Starting phenix.real_space_refine
on Tue Mar  3 20:33:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hk3_34843/03_2026/8hk3_34843.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hk3_34843/03_2026/8hk3_34843.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hk3_34843/03_2026/8hk3_34843.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hk3_34843/03_2026/8hk3_34843.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hk3_34843/03_2026/8hk3_34843.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hk3_34843/03_2026/8hk3_34843.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.033
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      69      5.16       5
     C    5585      2.51       5
     N    1488      2.21       5
     O    1604      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8746
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1801
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 220}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2561
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "C"
      Number of atoms: 2244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2244
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 15, 'TRANS': 268}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 404
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "H"
      Number of atoms: 1736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1736
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 32
  Time building chain proxies: 2.04, per 1000 atoms: 0.23
  Number of scatterers: 8746
  At special positions: 0
  Unit cell: (105.04, 115.44, 131.04, 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      69     16.00
     O    1604      8.00
     N    1488      7.00
     C    5585      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  95 " - pdb=" SG  CYS C 172 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 237.6 milliseconds
  

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2120

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      39.2% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 31
      removed outlier: 4.111A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 54
      removed outlier: 3.976A  pdb=" N   LYS A  46 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.661A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.020A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.855A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.597A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 3.552A  pdb=" N   LEU B   7 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.876A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 51
      removed outlier: 4.223A  pdb=" N   LEU C  38 " --> pdb=" O   PHE C  34 " (cutoff:3.500A)
      Proline residue:  C  39  - end of helix
    Processing helix  chain 'C' and resid 55 through 84
      Proline residue:  C  76  - end of helix
    Processing helix  chain 'C' and resid 91 through 126
      removed outlier: 4.043A  pdb=" N   CYS C  95 " --> pdb=" O   GLY C  91 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LYS C  96 " --> pdb=" O   ARG C  92 " (cutoff:3.500A)
      Proline residue:  C  99  - end of helix
      removed outlier: 3.772A  pdb=" N   VAL C 124 " --> pdb=" O   ARG C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 134
      removed outlier: 3.602A  pdb=" N   ASN C 132 " --> pdb=" O   ILE C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 161
      Proline residue:  C 156  - end of helix
    Processing helix  chain 'C' and resid 331 through 365
      removed outlier: 5.709A  pdb=" N   LEU C 347 " --> pdb=" O   VAL C 343 " (cutoff:3.500A)
      Proline residue:  C 348  - end of helix
    Processing helix  chain 'C' and resid 372 through 403
      removed outlier: 3.855A  pdb=" N   PHE C 376 " --> pdb=" O   GLN C 372 " (cutoff:3.500A)
      Proline residue:  C 392  - end of helix
      removed outlier: 3.552A  pdb=" N   LEU C 401 " --> pdb=" O   GLY C 397 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU C 402 " --> pdb=" O   VAL C 398 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 407 through 431
      removed outlier: 3.623A  pdb=" N   LYS C 411 " --> pdb=" O   THR C 407 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   HIS C 418 " --> pdb=" O   MET C 414 " (cutoff:3.500A)
      removed outlier: 5.434A  pdb=" N   VAL C 419 " --> pdb=" O   SER C 415 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   CYS C 420 " --> pdb=" O   TRP C 416 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE C 421 " --> pdb=" O   ASP C 417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 432 through 434
      No H-bonds generated for 'chain 'C' and resid 432 through 434'
    Processing helix  chain 'C' and resid 439 through 454
      removed outlier: 3.516A  pdb=" N   ARG C 443 " --> pdb=" O   GLY C 439 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LYS C 444 " --> pdb=" O   LYS C 440 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 23
      removed outlier: 3.704A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 220 through 224
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.510A  pdb=" N   ASP A 200 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR A 187 " --> pdb=" O   MET A 198 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.198A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.924A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.465A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
      removed outlier: 4.192A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.672A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.856A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.527A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ASN B 125 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.849A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.554A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.470A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.036A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.548A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 162 through 165
    Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.643A  pdb=" N   VAL H   5 " --> pdb=" O   SER H  23 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 7.107A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   TYR H  59 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 142
    Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148
      removed outlier: 3.587A  pdb=" N   GLU H 246 " --> pdb=" O   VAL H 147 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   GLY H 225 " --> pdb=" O   LEU H 245 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ILE H 189 " --> pdb=" O   TRP H 176 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LEU H 178 " --> pdb=" O   LEU H 187 " (cutoff:3.500A)
      removed outlier: 5.756A  pdb=" N   LEU H 187 " --> pdb=" O   LEU H 178 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ASN H 194 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)

    427 hydrogen bonds defined for protein.
    1194 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: 0.93

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1408
        1.31 -     1.43: 2456
        1.43 -     1.56: 4973
        1.56 -     1.69: 0
        1.69 -     1.81: 98
  Bond restraints: 8935
  Sorted by residual:
  bond pdb=" C   LEU C  32 "
       pdb=" O   LEU C  32 "
    ideal  model  delta    sigma   weight residual
    1.236  1.183  0.054 1.26e-02 6.30e+03 1.82e+01
  bond pdb=" C   PHE C 345 "
       pdb=" O   PHE C 345 "
    ideal  model  delta    sigma   weight residual
    1.237  1.185  0.052 1.36e-02 5.41e+03 1.46e+01
  bond pdb=" C   LEU C  38 "
       pdb=" O   LEU C  38 "
    ideal  model  delta    sigma   weight residual
    1.241  1.206  0.036 9.80e-03 1.04e+04 1.33e+01
  bond pdb=" CA  GLN C 372 "
       pdb=" C   GLN C 372 "
    ideal  model  delta    sigma   weight residual
    1.527  1.497  0.030 1.30e-02 5.92e+03 5.32e+00
  bond pdb=" C   THR C  33 "
       pdb=" O   THR C  33 "
    ideal  model  delta    sigma   weight residual
    1.237  1.211  0.025 1.16e-02 7.43e+03 4.76e+00
  ... (remaining 8930 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 12061
        2.45 -     4.90: 55
        4.90 -     7.34: 4
        7.34 -     9.79: 0
        9.79 -    12.24: 1
  Bond angle restraints: 12121
  Sorted by residual:
  angle pdb=" N   GLY C  91 "
        pdb=" CA  GLY C  91 "
        pdb=" C   GLY C  91 "
      ideal   model   delta    sigma   weight residual
     112.83  119.62   -6.79 1.70e+00 3.46e-01 1.60e+01
  angle pdb=" CA  LEU C  35 "
        pdb=" CB  LEU C  35 "
        pdb=" CG  LEU C  35 "
      ideal   model   delta    sigma   weight residual
     116.30  128.54  -12.24 3.50e+00 8.16e-02 1.22e+01
  angle pdb=" CA  GLN C 372 "
        pdb=" CB  GLN C 372 "
        pdb=" CG  GLN C 372 "
      ideal   model   delta    sigma   weight residual
     114.10  120.87   -6.77 2.00e+00 2.50e-01 1.15e+01
  angle pdb=" N   ARG C  92 "
        pdb=" CA  ARG C  92 "
        pdb=" C   ARG C  92 "
      ideal   model   delta    sigma   weight residual
     111.69  115.66   -3.97 1.23e+00 6.61e-01 1.04e+01
  angle pdb=" C   LEU C  38 "
        pdb=" N   PRO C  39 "
        pdb=" CA  PRO C  39 "
      ideal   model   delta    sigma   weight residual
     118.97  115.99    2.98 1.04e+00 9.25e-01 8.22e+00
  ... (remaining 12116 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.97: 5192
       15.97 -    31.94: 67
       31.94 -    47.92: 15
       47.92 -    63.89: 2
       63.89 -    79.86: 2
  Dihedral angle restraints: 5278
    sinusoidal: 1996
      harmonic: 3282
  Sorted by residual:
  dihedral pdb=" N   GLN C 372 "
           pdb=" C   GLN C 372 "
           pdb=" CA  GLN C 372 "
           pdb=" CB  GLN C 372 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.22   -8.42     0      2.50e+00 1.60e-01 1.13e+01
  dihedral pdb=" N   LEU C  38 "
           pdb=" C   LEU C  38 "
           pdb=" CA  LEU C  38 "
           pdb=" CB  LEU C  38 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.89   -8.09     0      2.50e+00 1.60e-01 1.05e+01
  dihedral pdb=" C   GLN C 372 "
           pdb=" N   GLN C 372 "
           pdb=" CA  GLN C 372 "
           pdb=" CB  GLN C 372 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.23    7.63     0      2.50e+00 1.60e-01 9.32e+00
  ... (remaining 5275 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1278
       0.073 -    0.147: 107
       0.147 -    0.220: 0
       0.220 -    0.293: 2
       0.293 -    0.367: 3
  Chirality restraints: 1390
  Sorted by residual:
  chirality pdb=" CA  LEU C  38 "
            pdb=" N   LEU C  38 "
            pdb=" C   LEU C  38 "
            pdb=" CB  LEU C  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.36e+00
  chirality pdb=" CA  GLN C 372 "
            pdb=" N   GLN C 372 "
            pdb=" C   GLN C 372 "
            pdb=" CB  GLN C 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CG  LEU C  38 "
            pdb=" CB  LEU C  38 "
            pdb=" CD1 LEU C  38 "
            pdb=" CD2 LEU C  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.24   -0.35 2.00e-01 2.50e+01 3.01e+00
  ... (remaining 1387 not shown)

  Planarity restraints: 1528
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C  90 "    0.017 2.00e-02 2.50e+03   3.41e-02 1.16e+01
        pdb=" C   TYR C  90 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   TYR C  90 "    0.022 2.00e-02 2.50e+03
        pdb=" N   GLY C  91 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C  31 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.82e+00
        pdb=" C   SER C  31 "    0.045 2.00e-02 2.50e+03
        pdb=" O   SER C  31 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LEU C  32 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 345 "   -0.008 2.00e-02 2.50e+03   1.69e-02 2.86e+00
        pdb=" C   PHE C 345 "    0.029 2.00e-02 2.50e+03
        pdb=" O   PHE C 345 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU C 346 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1525 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 82
        2.63 -     3.20: 8136
        3.20 -     3.77: 12881
        3.77 -     4.33: 18184
        4.33 -     4.90: 30718
  Nonbonded interactions: 70001
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.069 3.040
  nonbonded pdb=" OG1 THR C  55 "
            pdb=" OG1 THR C  58 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" OD1 ASP A 251 "
            pdb=" ND2 ASN A 255 "
     model   vdw
     2.181 3.120
  nonbonded pdb=" OH  TYR A 320 "
            pdb=" OD2 ASP A 341 "
     model   vdw
     2.197 3.040
  ... (remaining 69996 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.480
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     8.420
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   10.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
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      :  0.002   0.054   8936  Z= 0.150
  Angle     :  0.421  12.240  12123  Z= 0.233
  Chirality :  0.042   0.367   1390
  Planarity :  0.002   0.034   1528
  Dihedral  :  6.311  79.860   3155
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.81 %
    Favored  : 98.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.24), residues: 1119
  helix:  0.65 (0.26), residues: 397
  sheet: -1.05 (0.28), residues: 287
  loop : -1.56 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.003   0.000   TYR H 190 
 PHE   0.008   0.001   PHE C  34 
 TRP   0.003   0.000   TRP B  99 
 HIS   0.001   0.000   HIS C 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 8935)
  covalent geometry    : angle       0.42085 (12121)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       0.84684 (    2)
  hydrogen bonds       : bond        0.19944 (  427)
  hydrogen bonds       : angle       6.49706 ( 1194)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 280
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 LEU cc_start: 0.7685 (mt) cc_final: 0.7460 (mp)
REVERT: A  197 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7081 (mtpp)
REVERT: B   61 MET cc_start: 0.6755 (ppp) cc_final: 0.6376 (ppp)
REVERT: B  102 THR cc_start: 0.7984 (t) cc_final: 0.7770 (t)
REVERT: B  170 ASP cc_start: 0.6201 (t70) cc_final: 0.5998 (t0)
REVERT: B  246 ASP cc_start: 0.7460 (m-30) cc_final: 0.7216 (m-30)
REVERT: B  277 SER cc_start: 0.8547 (t) cc_final: 0.8102 (m)
REVERT: C  138 MET cc_start: 0.6859 (ttp) cc_final: 0.6429 (ttp)
REVERT: C  141 SER cc_start: 0.7926 (t) cc_final: 0.7724 (p)
REVERT: C  156 PRO cc_start: 0.7669 (Cg_exo) cc_final: 0.7437 (Cg_endo)
REVERT: C  399 LEU cc_start: 0.7811 (mp) cc_final: 0.7580 (mt)
REVERT: H  161 SER cc_start: 0.8318 (t) cc_final: 0.8116 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 281
  average time/residue: 0.0935
  time to fit residues: 35.7608
Evaluate side-chains
  229 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 228
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:    0.8980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B  75 GLN
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 ASN
B 220 GLN
B 295 ASN
C  63 HIS
H 179 GLN
H 194 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.130411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.111922 restraints weight = 12277.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 1.97
r_work: 0.3258 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8936  Z= 0.202
  Angle     :  0.606   8.880  12123  Z= 0.310
  Chirality :  0.045   0.162   1390
  Planarity :  0.005   0.043   1528
  Dihedral  :  4.286  57.667   1218
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  8.73 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.25), residues: 1119
  helix:  1.57 (0.27), residues: 404
  sheet: -0.48 (0.29), residues: 280
  loop : -1.42 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  49 
 TYR   0.023   0.003   TYR H 102 
 PHE   0.030   0.002   PHE B 199 
 TRP   0.021   0.002   TRP B 339 
 HIS   0.009   0.002   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 8935)
  covalent geometry    : angle       0.60580 (12121)
  SS BOND              : bond        0.00578 (    1)
  SS BOND              : angle       1.05668 (    2)
  hydrogen bonds       : bond        0.04298 (  427)
  hydrogen bonds       : angle       4.61968 ( 1194)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 234
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7780 (tp30) cc_final: 0.7494 (tp30)
REVERT: A  197 LYS cc_start: 0.8192 (mtpp) cc_final: 0.7967 (mtpt)
REVERT: A  240 MET cc_start: 0.4589 (mmm) cc_final: 0.4385 (mmm)
REVERT: B   14 LEU cc_start: 0.8027 (mm) cc_final: 0.7792 (mt)
REVERT: B   46 ARG cc_start: 0.7850 (mtp-110) cc_final: 0.7548 (mtp-110)
REVERT: B   50 THR cc_start: 0.8438 (m) cc_final: 0.8194 (t)
REVERT: B  119 ASN cc_start: 0.7928 (m-40) cc_final: 0.7636 (m-40)
REVERT: B  155 ASN cc_start: 0.7859 (t0) cc_final: 0.7491 (t0)
REVERT: B  170 ASP cc_start: 0.7404 (t70) cc_final: 0.6941 (t0)
REVERT: B  220 GLN cc_start: 0.8289 (mt0) cc_final: 0.7660 (mt0)
REVERT: B  254 ASP cc_start: 0.7762 (t70) cc_final: 0.7540 (t0)
REVERT: B  290 ASP cc_start: 0.7692 (m-30) cc_final: 0.7483 (m-30)
REVERT: B  304 ARG cc_start: 0.8061 (mtp-110) cc_final: 0.7380 (ttm-80)
REVERT: C  395 ILE cc_start: 0.8416 (mm) cc_final: 0.8173 (mt)
REVERT: C  399 LEU cc_start: 0.8144 (mp) cc_final: 0.7882 (mt)
REVERT: H  119 VAL cc_start: 0.7771 (t) cc_final: 0.7390 (p)
REVERT: H  161 SER cc_start: 0.8411 (t) cc_final: 0.8202 (p)
  outliers start: 14
  outliers final: 12
  residues processed: 241
  average time/residue: 0.0778
  time to fit residues: 26.5875
Evaluate side-chains
  222 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 210
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue  339 THR
Chi-restraints excluded: chain C residue  380 VAL
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 94 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  32 GLN
B  75 GLN
B 110 ASN
C 133 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.127784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.109406 restraints weight = 12137.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.96
r_work: 0.3220 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.3767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   8936  Z= 0.194
  Angle     :  0.550   8.755  12123  Z= 0.284
  Chirality :  0.043   0.152   1390
  Planarity :  0.004   0.045   1528
  Dihedral  :  4.295  59.309   1218
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 10.76 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.25), residues: 1119
  helix:  1.73 (0.26), residues: 409
  sheet: -0.16 (0.29), residues: 289
  loop : -1.19 (0.28), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  19 
 TYR   0.017   0.002   TYR H  95 
 PHE   0.022   0.002   PHE B 199 
 TRP   0.013   0.002   TRP B 339 
 HIS   0.007   0.002   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 8935)
  covalent geometry    : angle       0.54999 (12121)
  SS BOND              : bond        0.00375 (    1)
  SS BOND              : angle       0.52732 (    2)
  hydrogen bonds       : bond        0.04119 (  427)
  hydrogen bonds       : angle       4.48298 ( 1194)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 206
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7837 (tp30) cc_final: 0.7543 (tp30)
REVERT: A   29 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7863 (ttmm)
REVERT: A  225 VAL cc_start: 0.8688 (p) cc_final: 0.8358 (m)
REVERT: A  240 MET cc_start: 0.4599 (mmm) cc_final: 0.4270 (mmm)
REVERT: B   46 ARG cc_start: 0.7877 (mtp-110) cc_final: 0.7555 (mtp-110)
REVERT: B  155 ASN cc_start: 0.8030 (t0) cc_final: 0.7623 (t0)
REVERT: B  170 ASP cc_start: 0.7464 (t70) cc_final: 0.7039 (t0)
REVERT: B  234 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8402 (m-80)
REVERT: C  340 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7476 (ttp-170)
REVERT: C  391 THR cc_start: 0.8497 (m) cc_final: 0.8271 (m)
REVERT: C  399 LEU cc_start: 0.8161 (mp) cc_final: 0.7929 (mt)
REVERT: C  414 MET cc_start: 0.7990 (mtp) cc_final: 0.7501 (mpp)
REVERT: G   27 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.8055 (mtt-85)
REVERT: H  119 VAL cc_start: 0.7909 (t) cc_final: 0.7491 (p)
REVERT: H  161 SER cc_start: 0.8394 (t) cc_final: 0.8177 (p)
  outliers start: 18
  outliers final: 11
  residues processed: 214
  average time/residue: 0.1030
  time to fit residues: 29.5055
Evaluate side-chains
  211 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 199
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   25 LEU
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  339 THR
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 77 optimal weight:    0.2980
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 109 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 87 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 237 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.128182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.109558 restraints weight = 12216.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.00
r_work: 0.3212 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8936  Z= 0.136
  Angle     :  0.498   7.471  12123  Z= 0.258
  Chirality :  0.041   0.152   1390
  Planarity :  0.004   0.044   1528
  Dihedral  :  4.169  59.496   1218
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.93 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.25), residues: 1119
  helix:  1.90 (0.26), residues: 413
  sheet: -0.10 (0.29), residues: 290
  loop : -0.98 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  38 
 TYR   0.014   0.001   TYR H  95 
 PHE   0.020   0.001   PHE B 199 
 TRP   0.014   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8935)
  covalent geometry    : angle       0.49767 (12121)
  SS BOND              : bond        0.00323 (    1)
  SS BOND              : angle       0.47236 (    2)
  hydrogen bonds       : bond        0.03579 (  427)
  hydrogen bonds       : angle       4.25923 ( 1194)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 207
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7823 (ttmm)
REVERT: A   53 MET cc_start: 0.6909 (mpp) cc_final: 0.6233 (mpp)
REVERT: A  225 VAL cc_start: 0.8693 (p) cc_final: 0.8375 (m)
REVERT: A  240 MET cc_start: 0.4779 (mmm) cc_final: 0.4392 (mmm)
REVERT: B   46 ARG cc_start: 0.7898 (mtp-110) cc_final: 0.7573 (mtp-110)
REVERT: B   61 MET cc_start: 0.7804 (ppp) cc_final: 0.7575 (ppp)
REVERT: B  155 ASN cc_start: 0.8089 (t0) cc_final: 0.7566 (t0)
REVERT: B  170 ASP cc_start: 0.7424 (t70) cc_final: 0.7015 (t0)
REVERT: B  234 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8382 (m-80)
REVERT: B  304 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.8158 (ttp80)
REVERT: C  340 ARG cc_start: 0.7841 (ttp-170) cc_final: 0.7431 (ttp-170)
REVERT: C  391 THR cc_start: 0.8517 (m) cc_final: 0.8294 (m)
REVERT: C  414 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7478 (mpp)
REVERT: G   27 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.8108 (mtt-85)
REVERT: H  119 VAL cc_start: 0.7847 (t) cc_final: 0.7427 (p)
REVERT: H  161 SER cc_start: 0.8367 (t) cc_final: 0.8161 (p)
  outliers start: 16
  outliers final: 11
  residues processed: 214
  average time/residue: 0.1118
  time to fit residues: 31.9518
Evaluate side-chains
  212 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 199
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue  339 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain C residue  414 MET
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 89 optimal weight:    0.0970
   chunk 72 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0000
   chunk 67 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    0.8186

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.127417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.109512 restraints weight = 12319.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.93
r_work: 0.3221 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.4080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8936  Z= 0.134
  Angle     :  0.497   6.732  12123  Z= 0.258
  Chirality :  0.041   0.148   1390
  Planarity :  0.004   0.047   1528
  Dihedral  :  4.156  59.168   1218
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.21 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.25), residues: 1119
  helix:  2.07 (0.26), residues: 407
  sheet: -0.08 (0.29), residues: 290
  loop : -0.87 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 314 
 TYR   0.011   0.001   TYR A 320 
 PHE   0.019   0.001   PHE B 199 
 TRP   0.013   0.001   TRP B 339 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 8935)
  covalent geometry    : angle       0.49668 (12121)
  SS BOND              : bond        0.00324 (    1)
  SS BOND              : angle       0.41467 (    2)
  hydrogen bonds       : bond        0.03525 (  427)
  hydrogen bonds       : angle       4.18595 ( 1194)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 202
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7822 (ttmm)
REVERT: A   53 MET cc_start: 0.6901 (mpp) cc_final: 0.6224 (mpp)
REVERT: A  225 VAL cc_start: 0.8693 (p) cc_final: 0.8373 (m)
REVERT: A  240 MET cc_start: 0.4871 (mmm) cc_final: 0.4425 (mmm)
REVERT: B  155 ASN cc_start: 0.8083 (t0) cc_final: 0.7749 (t0)
REVERT: B  170 ASP cc_start: 0.7444 (t70) cc_final: 0.7029 (t0)
REVERT: B  230 ASN cc_start: 0.8363 (m110) cc_final: 0.8131 (m-40)
REVERT: B  234 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8291 (m-80)
REVERT: B  304 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8208 (ttp80)
REVERT: C  340 ARG cc_start: 0.7819 (ttp-170) cc_final: 0.7414 (ttp-170)
REVERT: C  391 THR cc_start: 0.8526 (m) cc_final: 0.8297 (m)
REVERT: C  414 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7508 (mpp)
REVERT: G   27 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.8076 (mtt90)
REVERT: H  119 VAL cc_start: 0.7902 (t) cc_final: 0.7471 (p)
  outliers start: 18
  outliers final: 16
  residues processed: 209
  average time/residue: 0.1137
  time to fit residues: 31.4118
Evaluate side-chains
  215 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 197
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue  339 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain C residue  414 MET
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 104 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 31 optimal weight:    0.4980
   chunk 51 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0570
   chunk 40 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.128140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.110163 restraints weight = 12317.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.97
r_work: 0.3238 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.4152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8936  Z= 0.115
  Angle     :  0.479   6.655  12123  Z= 0.249
  Chirality :  0.040   0.145   1390
  Planarity :  0.004   0.046   1528
  Dihedral  :  4.067  59.281   1218
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 13.21 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.25), residues: 1119
  helix:  2.17 (0.26), residues: 409
  sheet: -0.03 (0.29), residues: 290
  loop : -0.76 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 137 
 TYR   0.015   0.001   TYR H  95 
 PHE   0.018   0.001   PHE B 199 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8935)
  covalent geometry    : angle       0.47871 (12121)
  SS BOND              : bond        0.00262 (    1)
  SS BOND              : angle       0.35565 (    2)
  hydrogen bonds       : bond        0.03309 (  427)
  hydrogen bonds       : angle       4.08098 ( 1194)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 207
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7818 (ttmm)
REVERT: A  225 VAL cc_start: 0.8687 (p) cc_final: 0.8360 (m)
REVERT: A  240 MET cc_start: 0.5022 (mmm) cc_final: 0.4598 (mmm)
REVERT: A  341 ASP cc_start: 0.7719 (t70) cc_final: 0.7188 (t0)
REVERT: B   46 ARG cc_start: 0.7868 (mtp-110) cc_final: 0.7546 (mtp-110)
REVERT: B  136 SER cc_start: 0.8494 (t) cc_final: 0.8269 (p)
REVERT: B  155 ASN cc_start: 0.8132 (t0) cc_final: 0.7788 (t0)
REVERT: B  170 ASP cc_start: 0.7446 (t70) cc_final: 0.7039 (t0)
REVERT: B  213 VAL cc_start: 0.7797 (t) cc_final: 0.7487 (m)
REVERT: B  230 ASN cc_start: 0.8341 (m110) cc_final: 0.8113 (m-40)
REVERT: B  234 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8372 (m-80)
REVERT: C  340 ARG cc_start: 0.7808 (ttp-170) cc_final: 0.7372 (ttp-170)
REVERT: C  391 THR cc_start: 0.8516 (m) cc_final: 0.8287 (m)
REVERT: C  414 MET cc_start: 0.7920 (mtp) cc_final: 0.7445 (mpp)
REVERT: C  430 PHE cc_start: 0.7083 (m-10) cc_final: 0.6821 (m-80)
REVERT: G   27 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.8139 (mtt-85)
REVERT: H  119 VAL cc_start: 0.7851 (OUTLIER) cc_final: 0.7420 (p)
  outliers start: 20
  outliers final: 16
  residues processed: 213
  average time/residue: 0.1160
  time to fit residues: 32.7332
Evaluate side-chains
  222 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 204
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   25 LEU
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  339 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9980
   chunk 10 optimal weight:    0.2980
   chunk 1 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 237 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.128776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.110871 restraints weight = 12347.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.94
r_work: 0.3232 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.4234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8936  Z= 0.125
  Angle     :  0.492   6.886  12123  Z= 0.254
  Chirality :  0.041   0.154   1390
  Planarity :  0.004   0.047   1528
  Dihedral  :  4.090  59.317   1218
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 12.57 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.25), residues: 1119
  helix:  2.22 (0.26), residues: 407
  sheet: -0.03 (0.30), residues: 290
  loop : -0.71 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 137 
 TYR   0.010   0.001   TYR H 190 
 PHE   0.018   0.001   PHE B 199 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8935)
  covalent geometry    : angle       0.49215 (12121)
  SS BOND              : bond        0.00291 (    1)
  SS BOND              : angle       0.33893 (    2)
  hydrogen bonds       : bond        0.03401 (  427)
  hydrogen bonds       : angle       4.08948 ( 1194)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 212
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7864 (ttmm)
REVERT: A  225 VAL cc_start: 0.8714 (p) cc_final: 0.8382 (m)
REVERT: A  240 MET cc_start: 0.5079 (mmm) cc_final: 0.4663 (mmm)
REVERT: A  245 GLU cc_start: 0.7402 (tp30) cc_final: 0.6644 (tp30)
REVERT: A  341 ASP cc_start: 0.7714 (t70) cc_final: 0.7197 (t0)
REVERT: B  136 SER cc_start: 0.8434 (t) cc_final: 0.8223 (p)
REVERT: B  155 ASN cc_start: 0.8165 (t0) cc_final: 0.7831 (t0)
REVERT: B  170 ASP cc_start: 0.7544 (t70) cc_final: 0.7172 (t0)
REVERT: B  213 VAL cc_start: 0.7838 (t) cc_final: 0.7534 (m)
REVERT: B  234 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8423 (m-80)
REVERT: B  246 ASP cc_start: 0.8040 (m-30) cc_final: 0.7716 (m-30)
REVERT: C  340 ARG cc_start: 0.7850 (ttp-170) cc_final: 0.7420 (ttp-170)
REVERT: C  377 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7431 (ttt180)
REVERT: C  391 THR cc_start: 0.8502 (m) cc_final: 0.8268 (m)
REVERT: C  414 MET cc_start: 0.7936 (mtp) cc_final: 0.7471 (mpp)
REVERT: C  430 PHE cc_start: 0.7176 (m-10) cc_final: 0.6860 (m-80)
REVERT: G   27 ARG cc_start: 0.8445 (ttm-80) cc_final: 0.8228 (mtt-85)
REVERT: H   95 TYR cc_start: 0.8232 (m-80) cc_final: 0.8031 (m-80)
REVERT: H  119 VAL cc_start: 0.7890 (OUTLIER) cc_final: 0.7456 (p)
REVERT: H  192 MET cc_start: 0.7695 (ptm) cc_final: 0.7231 (ptm)
  outliers start: 26
  outliers final: 18
  residues processed: 221
  average time/residue: 0.1125
  time to fit residues: 32.9128
Evaluate side-chains
  228 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 207
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   25 LEU
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  339 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  377 ARG
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  189 ILE
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
C 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.125716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.107795 restraints weight = 12229.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 1.92
r_work: 0.3210 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.4444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8936  Z= 0.174
  Angle     :  0.526   6.735  12123  Z= 0.274
  Chirality :  0.042   0.177   1390
  Planarity :  0.004   0.048   1528
  Dihedral  :  4.303  59.357   1218
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.74 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.25), residues: 1119
  helix:  2.18 (0.26), residues: 405
  sheet: -0.08 (0.29), residues: 294
  loop : -0.74 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 137 
 TYR   0.013   0.001   TYR H 102 
 PHE   0.021   0.002   PHE B 199 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 8935)
  covalent geometry    : angle       0.52564 (12121)
  SS BOND              : bond        0.00355 (    1)
  SS BOND              : angle       0.35057 (    2)
  hydrogen bonds       : bond        0.03826 (  427)
  hydrogen bonds       : angle       4.26403 ( 1194)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 208
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.8094 (mmtt) cc_final: 0.7828 (ttmm)
REVERT: A  240 MET cc_start: 0.5222 (mmm) cc_final: 0.4831 (mmm)
REVERT: B   14 LEU cc_start: 0.7905 (mm) cc_final: 0.7674 (mt)
REVERT: B   46 ARG cc_start: 0.7891 (mtp-110) cc_final: 0.7561 (mtp-110)
REVERT: B   61 MET cc_start: 0.7896 (tmm) cc_final: 0.7562 (ppp)
REVERT: B  136 SER cc_start: 0.8471 (t) cc_final: 0.8224 (p)
REVERT: B  155 ASN cc_start: 0.8160 (t0) cc_final: 0.7880 (t0)
REVERT: B  234 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8257 (m-80)
REVERT: B  246 ASP cc_start: 0.8015 (m-30) cc_final: 0.7678 (m-30)
REVERT: C  340 ARG cc_start: 0.7850 (ttp-170) cc_final: 0.7426 (ttp-170)
REVERT: C  357 SER cc_start: 0.8303 (m) cc_final: 0.8078 (m)
REVERT: C  377 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7428 (ttt180)
REVERT: C  391 THR cc_start: 0.8498 (m) cc_final: 0.8275 (m)
REVERT: C  414 MET cc_start: 0.7920 (mtp) cc_final: 0.7409 (mpp)
REVERT: C  430 PHE cc_start: 0.7161 (m-10) cc_final: 0.6808 (m-80)
REVERT: G   27 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.8133 (mtt-85)
REVERT: H   95 TYR cc_start: 0.8213 (m-80) cc_final: 0.7956 (m-80)
REVERT: H  119 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7470 (p)
REVERT: H  192 MET cc_start: 0.7803 (ptm) cc_final: 0.7331 (ptm)
  outliers start: 23
  outliers final: 19
  residues processed: 215
  average time/residue: 0.1154
  time to fit residues: 32.7102
Evaluate side-chains
  224 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 202
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   25 LEU
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  131 GLN
Chi-restraints excluded: chain C residue  339 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  377 ARG
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  189 ILE
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 107 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0370
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.5256

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
C 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.128890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.111012 restraints weight = 12197.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.92
r_work: 0.3244 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.4419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8936  Z= 0.109
  Angle     :  0.488   7.311  12123  Z= 0.254
  Chirality :  0.040   0.152   1390
  Planarity :  0.004   0.046   1528
  Dihedral  :  4.127  59.646   1218
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 14.70 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.25), residues: 1119
  helix:  2.15 (0.26), residues: 412
  sheet: -0.03 (0.29), residues: 289
  loop : -0.71 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  32 
 TYR   0.009   0.001   TYR H 190 
 PHE   0.022   0.001   PHE A 191 
 TRP   0.012   0.001   TRP B 339 
 HIS   0.003   0.001   HIS C 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8935)
  covalent geometry    : angle       0.48824 (12121)
  SS BOND              : bond        0.00222 (    1)
  SS BOND              : angle       0.30623 (    2)
  hydrogen bonds       : bond        0.03308 (  427)
  hydrogen bonds       : angle       4.10752 ( 1194)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 209
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.8077 (mmtt) cc_final: 0.7807 (ttmm)
REVERT: A  240 MET cc_start: 0.5218 (mmm) cc_final: 0.4821 (mmm)
REVERT: B   61 MET cc_start: 0.7898 (tmm) cc_final: 0.7562 (ppp)
REVERT: B  136 SER cc_start: 0.8419 (t) cc_final: 0.8176 (p)
REVERT: B  137 ARG cc_start: 0.8005 (ttm170) cc_final: 0.7786 (ttm170)
REVERT: B  155 ASN cc_start: 0.8160 (t0) cc_final: 0.7842 (t0)
REVERT: B  170 ASP cc_start: 0.7497 (t70) cc_final: 0.7143 (t0)
REVERT: B  230 ASN cc_start: 0.8362 (m110) cc_final: 0.8027 (m-40)
REVERT: B  234 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8364 (m-80)
REVERT: B  246 ASP cc_start: 0.8015 (m-30) cc_final: 0.7692 (m-30)
REVERT: B  304 ARG cc_start: 0.8362 (ttp80) cc_final: 0.8014 (ttt-90)
REVERT: C  340 ARG cc_start: 0.7813 (ttp-170) cc_final: 0.7364 (ttp-170)
REVERT: C  357 SER cc_start: 0.8278 (m) cc_final: 0.8063 (m)
REVERT: C  391 THR cc_start: 0.8457 (m) cc_final: 0.8241 (m)
REVERT: C  414 MET cc_start: 0.7907 (mtp) cc_final: 0.7427 (mpp)
REVERT: C  430 PHE cc_start: 0.7048 (m-10) cc_final: 0.6750 (m-80)
REVERT: G   27 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.8106 (mtt-85)
REVERT: H  119 VAL cc_start: 0.7879 (t) cc_final: 0.7448 (p)
REVERT: H  192 MET cc_start: 0.7735 (ptm) cc_final: 0.7264 (ptm)
  outliers start: 22
  outliers final: 20
  residues processed: 215
  average time/residue: 0.1117
  time to fit residues: 31.8620
Evaluate side-chains
  229 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 208
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   25 LEU
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  131 GLN
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  189 ILE
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0570
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
C 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.128051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.110245 restraints weight = 12273.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.91
r_work: 0.3241 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.4446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8936  Z= 0.121
  Angle     :  0.495   7.027  12123  Z= 0.258
  Chirality :  0.041   0.155   1390
  Planarity :  0.004   0.047   1528
  Dihedral  :  4.128  59.469   1218
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.44 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.25), residues: 1119
  helix:  2.17 (0.26), residues: 412
  sheet:  0.03 (0.29), residues: 289
  loop : -0.74 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  32 
 TYR   0.009   0.001   TYR H 190 
 PHE   0.017   0.001   PHE B 199 
 TRP   0.011   0.001   TRP B 339 
 HIS   0.003   0.001   HIS C 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8935)
  covalent geometry    : angle       0.49517 (12121)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       0.32452 (    2)
  hydrogen bonds       : bond        0.03350 (  427)
  hydrogen bonds       : angle       4.11004 ( 1194)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 211
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7811 (ttmm)
REVERT: A  240 MET cc_start: 0.5223 (mmm) cc_final: 0.4827 (mmm)
REVERT: A  341 ASP cc_start: 0.7750 (t70) cc_final: 0.7197 (t0)
REVERT: B   50 THR cc_start: 0.8510 (m) cc_final: 0.8160 (t)
REVERT: B   61 MET cc_start: 0.7894 (tmm) cc_final: 0.7548 (ppp)
REVERT: B  136 SER cc_start: 0.8420 (t) cc_final: 0.8180 (p)
REVERT: B  155 ASN cc_start: 0.8191 (t0) cc_final: 0.7811 (t0)
REVERT: B  170 ASP cc_start: 0.7519 (t70) cc_final: 0.7167 (t0)
REVERT: B  230 ASN cc_start: 0.8367 (m110) cc_final: 0.8022 (m-40)
REVERT: B  234 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8333 (m-80)
REVERT: B  246 ASP cc_start: 0.8009 (m-30) cc_final: 0.7683 (m-30)
REVERT: B  304 ARG cc_start: 0.8388 (ttp80) cc_final: 0.8015 (ttt-90)
REVERT: C  340 ARG cc_start: 0.7841 (ttp-170) cc_final: 0.7407 (ttp-170)
REVERT: C  357 SER cc_start: 0.8293 (m) cc_final: 0.8073 (m)
REVERT: C  377 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7408 (ttt180)
REVERT: C  391 THR cc_start: 0.8460 (m) cc_final: 0.8237 (m)
REVERT: C  414 MET cc_start: 0.7982 (mtp) cc_final: 0.7470 (mpp)
REVERT: C  430 PHE cc_start: 0.7109 (m-10) cc_final: 0.6783 (m-80)
REVERT: G   27 ARG cc_start: 0.8445 (ttm-80) cc_final: 0.8138 (mtt-85)
REVERT: H   34 MET cc_start: 0.8417 (mmm) cc_final: 0.8194 (mmt)
REVERT: H  119 VAL cc_start: 0.7890 (t) cc_final: 0.7454 (p)
REVERT: H  192 MET cc_start: 0.7741 (ptm) cc_final: 0.7269 (ptm)
  outliers start: 21
  outliers final: 19
  residues processed: 217
  average time/residue: 0.1099
  time to fit residues: 31.6982
Evaluate side-chains
  234 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 213
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   25 LEU
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  131 GLN
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  377 ARG
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  189 ILE
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 48 optimal weight:    0.3980
   chunk 34 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 94 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
C 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.128339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.110609 restraints weight = 12197.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 1.91
r_work: 0.3237 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.4471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8936  Z= 0.129
  Angle     :  0.503   8.261  12123  Z= 0.260
  Chirality :  0.041   0.159   1390
  Planarity :  0.004   0.047   1528
  Dihedral  :  4.175  59.409   1218
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.02 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.25), residues: 1119
  helix:  2.28 (0.26), residues: 405
  sheet:  0.02 (0.30), residues: 290
  loop : -0.71 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  32 
 TYR   0.010   0.001   TYR A 320 
 PHE   0.018   0.001   PHE B 199 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS C 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8935)
  covalent geometry    : angle       0.50298 (12121)
  SS BOND              : bond        0.00265 (    1)
  SS BOND              : angle       0.29863 (    2)
  hydrogen bonds       : bond        0.03425 (  427)
  hydrogen bonds       : angle       4.09672 ( 1194)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2424.83 seconds
wall clock time: 42 minutes 14.46 seconds (2534.46 seconds total)