Starting phenix.real_space_refine
on Thu Sep 18 11:09:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bip_44597/09_2025/9bip_44597.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bip_44597/09_2025/9bip_44597.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bip_44597/09_2025/9bip_44597.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bip_44597/09_2025/9bip_44597.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bip_44597/09_2025/9bip_44597.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bip_44597/09_2025/9bip_44597.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.161
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: 5
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    5265      2.51       5
     N    1466      2.21       5
     O    1542      1.98       5
     H    8135      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16460
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3954
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 3954
          Classifications: {'peptide': 240}
          Link IDs: {'PTRANS': 6, 'TRANS': 233}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 5059
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "G"
      Number of atoms: 867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 867
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 1900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 1900
          Classifications: {'peptide': 128}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 4680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 4680
          Classifications: {'peptide': 290}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 277}
  Time building chain proxies: 2.69, per 1000 atoms: 0.16
  Number of scatterers: 16460
  At special positions: 0
  Unit cell: (75.68, 104.06, 141.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     O    1542      8.00
     N    1466      7.00
     C    5265      6.00
     H    8135      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R   9 " - pdb=" SG  CYS R 258 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  90 " - pdb=" SG  CYS R 168 " 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: 1.41
  Conformation dependent library (CDL) restraints added in 362.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1978

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 11 sheets defined
      42.8% alpha, 19.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 38
      removed outlier: 3.528A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.740A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE A 238 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 233 through 239'
    Processing helix  chain 'A' and resid 252 through 264
      No H-bonds generated for 'chain 'A' and resid 252 through 264'
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 3.581A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 311
      removed outlier: 3.577A  pdb=" N   ASP A 310 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.672A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.506A  pdb=" N   ARG A 389 " --> pdb=" O   ARG A 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.857A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.763A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 18 through 48
      removed outlier: 3.689A  pdb=" N   SER R  22 " --> pdb=" O   LEU R  18 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   GLY R  29 " --> pdb=" O   ILE R  25 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL R  30 " --> pdb=" O   PHE R  26 " (cutoff:3.500A)
      Proline residue:  R  33  - end of helix
    Processing helix  chain 'R' and resid 51 through 68
      removed outlier: 4.183A  pdb=" N   TYR R  55 " --> pdb=" O   GLU R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 69 through 79
      removed outlier: 4.124A  pdb=" N   TRP R  73 " --> pdb=" O   THR R  69 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 121
      removed outlier: 5.377A  pdb=" N   ILE R 101 " --> pdb=" O   PHE R  97 " (cutoff:3.500A)
      removed outlier: 5.669A  pdb=" N   TYR R 102 " --> pdb=" O   TYR R  98 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ILE R 103 " --> pdb=" O   THR R  99 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 130 through 150
    Processing helix  chain 'R' and resid 151 through 155
      removed outlier: 3.676A  pdb=" N   PHE R 154 " --> pdb=" O   ALA R 151 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   HIS R 155 " --> pdb=" O   PRO R 152 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 151 through 155'
    Processing helix  chain 'R' and resid 175 through 209
      removed outlier: 3.651A  pdb=" N   ALA R 179 " --> pdb=" O   GLU R 175 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   TRP R 180 " --> pdb=" O   GLY R 176 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   PHE R 192 " --> pdb=" O   VAL R 188 " (cutoff:3.500A)
      Proline residue:  R 193  - end of helix
    Processing helix  chain 'R' and resid 215 through 254
      removed outlier: 3.794A  pdb=" N   VAL R 233 " --> pdb=" O   LEU R 229 " (cutoff:3.500A)
      Proline residue:  R 239  - end of helix
    Processing helix  chain 'R' and resid 258 through 264
      removed outlier: 3.594A  pdb=" N   ARG R 263 " --> pdb=" O   GLY R 259 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL R 264 " --> pdb=" O   PHE R 260 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 264 through 275
      removed outlier: 3.624A  pdb=" N   THR R 275 " --> pdb=" O   SER R 271 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 277 through 288
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 292 through 296
      removed outlier: 3.838A  pdb=" N   ASP R 296 " --> pdb=" O   ALA R 293 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.601A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 10.036A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.363A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.543A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLY B 330 " --> pdb=" O   CYS B 317 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.828A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.671A  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: 7.212A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.194A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.054A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.760A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.977A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.442A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.872A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.551A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   SER N  71 " --> pdb=" O   TYR N  80 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 3.585A  pdb=" N   VAL N  93 " --> pdb=" O   GLN N  39 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA N  97 " --> pdb=" O   ASN N  35 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 158 through 160

    401 hydrogen bonds defined for protein.
    1146 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: 3.50

  Time building geometry restraints manager: 1.91 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8109
        1.03 -     1.23: 132
        1.23 -     1.43: 3575
        1.43 -     1.62: 4757
        1.62 -     1.82: 70
  Bond restraints: 16643
  Sorted by residual:
  bond pdb=" N   GLY B   1 "
       pdb=" CA  GLY B   1 "
    ideal  model  delta    sigma   weight residual
    1.451  1.490 -0.039 1.60e-02 3.91e+03 6.09e+00
  bond pdb=" N   ASN G   5 "
       pdb=" CA  ASN G   5 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.04e+00
  bond pdb=" N   THR A   9 "
       pdb=" CA  THR A   9 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.01e+00
  bond pdb=" N   THR A   9 "
       pdb=" H   THR A   9 "
    ideal  model  delta    sigma   weight residual
    0.860  0.891 -0.031 2.00e-02 2.50e+03 2.33e+00
  bond pdb=" N   ASN G   5 "
       pdb=" H   ASN G   5 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.23e+00
  ... (remaining 16638 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 27626
        1.02 -     2.03: 2143
        2.03 -     3.05: 94
        3.05 -     4.06: 31
        4.06 -     5.08: 7
  Bond angle restraints: 29901
  Sorted by residual:
  angle pdb=" N   ALA N  92 "
        pdb=" CA  ALA N  92 "
        pdb=" C   ALA N  92 "
      ideal   model   delta    sigma   weight residual
     107.73  111.33   -3.60 1.61e+00 3.86e-01 4.99e+00
  angle pdb=" N   ARG R  14 "
        pdb=" CA  ARG R  14 "
        pdb=" C   ARG R  14 "
      ideal   model   delta    sigma   weight residual
     114.56  111.82    2.74 1.27e+00 6.20e-01 4.66e+00
  angle pdb=" C   GLN A  59 "
        pdb=" N   MET A  60 "
        pdb=" CA  MET A  60 "
      ideal   model   delta    sigma   weight residual
     121.14  117.95    3.19 1.75e+00 3.27e-01 3.33e+00
  angle pdb=" N   PRO N 102 "
        pdb=" CA  PRO N 102 "
        pdb=" C   PRO N 102 "
      ideal   model   delta    sigma   weight residual
     112.47  116.16   -3.69 2.06e+00 2.36e-01 3.21e+00
  angle pdb=" N   ASP B 291 "
        pdb=" CA  ASP B 291 "
        pdb=" C   ASP B 291 "
      ideal   model   delta    sigma   weight residual
     110.53  108.17    2.36 1.32e+00 5.74e-01 3.21e+00
  ... (remaining 29896 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 7014
       17.88 -    35.75: 605
       35.75 -    53.63: 190
       53.63 -    71.51: 41
       71.51 -    89.39: 14
  Dihedral angle restraints: 7864
    sinusoidal: 4181
      harmonic: 3683
  Sorted by residual:
  dihedral pdb=" CA  LEU A 291 "
           pdb=" C   LEU A 291 "
           pdb=" N   ASN A 292 "
           pdb=" CA  ASN A 292 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.87  -29.13     0      5.00e+00 4.00e-02 3.39e+01
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.33   40.33     1      1.00e+01 1.00e-02 2.28e+01
  dihedral pdb=" CA  ASP B 291 "
           pdb=" C   ASP B 291 "
           pdb=" N   PHE B 292 "
           pdb=" CA  PHE B 292 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.53  -22.47     0      5.00e+00 4.00e-02 2.02e+01
  ... (remaining 7861 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 765
       0.028 -    0.055: 314
       0.055 -    0.083: 105
       0.083 -    0.110: 62
       0.110 -    0.138: 28
  Chirality restraints: 1274
  Sorted by residual:
  chirality pdb=" CA  VAL G  54 "
            pdb=" N   VAL G  54 "
            pdb=" C   VAL G  54 "
            pdb=" CB  VAL G  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  ILE B 157 "
            pdb=" N   ILE B 157 "
            pdb=" C   ILE B 157 "
            pdb=" CB  ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.56e-01
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.54e-01
  ... (remaining 1271 not shown)

  Planarity restraints: 2504
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 186 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.06e+00
        pdb=" C   VAL R 186 "    0.035 2.00e-02 2.50e+03
        pdb=" O   VAL R 186 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   PHE R 187 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.029 5.00e-02 4.00e+02   4.42e-02 3.13e+00
        pdb=" N   PRO B 236 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 360 "   -0.028 5.00e-02 4.00e+02   4.21e-02 2.84e+00
        pdb=" N   PRO A 361 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 361 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 361 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 2501 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 1203
        2.21 -     2.81: 33078
        2.81 -     3.41: 41571
        3.41 -     4.00: 55986
        4.00 -     4.60: 87210
  Nonbonded interactions: 219048
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN N  53 "
            pdb=" H   GLN N  53 "
     model   vdw
     1.616 2.450
  nonbonded pdb="HE21 GLN N  39 "
            pdb=" O   LYS N  43 "
     model   vdw
     1.626 2.450
  nonbonded pdb=" O   ASP B 163 "
            pdb=" HG1 THR B 164 "
     model   vdw
     1.671 2.450
  nonbonded pdb=" O   ARG A 283 "
            pdb=" HG1 THR A 284 "
     model   vdw
     1.678 2.450
  nonbonded pdb=" O   ASP B 333 "
            pdb=" HG  SER B 334 "
     model   vdw
     1.683 2.450
  ... (remaining 219043 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.080
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     14.640
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
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      :  0.003   0.039   8512  Z= 0.125
  Angle     :  0.513   5.079  11540  Z= 0.283
  Chirality :  0.041   0.138   1274
  Planarity :  0.003   0.044   1486
  Dihedral  : 16.505  89.385   3060
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 18.97 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.26), residues: 1044
  helix:  2.03 (0.27), residues: 402
  sheet: -0.54 (0.34), residues: 223
  loop : -1.57 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 333 
 TYR   0.008   0.001   TYR N  95 
 PHE   0.010   0.001   PHE R 159 
 TRP   0.011   0.001   TRP R  73 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8508)
  covalent geometry    : angle       0.51211 (11532)
  SS BOND              : bond        0.00325 (    4)
  SS BOND              : angle       0.98697 (    8)
  hydrogen bonds       : bond        0.18167 (  401)
  hydrogen bonds       : angle       5.75308 ( 1146)

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   46 is missing expected H atoms. Skipping.
Residue SER  112 is missing expected H atoms. Skipping.
Residue THR  113 is missing expected H atoms. Skipping.
Evaluate side-chains
  91 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.470 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7069 (mp0)
REVERT: A   64 HIS cc_start: 0.3312 (OUTLIER) cc_final: 0.2271 (t70)
REVERT: A  266 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8437 (mp)
REVERT: A  327 GLU cc_start: 0.4712 (OUTLIER) cc_final: 0.2372 (mp0)
REVERT: B   59 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8482 (t80)
REVERT: B  259 GLN cc_start: 0.7940 (tt0) cc_final: 0.7627 (mt0)
REVERT: R  181 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.6501 (tmm)
  outliers start: 17
  outliers final: 11
  residues processed: 88
  average time/residue: 1.3433
  time to fit residues: 125.1600
Evaluate side-chains
  88 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  156 ASP
Chi-restraints excluded: chain R residue  181 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
R  79 HIS
R 100 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.172033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.131331 restraints weight = 26104.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 2.14
r_work: 0.3399 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.0665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8512  Z= 0.127
  Angle     :  0.535   5.437  11540  Z= 0.294
  Chirality :  0.041   0.145   1274
  Planarity :  0.004   0.046   1486
  Dihedral  :  6.931  58.778   1193
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 17.28 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.26), residues: 1044
  helix:  2.04 (0.27), residues: 407
  sheet: -0.35 (0.35), residues: 211
  loop : -1.46 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 294 
 TYR   0.011   0.001   TYR N  95 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.010   0.001   TRP B 297 
 HIS   0.009   0.001   HIS R  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8508)
  covalent geometry    : angle       0.53443 (11532)
  SS BOND              : bond        0.00411 (    4)
  SS BOND              : angle       0.93844 (    8)
  hydrogen bonds       : bond        0.05996 (  401)
  hydrogen bonds       : angle       4.61809 ( 1146)

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   46 is missing expected H atoms. Skipping.
Residue SER  112 is missing expected H atoms. Skipping.
Residue THR  113 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7012 (mt-10)
REVERT: B   59 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8414 (t80)
REVERT: B  175 GLN cc_start: 0.7880 (mm110) cc_final: 0.7442 (mt0)
REVERT: B  259 GLN cc_start: 0.7639 (tt0) cc_final: 0.7274 (mt0)
REVERT: B  284 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8004 (mp)
REVERT: N   98 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8384 (ppt90)
REVERT: R  115 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7873 (mtt180)
REVERT: R  123 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6894 (mt)
  outliers start: 29
  outliers final: 11
  residues processed: 104
  average time/residue: 1.3820
  time to fit residues: 151.6019
Evaluate side-chains
  91 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   98 ARG
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   69 THR
Chi-restraints excluded: chain R residue  115 ARG
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  211 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B  36 ASN
N  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.171261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.130531 restraints weight = 26333.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.15
r_work: 0.3383 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.0962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8512  Z= 0.138
  Angle     :  0.539   5.071  11540  Z= 0.296
  Chirality :  0.042   0.156   1274
  Planarity :  0.004   0.046   1486
  Dihedral  :  5.790  59.861   1170
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 17.62 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.26), residues: 1044
  helix:  2.02 (0.26), residues: 407
  sheet: -0.50 (0.34), residues: 222
  loop : -1.41 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  98 
 TYR   0.013   0.001   TYR N  95 
 PHE   0.016   0.001   PHE R  19 
 TRP   0.009   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8508)
  covalent geometry    : angle       0.53866 (11532)
  SS BOND              : bond        0.00428 (    4)
  SS BOND              : angle       1.09865 (    8)
  hydrogen bonds       : bond        0.06046 (  401)
  hydrogen bonds       : angle       4.44212 ( 1146)

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   46 is missing expected H atoms. Skipping.
Residue SER  112 is missing expected H atoms. Skipping.
Residue THR  113 is missing expected H atoms. Skipping.
Evaluate side-chains
  102 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 73
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  327 GLU cc_start: 0.4595 (OUTLIER) cc_final: 0.4349 (mt-10)
REVERT: A  344 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7438 (mm-30)
REVERT: B   59 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8425 (t80)
REVERT: B  175 GLN cc_start: 0.7860 (mm110) cc_final: 0.7447 (mt0)
REVERT: B  259 GLN cc_start: 0.7651 (tt0) cc_final: 0.7270 (mt0)
REVERT: B  284 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8021 (mp)
REVERT: N   98 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8281 (ppt170)
REVERT: R  123 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6934 (mt)
  outliers start: 29
  outliers final: 15
  residues processed: 99
  average time/residue: 1.3639
  time to fit residues: 142.5347
Evaluate side-chains
  92 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain N residue   98 ARG
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   69 THR
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  211 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
N  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.173646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.132986 restraints weight = 26342.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.17
r_work: 0.3446 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8512  Z= 0.106
  Angle     :  0.493   4.917  11540  Z= 0.269
  Chirality :  0.040   0.139   1274
  Planarity :  0.003   0.046   1486
  Dihedral  :  5.479  58.921   1169
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.29 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.26), residues: 1044
  helix:  2.24 (0.27), residues: 407
  sheet: -0.34 (0.34), residues: 211
  loop : -1.43 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N 105 
 TYR   0.012   0.001   TYR N  95 
 PHE   0.017   0.001   PHE R  19 
 TRP   0.009   0.001   TRP B 297 
 HIS   0.005   0.001   HIS R  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 8508)
  covalent geometry    : angle       0.49253 (11532)
  SS BOND              : bond        0.00326 (    4)
  SS BOND              : angle       0.93893 (    8)
  hydrogen bonds       : bond        0.05049 (  401)
  hydrogen bonds       : angle       4.23725 ( 1146)

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   46 is missing expected H atoms. Skipping.
Residue SER  112 is missing expected H atoms. Skipping.
Residue THR  113 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6377 (mp0)
REVERT: A  229 ASP cc_start: 0.7626 (m-30) cc_final: 0.7275 (p0)
REVERT: A  266 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8346 (mp)
REVERT: A  309 GLU cc_start: 0.5532 (pm20) cc_final: 0.5265 (pp20)
REVERT: A  327 GLU cc_start: 0.4561 (OUTLIER) cc_final: 0.4270 (mt-10)
REVERT: B   59 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8370 (t80)
REVERT: B  175 GLN cc_start: 0.7790 (mm110) cc_final: 0.7324 (mt0)
REVERT: B  259 GLN cc_start: 0.7663 (tt0) cc_final: 0.7307 (mt0)
REVERT: N   98 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8405 (ppt90)
REVERT: R  115 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7748 (mtt180)
REVERT: R  123 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6783 (mt)
REVERT: R  181 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.5943 (tmm)
  outliers start: 25
  outliers final: 12
  residues processed: 98
  average time/residue: 1.4312
  time to fit residues: 148.0497
Evaluate side-chains
  96 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   98 ARG
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   69 THR
Chi-restraints excluded: chain R residue  115 ARG
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  211 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 90 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
N  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.172868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.132215 restraints weight = 26124.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 2.15
r_work: 0.3421 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.1182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8512  Z= 0.118
  Angle     :  0.507   4.992  11540  Z= 0.276
  Chirality :  0.041   0.144   1274
  Planarity :  0.004   0.045   1486
  Dihedral  :  5.494  58.646   1169
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 1.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.28 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.26), residues: 1044
  helix:  2.24 (0.27), residues: 407
  sheet: -0.33 (0.35), residues: 211
  loop : -1.41 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N 105 
 TYR   0.013   0.001   TYR N  95 
 PHE   0.018   0.001   PHE R  19 
 TRP   0.008   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8508)
  covalent geometry    : angle       0.50610 (11532)
  SS BOND              : bond        0.00391 (    4)
  SS BOND              : angle       0.99349 (    8)
  hydrogen bonds       : bond        0.05302 (  401)
  hydrogen bonds       : angle       4.22046 ( 1146)

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   46 is missing expected H atoms. Skipping.
Residue SER  112 is missing expected H atoms. Skipping.
Residue THR  113 is missing expected H atoms. Skipping.
Evaluate side-chains
  110 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 79
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6442 (mp0)
REVERT: A  266 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8388 (mp)
REVERT: A  309 GLU cc_start: 0.5609 (pm20) cc_final: 0.5336 (pp20)
REVERT: A  327 GLU cc_start: 0.4579 (OUTLIER) cc_final: 0.4285 (mt-10)
REVERT: A  344 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7568 (mm-30)
REVERT: B   22 ARG cc_start: 0.5565 (mtt180) cc_final: 0.5324 (mtt90)
REVERT: B   59 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8406 (t80)
REVERT: B  146 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8504 (mm)
REVERT: B  175 GLN cc_start: 0.7844 (mm110) cc_final: 0.7408 (mt0)
REVERT: B  259 GLN cc_start: 0.7742 (tt0) cc_final: 0.7369 (mt0)
REVERT: B  284 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8065 (mp)
REVERT: B  318 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8690 (tt)
REVERT: N   98 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8451 (ppt90)
REVERT: R  115 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7994 (mtt180)
REVERT: R  123 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6819 (mt)
REVERT: R  181 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6029 (tmm)
  outliers start: 31
  outliers final: 13
  residues processed: 106
  average time/residue: 1.4666
  time to fit residues: 163.8906
Evaluate side-chains
  102 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   98 ARG
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   69 THR
Chi-restraints excluded: chain R residue  115 ARG
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  211 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 390 GLN
B  36 ASN
N  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.170172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.128262 restraints weight = 26234.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.94
r_work: 0.3377 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8512  Z= 0.162
  Angle     :  0.570   5.664  11540  Z= 0.311
  Chirality :  0.043   0.180   1274
  Planarity :  0.004   0.050   1486
  Dihedral  :  5.823  58.374   1169
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 16.95 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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 aren not related in a simple way.
  whole:  0.26 (0.26), residues: 1044
  helix:  2.03 (0.26), residues: 408
  sheet: -0.29 (0.34), residues: 211
  loop : -1.46 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG R 206 
 TYR   0.017   0.002   TYR N  95 
 PHE   0.020   0.002   PHE R  19 
 TRP   0.009   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8508)
  covalent geometry    : angle       0.56869 (11532)
  SS BOND              : bond        0.00466 (    4)
  SS BOND              : angle       1.33396 (    8)
  hydrogen bonds       : bond        0.06371 (  401)
  hydrogen bonds       : angle       4.40544 ( 1146)

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   46 is missing expected H atoms. Skipping.
Residue SER  112 is missing expected H atoms. Skipping.
Residue THR  113 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 78
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7990 (mm-30)
REVERT: A  266 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8409 (mp)
REVERT: A  309 GLU cc_start: 0.5642 (pm20) cc_final: 0.5429 (pp20)
REVERT: A  327 GLU cc_start: 0.4603 (OUTLIER) cc_final: 0.2961 (mp0)
REVERT: A  331 ASP cc_start: 0.6401 (OUTLIER) cc_final: 0.6046 (m-30)
REVERT: A  344 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7089 (mt-10)
REVERT: B   22 ARG cc_start: 0.5801 (mtt180) cc_final: 0.5570 (mtt90)
REVERT: B   59 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8534 (t80)
REVERT: B  175 GLN cc_start: 0.7935 (mm110) cc_final: 0.7557 (mt0)
REVERT: B  259 GLN cc_start: 0.7798 (tt0) cc_final: 0.7460 (mt0)
REVERT: B  284 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8003 (mp)
REVERT: B  318 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8820 (tt)
REVERT: N   98 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8277 (ppt170)
REVERT: R  115 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7793 (mtt180)
REVERT: R  123 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7123 (mt)
  outliers start: 37
  outliers final: 18
  residues processed: 111
  average time/residue: 1.4256
  time to fit residues: 166.9007
Evaluate side-chains
  102 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain A residue  331 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   98 ARG
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   69 THR
Chi-restraints excluded: chain R residue  115 ARG
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  211 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 46 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
N  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.170700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.130413 restraints weight = 26174.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 2.15
r_work: 0.3407 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8512  Z= 0.148
  Angle     :  0.552   5.136  11540  Z= 0.302
  Chirality :  0.042   0.168   1274
  Planarity :  0.004   0.046   1486
  Dihedral  :  5.789  57.162   1169
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 17.28 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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 aren not related in a simple way.
  whole:  0.23 (0.26), residues: 1044
  helix:  2.03 (0.26), residues: 408
  sheet: -0.37 (0.34), residues: 213
  loop : -1.48 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N 105 
 TYR   0.014   0.002   TYR N  95 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.009   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8508)
  covalent geometry    : angle       0.55015 (11532)
  SS BOND              : bond        0.00357 (    4)
  SS BOND              : angle       1.67093 (    8)
  hydrogen bonds       : bond        0.06090 (  401)
  hydrogen bonds       : angle       4.35959 ( 1146)

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   46 is missing expected H atoms. Skipping.
Residue SER  112 is missing expected H atoms. Skipping.
Residue THR  113 is missing expected H atoms. Skipping.
Evaluate side-chains
  110 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 76
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8332 (mp)
REVERT: A  309 GLU cc_start: 0.5614 (pm20) cc_final: 0.5318 (pp20)
REVERT: A  327 GLU cc_start: 0.4556 (OUTLIER) cc_final: 0.4334 (mt-10)
REVERT: A  331 ASP cc_start: 0.6211 (OUTLIER) cc_final: 0.5916 (m-30)
REVERT: A  344 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7582 (mm-30)
REVERT: B   22 ARG cc_start: 0.5628 (mtt180) cc_final: 0.5393 (mtt90)
REVERT: B   59 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8495 (t80)
REVERT: B  175 GLN cc_start: 0.7814 (mm110) cc_final: 0.7340 (mt0)
REVERT: B  259 GLN cc_start: 0.7679 (tt0) cc_final: 0.7382 (mt0)
REVERT: B  284 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7947 (mp)
REVERT: B  318 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8760 (tt)
REVERT: N   98 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8218 (ppt170)
REVERT: R  115 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7634 (mtt180)
REVERT: R  123 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6958 (mt)
  outliers start: 34
  outliers final: 19
  residues processed: 106
  average time/residue: 1.5654
  time to fit residues: 175.0900
Evaluate side-chains
  102 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 73
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain A residue  331 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   98 ARG
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   69 THR
Chi-restraints excluded: chain R residue   90 CYS
Chi-restraints excluded: chain R residue  115 ARG
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  211 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0570
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    1.5904

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

Flipped N/Q/H residues before XYZ refinement:
N  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.170544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.128468 restraints weight = 26351.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 1.96
r_work: 0.3393 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8512  Z= 0.151
  Angle     :  0.556   5.041  11540  Z= 0.304
  Chirality :  0.042   0.168   1274
  Planarity :  0.004   0.046   1486
  Dihedral  :  5.813  57.170   1169
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 17.28 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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 aren not related in a simple way.
  whole:  0.23 (0.26), residues: 1044
  helix:  2.01 (0.26), residues: 408
  sheet: -0.32 (0.34), residues: 211
  loop : -1.49 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  98 
 TYR   0.015   0.002   TYR N  95 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.010   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8508)
  covalent geometry    : angle       0.55439 (11532)
  SS BOND              : bond        0.00404 (    4)
  SS BOND              : angle       1.50482 (    8)
  hydrogen bonds       : bond        0.06151 (  401)
  hydrogen bonds       : angle       4.35920 ( 1146)

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   46 is missing expected H atoms. Skipping.
Residue SER  112 is missing expected H atoms. Skipping.
Residue THR  113 is missing expected H atoms. Skipping.
Evaluate side-chains
  109 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 73
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8427 (mp)
REVERT: A  309 GLU cc_start: 0.5603 (pm20) cc_final: 0.5401 (pp20)
REVERT: A  327 GLU cc_start: 0.4650 (OUTLIER) cc_final: 0.3135 (mp0)
REVERT: A  331 ASP cc_start: 0.6334 (OUTLIER) cc_final: 0.6009 (m-30)
REVERT: A  344 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7769 (mm-30)
REVERT: B   59 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.8542 (t80)
REVERT: B  175 GLN cc_start: 0.7952 (mm110) cc_final: 0.7515 (mt0)
REVERT: B  259 GLN cc_start: 0.7801 (tt0) cc_final: 0.7515 (mt0)
REVERT: B  284 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8001 (mp)
REVERT: B  318 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8803 (tt)
REVERT: N   98 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8283 (ppt170)
REVERT: R  115 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7789 (mtt180)
REVERT: R  123 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7105 (mt)
  outliers start: 36
  outliers final: 19
  residues processed: 105
  average time/residue: 1.5069
  time to fit residues: 167.1675
Evaluate side-chains
  101 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 72
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain A residue  331 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   98 ARG
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   69 THR
Chi-restraints excluded: chain R residue   90 CYS
Chi-restraints excluded: chain R residue  115 ARG
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  211 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B  36 ASN
N  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.171226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.129307 restraints weight = 26334.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.95
r_work: 0.3375 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8512  Z= 0.134
  Angle     :  0.534   5.063  11540  Z= 0.292
  Chirality :  0.042   0.156   1274
  Planarity :  0.004   0.047   1486
  Dihedral  :  5.707  57.108   1169
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.51 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.26), residues: 1044
  helix:  2.10 (0.27), residues: 407
  sheet: -0.30 (0.34), residues: 211
  loop : -1.48 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N 105 
 TYR   0.014   0.001   TYR N  95 
 PHE   0.025   0.001   PHE R  19 
 TRP   0.009   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8508)
  covalent geometry    : angle       0.53311 (11532)
  SS BOND              : bond        0.00341 (    4)
  SS BOND              : angle       1.43596 (    8)
  hydrogen bonds       : bond        0.05772 (  401)
  hydrogen bonds       : angle       4.30645 ( 1146)

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   46 is missing expected H atoms. Skipping.
Residue SER  112 is missing expected H atoms. Skipping.
Residue THR  113 is missing expected H atoms. Skipping.
Evaluate side-chains
  104 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 72
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8438 (mp)
REVERT: A  327 GLU cc_start: 0.4556 (OUTLIER) cc_final: 0.4336 (mt-10)
REVERT: A  331 ASP cc_start: 0.6254 (OUTLIER) cc_final: 0.6019 (m-30)
REVERT: A  344 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7779 (mm-30)
REVERT: B   22 ARG cc_start: 0.5744 (mtt180) cc_final: 0.5541 (mtt90)
REVERT: B   59 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8527 (t80)
REVERT: B  175 GLN cc_start: 0.7996 (mm110) cc_final: 0.7569 (mt0)
REVERT: B  259 GLN cc_start: 0.7844 (tt0) cc_final: 0.7576 (mt0)
REVERT: B  284 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8065 (mp)
REVERT: B  318 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8771 (tt)
REVERT: N   98 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8300 (ppt170)
REVERT: R  115 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8061 (mtt180)
REVERT: R  123 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7053 (mt)
  outliers start: 32
  outliers final: 19
  residues processed: 101
  average time/residue: 1.3255
  time to fit residues: 141.9865
Evaluate side-chains
  99 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 70
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain A residue  331 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   98 ARG
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   69 THR
Chi-restraints excluded: chain R residue   90 CYS
Chi-restraints excluded: chain R residue  115 ARG
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  211 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 101 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
N  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.171312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.129400 restraints weight = 26262.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.96
r_work: 0.3383 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8512  Z= 0.129
  Angle     :  0.529   5.010  11540  Z= 0.289
  Chirality :  0.041   0.154   1274
  Planarity :  0.004   0.047   1486
  Dihedral  :  5.652  56.972   1169
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.62 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.26), residues: 1044
  helix:  2.14 (0.27), residues: 407
  sheet: -0.35 (0.34), residues: 212
  loop : -1.47 (0.27), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N 105 
 TYR   0.014   0.001   TYR N  95 
 PHE   0.027   0.001   PHE R  19 
 TRP   0.010   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8508)
  covalent geometry    : angle       0.52744 (11532)
  SS BOND              : bond        0.00331 (    4)
  SS BOND              : angle       1.39503 (    8)
  hydrogen bonds       : bond        0.05644 (  401)
  hydrogen bonds       : angle       4.27724 ( 1146)

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

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

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   46 is missing expected H atoms. Skipping.
Residue SER  112 is missing expected H atoms. Skipping.
Residue THR  113 is missing expected H atoms. Skipping.
Evaluate side-chains
  103 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 71
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  327 GLU cc_start: 0.4661 (OUTLIER) cc_final: 0.4364 (mt-10)
REVERT: A  331 ASP cc_start: 0.6150 (OUTLIER) cc_final: 0.5932 (m-30)
REVERT: A  344 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7060 (mt-10)
REVERT: B   22 ARG cc_start: 0.5722 (mtt180) cc_final: 0.5511 (mtt90)
REVERT: B   59 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8502 (t80)
REVERT: B  175 GLN cc_start: 0.7986 (mm110) cc_final: 0.7525 (mt0)
REVERT: B  259 GLN cc_start: 0.7809 (tt0) cc_final: 0.7498 (mt0)
REVERT: B  284 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8051 (mp)
REVERT: B  318 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8752 (tt)
REVERT: N   98 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8317 (ppt170)
REVERT: R  115 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8022 (mtt180)
REVERT: R  123 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6971 (mt)
  outliers start: 32
  outliers final: 19
  residues processed: 100
  average time/residue: 1.3779
  time to fit residues: 145.8482
Evaluate side-chains
  100 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 72
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain A residue  331 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   98 ARG
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   11 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   69 THR
Chi-restraints excluded: chain R residue   90 CYS
Chi-restraints excluded: chain R residue  115 ARG
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  211 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
N  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.171270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.129460 restraints weight = 26175.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.95
r_work: 0.3395 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8512  Z= 0.136
  Angle     :  0.537   5.048  11540  Z= 0.294
  Chirality :  0.042   0.159   1274
  Planarity :  0.004   0.047   1486
  Dihedral  :  5.680  57.028   1169
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 2.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.73 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.26), residues: 1044
  helix:  2.12 (0.27), residues: 407
  sheet: -0.35 (0.34), residues: 213
  loop : -1.49 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  98 
 TYR   0.014   0.001   TYR N  95 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.009   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8508)
  covalent geometry    : angle       0.53629 (11532)
  SS BOND              : bond        0.00352 (    4)
  SS BOND              : angle       1.42128 (    8)
  hydrogen bonds       : bond        0.05781 (  401)
  hydrogen bonds       : angle       4.29740 ( 1146)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5596.03 seconds
wall clock time: 95 minutes 11.97 seconds (5711.97 seconds total)