (p0) cc_final: 0.8435 (p0)
REVERT: G   46 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8313 (tppt)
REVERT: H    6 GLU cc_start: 0.7950 (mp0) cc_final: 0.7701 (mp0)
REVERT: H   80 PHE cc_start: 0.8553 (m-80) cc_final: 0.8109 (m-80)
REVERT: H   85 SER cc_start: 0.8622 (m) cc_final: 0.8245 (t)
REVERT: H  160 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7406 (ttm110)
REVERT: H  192 MET cc_start: 0.8711 (ptm) cc_final: 0.8426 (ppp)
REVERT: H  201 ASP cc_start: 0.8357 (p0) cc_final: 0.8073 (t0)
  outliers start: 37
  outliers final: 15
  residues processed: 181
  average time/residue: 1.2337
  time to fit residues: 238.5038
Evaluate side-chains
  167 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  169 LEU
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  287 VAL
Chi-restraints excluded: chain U residue   10 THR
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  146 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 79 optimal weight:    0.0970
   chunk 64 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 69 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 114 optimal weight:    3.9990
   chunk 78 optimal weight:    6.9990
   chunk 111 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 101 optimal weight:    0.5980
   chunk 87 optimal weight:    3.9990
   overall best weight:    1.5182

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

Flipped N/Q/H residues before XYZ refinement:
H 171 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.146317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.100940 restraints weight = 18910.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 2.86
r_work: 0.3038 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2922
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2922 r_free = 0.2922    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 = 0.2922 r_free = 0.2922    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2922
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.4388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9588  Z= 0.239
  Angle     :  0.533   8.282  12987  Z= 0.282
  Chirality :  0.041   0.150   1457
  Planarity :  0.004   0.042   1649
  Dihedral  :  3.940  17.325   1290
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 15.75 %
    Favored  : 80.23 %
  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:  1.46 (0.25), residues: 1167
  helix:  2.94 (0.25), residues: 415
  sheet:  0.26 (0.29), residues: 282
  loop : -0.36 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP H 111 
 HIS   0.005   0.001   HIS P 174 
 PHE   0.013   0.002   PHE A 190 
 TYR   0.028   0.002   TYR H  94 
 ARG   0.003   0.000   ARG B 197 

*********************** 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
  201 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 160
  time to evaluate  : 1.255 
Fit side-chains
REVERT: P  175 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7740 (mm-30)
REVERT: P  215 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.6663 (tpt)
REVERT: P  372 LYS cc_start: 0.7521 (mtpt) cc_final: 0.6645 (mmmt)
REVERT: U   24 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7435 (tp40)
REVERT: A   44 SER cc_start: 0.8609 (t) cc_final: 0.8196 (p)
REVERT: A  261 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8487 (pp)
REVERT: A  278 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7881 (ptmt)
REVERT: A  298 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7413 (tp30)
REVERT: B   46 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8047 (mtp-110)
REVERT: B  101 MET cc_start: 0.9398 (mtp) cc_final: 0.9152 (mtm)
REVERT: B  130 GLU cc_start: 0.8330 (mp0) cc_final: 0.7830 (mp0)
REVERT: B  150 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8434 (mmt90)
REVERT: B  197 ARG cc_start: 0.8040 (mmt180) cc_final: 0.7696 (mmm160)
REVERT: B  217 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7942 (pmt)
REVERT: B  234 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8915 (t80)
REVERT: G   46 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8328 (tppt)
REVERT: H   80 PHE cc_start: 0.8533 (m-80) cc_final: 0.8052 (m-80)
REVERT: H   85 SER cc_start: 0.8651 (m) cc_final: 0.8192 (t)
REVERT: H  160 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7416 (ttm-80)
REVERT: H  192 MET cc_start: 0.8810 (ptm) cc_final: 0.8484 (ppp)
REVERT: H  201 ASP cc_start: 0.8354 (p0) cc_final: 0.7957 (t0)
  outliers start: 41
  outliers final: 22
  residues processed: 185
  average time/residue: 1.2692
  time to fit residues: 250.9013
Evaluate side-chains
  174 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
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  244 ILE
Chi-restraints excluded: chain P residue  287 VAL
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 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  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   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  206 SER
Chi-restraints excluded: chain H residue  208 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 104 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 111 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 39 optimal weight:    0.2980
   overall best weight:    1.4588

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 189 HIS
A 295 ASN
B  44 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.145528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.101744 restraints weight = 13922.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.48
r_work: 0.3035 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.4584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9588  Z= 0.227
  Angle     :  0.520   8.332  12987  Z= 0.273
  Chirality :  0.041   0.152   1457
  Planarity :  0.004   0.042   1649
  Dihedral  :  3.892  17.330   1290
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 16.05 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.55 (0.25), residues: 1167
  helix:  3.02 (0.25), residues: 414
  sheet:  0.30 (0.29), residues: 288
  loop : -0.32 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS P 174 
 PHE   0.014   0.001   PHE P 256 
 TYR   0.028   0.002   TYR H  94 
 ARG   0.003   0.000   ARG B 197 

*********************** 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
  198 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 156
  time to evaluate  : 1.008 
Fit side-chains
REVERT: P  175 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7774 (mm-30)
REVERT: P  178 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7402 (mm-30)
REVERT: P  215 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.6758 (tpt)
REVERT: P  250 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7388 (pt0)
REVERT: P  372 LYS cc_start: 0.7581 (mtpt) cc_final: 0.6686 (mmmt)
REVERT: U   24 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7381 (tp40)
REVERT: A   44 SER cc_start: 0.8626 (t) cc_final: 0.8221 (p)
REVERT: A  198 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7029 (mtm-85)
REVERT: A  261 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8523 (pp)
REVERT: A  278 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7797 (ptmt)
REVERT: A  284 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8012 (tt)
REVERT: A  298 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7336 (tp30)
REVERT: B   46 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8024 (mtp180)
REVERT: B  130 GLU cc_start: 0.8405 (mp0) cc_final: 0.8049 (mp0)
REVERT: B  132 ASN cc_start: 0.7692 (t0) cc_final: 0.6957 (p0)
REVERT: B  150 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8457 (mmt90)
REVERT: B  197 ARG cc_start: 0.8052 (mmt180) cc_final: 0.7627 (mmm160)
REVERT: B  217 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8006 (pmt)
REVERT: B  280 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8669 (tmtm)
REVERT: G   46 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8301 (tppt)
REVERT: H   80 PHE cc_start: 0.8621 (m-80) cc_final: 0.8112 (m-80)
REVERT: H   85 SER cc_start: 0.8677 (m) cc_final: 0.8220 (t)
REVERT: H  160 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7336 (ttm-80)
REVERT: H  192 MET cc_start: 0.8725 (ptm) cc_final: 0.8464 (ppp)
REVERT: H  201 ASP cc_start: 0.8344 (p0) cc_final: 0.7950 (t0)
  outliers start: 42
  outliers final: 25
  residues processed: 183
  average time/residue: 1.3139
  time to fit residues: 256.4344
Evaluate side-chains
  181 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 144
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
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  250 GLU
Chi-restraints excluded: chain U residue    7 ILE
Chi-restraints excluded: chain U residue   10 THR
Chi-restraints excluded: chain U residue   23 THR
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  198 ARG
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  284 LEU
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  217 MET
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   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  208 SER
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0970
   chunk 43 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9980
   chunk 76 optimal weight:    6.9990
   chunk 98 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
P 152 HIS
P 177 HIS
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 242 ASN
A 295 ASN
B   6 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.146060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.101025 restraints weight = 20292.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 2.92
r_work: 0.3011 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.4734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9588  Z= 0.192
  Angle     :  0.491   8.302  12987  Z= 0.260
  Chirality :  0.040   0.148   1457
  Planarity :  0.004   0.040   1649
  Dihedral  :  3.769  16.880   1290
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 15.75 %
    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:  1.63 (0.25), residues: 1167
  helix:  3.10 (0.25), residues: 416
  sheet:  0.37 (0.29), residues: 282
  loop : -0.32 (0.29), residues: 469

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   0.025   0.001   TYR H  94 
 ARG   0.002   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
  201 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 153
  time to evaluate  : 0.969 
Fit side-chains
REVERT: P  175 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7707 (mm-30)
REVERT: P  215 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.6946 (tpt)
REVERT: P  250 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7282 (pt0)
REVERT: P  252 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8319 (pt0)
REVERT: P  372 LYS cc_start: 0.7463 (mtpt) cc_final: 0.6560 (mmmt)
REVERT: U   24 GLN cc_start: 0.7577 (tm-30) cc_final: 0.7355 (tp40)
REVERT: A   44 SER cc_start: 0.8517 (t) cc_final: 0.8117 (p)
REVERT: A  198 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.6736 (mtm-85)
REVERT: A  261 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8499 (pp)
REVERT: A  278 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7752 (ptmt)
REVERT: A  298 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7312 (tp30)
REVERT: A  332 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7745 (mt)
REVERT: B   46 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7826 (mtp180)
REVERT: B  130 GLU cc_start: 0.8299 (mp0) cc_final: 0.8009 (mp0)
REVERT: B  132 ASN cc_start: 0.7590 (t0) cc_final: 0.6922 (p0)
REVERT: B  150 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8394 (mmt90)
REVERT: B  197 ARG cc_start: 0.8002 (mmt180) cc_final: 0.7550 (mmm160)
REVERT: B  217 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7872 (pmt)
REVERT: B  280 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8587 (tmtm)
REVERT: G   46 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8260 (tppt)
REVERT: H   80 PHE cc_start: 0.8579 (m-80) cc_final: 0.8073 (m-80)
REVERT: H   85 SER cc_start: 0.8774 (m) cc_final: 0.8320 (t)
REVERT: H  145 SER cc_start: 0.7313 (OUTLIER) cc_final: 0.6889 (p)
REVERT: H  160 ARG cc_start: 0.7740 (ttp80) cc_final: 0.7252 (ttm-80)
REVERT: H  192 MET cc_start: 0.8600 (ptm) cc_final: 0.8333 (ppp)
REVERT: H  201 ASP cc_start: 0.8166 (p0) cc_final: 0.7833 (t0)
REVERT: H  206 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.7788 (t)
  outliers start: 48
  outliers final: 22
  residues processed: 186
  average time/residue: 1.2671
  time to fit residues: 251.6281
Evaluate side-chains
  182 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 146
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
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 P residue  252 GLU
Chi-restraints excluded: chain U residue    7 ILE
Chi-restraints excluded: chain U residue   10 THR
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  198 ARG
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   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  217 MET
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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 107 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 92 optimal weight:    0.2980
   overall best weight:    2.0386

-------------------------------------------------------------------------------
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 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 242 ASN
A 295 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.143259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.098845 restraints weight = 17421.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 2.70
r_work: 0.2978 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2851
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2851
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.4992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9588  Z= 0.298
  Angle     :  0.560   8.354  12987  Z= 0.292
  Chirality :  0.042   0.154   1457
  Planarity :  0.004   0.043   1649
  Dihedral  :  4.032  18.136   1290
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 16.34 %
    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:  1.48 (0.25), residues: 1167
  helix:  2.94 (0.25), residues: 417
  sheet:  0.21 (0.29), residues: 287
  loop : -0.31 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP H 111 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.015   0.002   PHE P 256 
 TYR   0.035   0.002   TYR H  94 
 ARG   0.003   0.000   ARG B 314 

*********************** 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
  197 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 150
  time to evaluate  : 1.010 
Fit side-chains
REVERT: P  175 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7774 (mm-30)
REVERT: P  178 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7414 (mm-30)
REVERT: P  215 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7047 (tpt)
REVERT: P  250 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7572 (pt0)
REVERT: P  372 LYS cc_start: 0.7542 (mtpt) cc_final: 0.6690 (mmmt)
REVERT: A   44 SER cc_start: 0.8578 (t) cc_final: 0.8162 (p)
REVERT: A  198 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7128 (mtm-85)
REVERT: A  246 GLU cc_start: 0.8185 (tt0) cc_final: 0.7478 (tp30)
REVERT: A  261 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8548 (pp)
REVERT: A  278 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7726 (ptmt)
REVERT: A  295 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7399 (t0)
REVERT: A  298 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7338 (tp30)
REVERT: A  332 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7895 (mt)
REVERT: B   46 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8067 (mtp180)
REVERT: B  130 GLU cc_start: 0.8438 (mp0) cc_final: 0.8168 (mp0)
REVERT: B  132 ASN cc_start: 0.7692 (t0) cc_final: 0.7023 (p0)
REVERT: B  150 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8407 (mmt90)
REVERT: B  217 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7996 (pmt)
REVERT: B  226 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8061 (mt-10)
REVERT: G   46 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8288 (tppt)
REVERT: H   85 SER cc_start: 0.8722 (m) cc_final: 0.8256 (t)
REVERT: H  145 SER cc_start: 0.7355 (OUTLIER) cc_final: 0.6932 (p)
REVERT: H  160 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7310 (ttm-80)
REVERT: H  192 MET cc_start: 0.8733 (ptm) cc_final: 0.8399 (ppp)
REVERT: H  201 ASP cc_start: 0.8253 (p0) cc_final: 0.7829 (t0)
REVERT: H  206 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.7811 (t)
  outliers start: 47
  outliers final: 25
  residues processed: 178
  average time/residue: 1.3388
  time to fit residues: 253.7030
Evaluate side-chains
  181 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 141
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  169 LEU
Chi-restraints excluded: chain P residue  178 GLU
Chi-restraints excluded: chain P residue  182 VAL
Chi-restraints excluded: chain P residue  197 THR
Chi-restraints excluded: chain P residue  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 P residue  263 LEU
Chi-restraints excluded: chain U residue   10 THR
Chi-restraints excluded: chain U residue   23 THR
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  198 ARG
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  150 ARG
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
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
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 16 optimal weight:    0.1980
   chunk 86 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 113 optimal weight:    8.9990
   chunk 39 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 93 optimal weight:    0.0060
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
P 170 GLN
P 198 ASN
** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 242 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.146875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.104200 restraints weight = 13891.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.43
r_work: 0.3081 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2960
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.4915

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= 0.137
  Angle     :  0.490   8.589  12987  Z= 0.254
  Chirality :  0.039   0.143   1457
  Planarity :  0.003   0.040   1649
  Dihedral  :  3.703  17.096   1290
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 17.91 %
    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:  1.64 (0.25), residues: 1167
  helix:  3.18 (0.25), residues: 417
  sheet:  0.31 (0.29), residues: 274
  loop : -0.35 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.003   0.001   HIS P 174 
 PHE   0.015   0.001   PHE P 256 
 TYR   0.018   0.001   TYR H  94 
 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
  185 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 154
  time to evaluate  : 1.032 
Fit side-chains
REVERT: P  109 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.4664 (p90)
REVERT: P  175 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7740 (mm-30)
REVERT: P  215 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.6912 (tpt)
REVERT: P  250 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7479 (pt0)
REVERT: P  372 LYS cc_start: 0.7587 (mtpt) cc_final: 0.6706 (mmmt)
REVERT: A   44 SER cc_start: 0.8518 (t) cc_final: 0.8128 (p)
REVERT: A  198 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.6902 (mtm-85)
REVERT: A  278 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7900 (ptmt)
REVERT: A  298 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7319 (tp30)
REVERT: A  332 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7732 (mt)
REVERT: B   46 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8004 (mtp180)
REVERT: B  132 ASN cc_start: 0.7627 (t0) cc_final: 0.7061 (p0)
REVERT: B  150 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8399 (mmt90)
REVERT: B  197 ARG cc_start: 0.8103 (mmt180) cc_final: 0.7661 (mmm160)
REVERT: G   46 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8270 (tppt)
REVERT: H   80 PHE cc_start: 0.8617 (m-80) cc_final: 0.8146 (m-80)
REVERT: H   85 SER cc_start: 0.8640 (m) cc_final: 0.8207 (t)
REVERT: H  145 SER cc_start: 0.7337 (t) cc_final: 0.6921 (p)
REVERT: H  160 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7300 (ttm-80)
REVERT: H  186 GLN cc_start: 0.8413 (tt0) cc_final: 0.8091 (pt0)
REVERT: H  192 MET cc_start: 0.8675 (ptm) cc_final: 0.8392 (ppp)
REVERT: H  201 ASP cc_start: 0.8228 (p0) cc_final: 0.7892 (t0)
  outliers start: 31
  outliers final: 14
  residues processed: 173
  average time/residue: 1.3649
  time to fit residues: 251.0316
Evaluate side-chains
  168 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 145
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  109 TYR
Chi-restraints excluded: chain P residue  138 PHE
Chi-restraints excluded: chain P residue  165 MET
Chi-restraints excluded: chain P residue  169 LEU
Chi-restraints excluded: chain P residue  197 THR
Chi-restraints excluded: chain P residue  215 MET
Chi-restraints excluded: chain P residue  250 GLU
Chi-restraints excluded: chain A residue  198 ARG
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
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  146 SER
Chi-restraints excluded: chain H residue  208 SER
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 107 optimal weight:    9.9990
   chunk 95 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 1 optimal weight:    9.9990
   chunk 91 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 189 HIS
A 242 ASN
A 295 ASN
B  44 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.146623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.102433 restraints weight = 19041.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 2.82
r_work: 0.3047 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2924
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2924
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.4940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051   9588  Z= 0.156
  Angle     :  0.496   8.738  12987  Z= 0.258
  Chirality :  0.040   0.146   1457
  Planarity :  0.003   0.040   1649
  Dihedral  :  3.714  17.199   1290
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.18 %
    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:  1.66 (0.25), residues: 1167
  helix:  3.22 (0.25), residues: 417
  sheet:  0.28 (0.29), residues: 276
  loop : -0.32 (0.29), residues: 474

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   0.016   0.001   PHE P 256 
 TYR   0.021   0.001   TYR H  94 
 ARG   0.003   0.000   ARG B 197 

*********************** 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
  173 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 1.006 
Fit side-chains
REVERT: P  175 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7713 (mm-30)
REVERT: P  215 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.6919 (tpt)
REVERT: P  250 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7515 (pt0)
REVERT: P  252 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8416 (pt0)
REVERT: P  372 LYS cc_start: 0.7569 (mtpt) cc_final: 0.6694 (mmmt)
REVERT: U   27 ARG cc_start: 0.8116 (tmm-80) cc_final: 0.7887 (tmm-80)
REVERT: A   44 SER cc_start: 0.8526 (t) cc_final: 0.8091 (p)
REVERT: A  198 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.6954 (mtm-85)
REVERT: A  278 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7863 (ptmt)
REVERT: A  295 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7568 (t0)
REVERT: A  298 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7303 (tp30)
REVERT: A  332 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7699 (mt)
REVERT: B   46 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8049 (mtp180)
REVERT: B  130 GLU cc_start: 0.8455 (mp0) cc_final: 0.8174 (mp0)
REVERT: B  132 ASN cc_start: 0.7649 (t0) cc_final: 0.7025 (p0)
REVERT: B  150 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8403 (mmt90)
REVERT: B  197 ARG cc_start: 0.8105 (mmt180) cc_final: 0.7652 (mmm160)
REVERT: G   46 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8232 (tppt)
REVERT: H   80 PHE cc_start: 0.8597 (m-80) cc_final: 0.8099 (m-80)
REVERT: H   85 SER cc_start: 0.8572 (m) cc_final: 0.8167 (t)
REVERT: H  145 SER cc_start: 0.7268 (t) cc_final: 0.6860 (p)
REVERT: H  160 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7317 (ttm-80)
REVERT: H  186 GLN cc_start: 0.8471 (tt0) cc_final: 0.8178 (pt0)
REVERT: H  192 MET cc_start: 0.8657 (ptm) cc_final: 0.8385 (ppp)
REVERT: H  201 ASP cc_start: 0.8260 (p0) cc_final: 0.7890 (t0)
  outliers start: 24
  outliers final: 13
  residues processed: 163
  average time/residue: 1.4044
  time to fit residues: 243.7714
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  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  169 LEU
Chi-restraints excluded: chain P residue  197 THR
Chi-restraints excluded: chain P residue  215 MET
Chi-restraints excluded: chain P residue  250 GLU
Chi-restraints excluded: chain P residue  252 GLU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  198 ARG
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  150 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
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  146 SER
Chi-restraints excluded: chain H residue  208 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 23 optimal weight:    0.1980
   chunk 27 optimal weight:    8.9990
   chunk 54 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 101 optimal weight:    6.9990
   overall best weight:    2.0386

-------------------------------------------------------------------------------
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 ** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.143408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.100479 restraints weight = 12796.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.34
r_work: 0.3039 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2927
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2927
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.5096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   9588  Z= 0.296
  Angle     :  0.569   8.942  12987  Z= 0.296
  Chirality :  0.042   0.153   1457
  Planarity :  0.004   0.043   1649
  Dihedral  :  3.971  18.304   1290
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.18 %
    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:  1.52 (0.25), residues: 1167
  helix:  2.99 (0.25), residues: 419
  sheet:  0.19 (0.29), residues: 288
  loop : -0.30 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H 111 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.015   0.002   PHE P 256 
 TYR   0.035   0.002   TYR H  94 
 ARG   0.003   0.000   ARG B 197 

********************** 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
  173 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.985 
Fit side-chains
REVERT: P  109 TYR cc_start: 0.6471 (OUTLIER) cc_final: 0.4950 (p90)
REVERT: P  175 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7697 (mm-30)
REVERT: P  215 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7037 (tpt)
REVERT: P  250 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7491 (pt0)
REVERT: P  252 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8419 (pt0)
REVERT: P  372 LYS cc_start: 0.7489 (mtpt) cc_final: 0.6635 (mmmt)
REVERT: U   27 ARG cc_start: 0.8082 (tmm-80) cc_final: 0.7858 (tmm-80)
REVERT: A   44 SER cc_start: 0.8562 (t) cc_final: 0.8120 (p)
REVERT: A  198 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7081 (mtm-85)
REVERT: A  246 GLU cc_start: 0.8132 (tt0) cc_final: 0.7447 (tp30)
REVERT: A  278 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7811 (ptmt)
REVERT: A  298 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7254 (tp30)
REVERT: B   46 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7988 (mtp180)
REVERT: B  130 GLU cc_start: 0.8367 (mp0) cc_final: 0.8165 (mp0)
REVERT: B  132 ASN cc_start: 0.7604 (t0) cc_final: 0.7081 (p0)
REVERT: B  150 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8396 (mmt90)
REVERT: G   46 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8261 (tppt)
REVERT: H   85 SER cc_start: 0.8659 (m) cc_final: 0.8208 (t)
REVERT: H  145 SER cc_start: 0.7354 (t) cc_final: 0.6938 (p)
REVERT: H  160 ARG cc_start: 0.7849 (ttp80) cc_final: 0.7326 (ttm-80)
REVERT: H  186 GLN cc_start: 0.8472 (tt0) cc_final: 0.8225 (pt0)
REVERT: H  192 MET cc_start: 0.8713 (ptm) cc_final: 0.8408 (ppp)
  outliers start: 26
  outliers final: 15
  residues processed: 161
  average time/residue: 1.3949
  time to fit residues: 238.3521
Evaluate side-chains
  168 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
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  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 P residue  252 GLU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  198 ARG
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain B residue   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   46 LYS
Chi-restraints excluded: chain G residue   54 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 57 optimal weight:    0.0870
   chunk 6 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0570
   overall best weight:    0.5076

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

Flipped N/Q/H residues before XYZ refinement:
P 177 HIS
P 198 ASN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 189 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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.147360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.104685 restraints weight = 13748.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.43
r_work: 0.3081 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2967
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2967
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.5003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   9588  Z= 0.136
  Angle     :  0.490   8.895  12987  Z= 0.254
  Chirality :  0.040   0.148   1457
  Planarity :  0.003   0.040   1649
  Dihedral  :  3.724  17.729   1290
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 19.57 %
    Favored  : 78.18 %
  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:  1.68 (0.25), residues: 1167
  helix:  3.25 (0.25), residues: 417
  sheet:  0.27 (0.29), residues: 280
  loop : -0.33 (0.30), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 189 
 PHE   0.015   0.001   PHE P 256 
 TYR   0.017   0.001   TYR H  94 
 ARG   0.002   0.000   ARG B  42 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10141.81 seconds
wall clock time: 178 minutes 54.94 seconds (10734.94 seconds total)