Starting phenix.real_space_refine
on Sat May 17 23:39:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bip_44597/05_2025/9bip_44597.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bip_44597/05_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_44597/05_2025/9bip_44597.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bip_44597/05_2025/9bip_44597.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bip_44597/05_2025/9bip_44597.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bip_44597/05_2025/9bip_44597.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 2, 'ARG:plan': 3}
          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: 8.11, per 1000 atoms: 0.49
  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: 4.30
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.56
  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: 5.26

  Time building geometry restraints manager: 5.16 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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.280
  Extract box with map and model:          0.660
  Check model and map are aligned:         0.140
  Set scattering table:                    0.160
  Process input model:                     35.910
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.410
-------------------------------------------------------------------------------
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 : 2.73
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (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
 TRP   0.011   0.001   TRP R  73 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.010   0.001   PHE R 159 
 TYR   0.008   0.001   TYR N  95 
 ARG   0.002   0.000   ARG A 333 

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

*********************** 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  : 1.345 
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: 2.7784
  time to fit residues: 259.6436
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  : 1.280 
-------------------------------------------------------------------------------
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 87 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.169545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.128592 restraints weight = 26157.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.12
r_work: 0.3375 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.0743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8512  Z= 0.178
  Angle     :  0.600   6.072  11540  Z= 0.329
  Chirality :  0.044   0.180   1274
  Planarity :  0.004   0.048   1486
  Dihedral  :  7.248  58.476   1193
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 2.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 16.95 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.26), residues: 1044
  helix:  1.79 (0.26), residues: 408
  sheet: -0.47 (0.34), residues: 216
  loop : -1.53 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 234 
 HIS   0.009   0.001   HIS R  79 
 PHE   0.014   0.002   PHE B 151 
 TYR   0.012   0.002   TYR N  95 
 ARG   0.004   0.000   ARG N  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07054 (  401)
  hydrogen bonds       : angle       4.73827 ( 1146)
  SS BOND              : bond        0.00580 (    4)
  SS BOND              : angle       1.23108 (    8)
  covalent geometry    : bond        0.00407 ( 8508)
  covalent geometry    : angle       0.59968 (11532)

*********************** 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: 32
    poor density    : 76
  time to evaluate  : 1.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.6938 (mt-10)
REVERT: B   59 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8513 (t80)
REVERT: B  175 GLN cc_start: 0.7873 (mm110) cc_final: 0.7432 (mt0)
REVERT: B  259 GLN cc_start: 0.7708 (tt0) cc_final: 0.7340 (mt0)
REVERT: B  284 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8003 (mp)
REVERT: N   98 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8370 (ppt90)
REVERT: R  115 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8080 (mtm-85)
REVERT: R  123 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7101 (mt)
  outliers start: 32
  outliers final: 12
  residues processed: 102
  average time/residue: 2.9075
  time to fit residues: 313.8320
Evaluate side-chains
  91 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 1.334 
-------------------------------------------------------------------------------
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  276 ILE
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  356 ARG
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 N residue   12 VAL
Chi-restraints excluded: chain N residue   98 ARG
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 14 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   chunk 23 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 99 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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
R 100 ASN
R 165 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.172028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.131470 restraints weight = 25904.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.14
r_work: 0.3400 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.0987

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= 0.122
  Angle     :  0.520   5.028  11540  Z= 0.285
  Chirality :  0.041   0.142   1274
  Planarity :  0.004   0.047   1486
  Dihedral  :  5.749  59.906   1170
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 1.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 17.85 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.26), residues: 1044
  helix:  2.05 (0.26), residues: 407
  sheet: -0.46 (0.34), residues: 219
  loop : -1.42 (0.27), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 297 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.016   0.001   PHE R  19 
 TYR   0.012   0.001   TYR N  95 
 ARG   0.002   0.000   ARG N 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05655 (  401)
  hydrogen bonds       : angle       4.40293 ( 1146)
  SS BOND              : bond        0.00368 (    4)
  SS BOND              : angle       1.05693 (    8)
  covalent geometry    : bond        0.00259 ( 8508)
  covalent geometry    : angle       0.51920 (11532)

*********************** 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
  106 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 1.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  327 GLU cc_start: 0.4615 (OUTLIER) cc_final: 0.4345 (mp0)
REVERT: A  344 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7645 (mm-30)
REVERT: B   59 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8413 (t80)
REVERT: B  175 GLN cc_start: 0.7851 (mm110) cc_final: 0.7418 (mt0)
REVERT: B  259 GLN cc_start: 0.7620 (tt0) cc_final: 0.7301 (mt0)
REVERT: B  284 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8073 (mp)
REVERT: N   98 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8249 (ppt170)
REVERT: R  123 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6869 (mt)
REVERT: R  181 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6037 (tmm)
  outliers start: 29
  outliers final: 14
  residues processed: 103
  average time/residue: 2.7084
  time to fit residues: 296.6259
Evaluate side-chains
  94 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
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  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 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 86 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 85 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 62 optimal weight:    0.4980
   chunk 89 optimal weight:    0.0980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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
R 100 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.173154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.132568 restraints weight = 26198.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.15
r_work: 0.3412 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8512  Z= 0.110
  Angle     :  0.500   4.974  11540  Z= 0.273
  Chirality :  0.041   0.140   1274
  Planarity :  0.003   0.046   1486
  Dihedral  :  5.513  59.291   1169
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 1.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.40 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.26), residues: 1044
  helix:  2.22 (0.27), residues: 407
  sheet: -0.34 (0.35), residues: 209
  loop : -1.45 (0.27), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 297 
 HIS   0.005   0.001   HIS R  79 
 PHE   0.018   0.001   PHE R  19 
 TYR   0.012   0.001   TYR N  95 
 ARG   0.001   0.000   ARG A 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05178 (  401)
  hydrogen bonds       : angle       4.24308 ( 1146)
  SS BOND              : bond        0.00334 (    4)
  SS BOND              : angle       1.00030 (    8)
  covalent geometry    : bond        0.00234 ( 8508)
  covalent geometry    : angle       0.49948 (11532)

*********************** 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
  111 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 79
  time to evaluate  : 1.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8376 (mp)
REVERT: A  309 GLU cc_start: 0.5547 (pm20) cc_final: 0.5302 (pp20)
REVERT: A  327 GLU cc_start: 0.4623 (OUTLIER) cc_final: 0.4337 (mt-10)
REVERT: B   59 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8390 (t80)
REVERT: B  175 GLN cc_start: 0.7836 (mm110) cc_final: 0.7383 (mt0)
REVERT: B  259 GLN cc_start: 0.7624 (tt0) cc_final: 0.7257 (mt0)
REVERT: B  318 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8685 (tt)
REVERT: N   98 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8439 (ppt90)
REVERT: R  115 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7784 (mtt180)
REVERT: R  123 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6840 (mt)
  outliers start: 32
  outliers final: 17
  residues processed: 107
  average time/residue: 2.6285
  time to fit residues: 298.8111
Evaluate side-chains
  99 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
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  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  189 SER
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 83 optimal weight:    0.4980
   chunk 19 optimal weight:    0.1980
   chunk 34 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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
R 100 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.174639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.133042 restraints weight = 26546.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.96
r_work: 0.3446 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3337 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8512  Z= 0.100
  Angle     :  0.480   4.934  11540  Z= 0.261
  Chirality :  0.040   0.139   1274
  Planarity :  0.003   0.045   1486
  Dihedral  :  5.337  58.762   1169
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.62 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.26), residues: 1044
  helix:  2.36 (0.27), residues: 407
  sheet: -0.30 (0.34), residues: 220
  loop : -1.40 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 297 
 HIS   0.003   0.001   HIS R  79 
 PHE   0.019   0.001   PHE R  19 
 TYR   0.012   0.001   TYR N  95 
 ARG   0.002   0.000   ARG N 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04722 (  401)
  hydrogen bonds       : angle       4.11842 ( 1146)
  SS BOND              : bond        0.00313 (    4)
  SS BOND              : angle       0.90461 (    8)
  covalent geometry    : bond        0.00206 ( 8508)
  covalent geometry    : angle       0.47930 (11532)

*********************** 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
  105 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 77
  time to evaluate  : 1.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6545 (mp0)
REVERT: A  229 ASP cc_start: 0.7641 (m-30) cc_final: 0.7440 (p0)
REVERT: A  327 GLU cc_start: 0.4701 (OUTLIER) cc_final: 0.4395 (mt-10)
REVERT: A  344 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7695 (mm-30)
REVERT: B   22 ARG cc_start: 0.5624 (mtt180) cc_final: 0.5394 (mtt90)
REVERT: B   59 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8425 (t80)
REVERT: B  175 GLN cc_start: 0.7946 (mm110) cc_final: 0.7598 (mt0)
REVERT: B  259 GLN cc_start: 0.7786 (tt0) cc_final: 0.7484 (mt0)
REVERT: N   98 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8521 (ppt90)
REVERT: R  115 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7897 (mtt180)
REVERT: R  123 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6887 (mt)
  outliers start: 28
  outliers final: 13
  residues processed: 101
  average time/residue: 2.9961
  time to fit residues: 319.5650
Evaluate side-chains
  97 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
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  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  189 SER
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 41 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 90 optimal weight:    9.9990
   chunk 2 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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
R 100 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.172608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.130826 restraints weight = 26276.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.96
r_work: 0.3414 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1324

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= 0.122
  Angle     :  0.512   4.951  11540  Z= 0.279
  Chirality :  0.041   0.150   1274
  Planarity :  0.004   0.049   1486
  Dihedral  :  5.358  58.647   1167
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  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 : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.26), residues: 1044
  helix:  2.31 (0.27), residues: 407
  sheet: -0.33 (0.35), residues: 211
  loop : -1.43 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.021   0.001   PHE R  19 
 TYR   0.015   0.001   TYR N  95 
 ARG   0.007   0.000   ARG R 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05319 (  401)
  hydrogen bonds       : angle       4.19868 ( 1146)
  SS BOND              : bond        0.00338 (    4)
  SS BOND              : angle       1.36129 (    8)
  covalent geometry    : bond        0.00267 ( 8508)
  covalent geometry    : angle       0.51071 (11532)

*********************** 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
  110 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 76
  time to evaluate  : 1.312 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.6589 (mp0)
REVERT: A  327 GLU cc_start: 0.4643 (OUTLIER) cc_final: 0.4344 (mt-10)
REVERT: A  344 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7099 (mt-10)
REVERT: B   22 ARG cc_start: 0.5644 (mtt180) cc_final: 0.5425 (mtt90)
REVERT: B   59 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8427 (t80)
REVERT: B  175 GLN cc_start: 0.7975 (mm110) cc_final: 0.7591 (mt0)
REVERT: B  259 GLN cc_start: 0.7822 (tt0) cc_final: 0.7500 (mt0)
REVERT: B  318 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8733 (tt)
REVERT: N   98 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8280 (ppt90)
REVERT: R  115 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8134 (mtt180)
REVERT: R  123 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7015 (mt)
  outliers start: 34
  outliers final: 18
  residues processed: 106
  average time/residue: 2.8686
  time to fit residues: 322.3147
Evaluate side-chains
  100 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 1.348 
-------------------------------------------------------------------------------
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  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  189 SER
Chi-restraints excluded: chain B residue  275 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 73 optimal weight:    0.4980
   chunk 81 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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
R 100 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.171404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.129518 restraints weight = 26378.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.95
r_work: 0.3384 rms_B_bonded: 2.22 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: 0.8113
moved from start:          0.1313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8512  Z= 0.141
  Angle     :  0.540   5.024  11540  Z= 0.295
  Chirality :  0.042   0.167   1274
  Planarity :  0.004   0.059   1486
  Dihedral  :  5.539  58.123   1167
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 16.95 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.26), residues: 1044
  helix:  2.20 (0.27), residues: 408
  sheet: -0.25 (0.34), residues: 211
  loop : -1.47 (0.27), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.015   0.001   TYR N  95 
 ARG   0.010   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05861 (  401)
  hydrogen bonds       : angle       4.28083 ( 1146)
  SS BOND              : bond        0.00352 (    4)
  SS BOND              : angle       1.59976 (    8)
  covalent geometry    : bond        0.00317 ( 8508)
  covalent geometry    : angle       0.53826 (11532)

*********************** 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
  112 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 74
  time to evaluate  : 1.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 GLU cc_start: 0.5394 (OUTLIER) cc_final: 0.4915 (pp20)
REVERT: A  327 GLU cc_start: 0.4692 (OUTLIER) cc_final: 0.4365 (mt-10)
REVERT: A  344 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7625 (mm-30)
REVERT: B   22 ARG cc_start: 0.5670 (mtt180) cc_final: 0.5448 (mtt90)
REVERT: B   59 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8440 (t80)
REVERT: B  175 GLN cc_start: 0.7961 (mm110) cc_final: 0.7523 (mt0)
REVERT: B  259 GLN cc_start: 0.7743 (tt0) cc_final: 0.7429 (mt0)
REVERT: B  284 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8006 (mp)
REVERT: B  318 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8772 (tt)
REVERT: N   98 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8343 (ppt170)
REVERT: R  115 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8054 (mtt180)
REVERT: R  123 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6984 (mt)
  outliers start: 38
  outliers final: 20
  residues processed: 108
  average time/residue: 2.5337
  time to fit residues: 291.5339
Evaluate side-chains
  103 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 74
  time to evaluate  : 1.360 
-------------------------------------------------------------------------------
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  309 GLU
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  189 SER
Chi-restraints excluded: chain B residue  275 SER
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 35 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 97 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
N  39 GLN
R 100 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.170948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.129053 restraints weight = 26107.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.95
r_work: 0.3371 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1318

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= 0.147
  Angle     :  0.548   4.968  11540  Z= 0.299
  Chirality :  0.042   0.171   1274
  Planarity :  0.004   0.070   1486
  Dihedral  :  5.616  57.252   1167
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 17.62 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.26), residues: 1044
  helix:  2.12 (0.26), residues: 408
  sheet: -0.35 (0.34), residues: 213
  loop : -1.48 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 362 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.015   0.002   TYR N  95 
 ARG   0.010   0.000   ARG R 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05998 (  401)
  hydrogen bonds       : angle       4.30880 ( 1146)
  SS BOND              : bond        0.00395 (    4)
  SS BOND              : angle       1.47791 (    8)
  covalent geometry    : bond        0.00331 ( 8508)
  covalent geometry    : angle       0.54651 (11532)

*********************** 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
  111 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 76
  time to evaluate  : 1.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 GLU cc_start: 0.5412 (OUTLIER) cc_final: 0.4924 (pp20)
REVERT: A  327 GLU cc_start: 0.4549 (OUTLIER) cc_final: 0.4309 (mt-10)
REVERT: A  344 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7659 (mm-30)
REVERT: B   22 ARG cc_start: 0.5752 (mtt180) cc_final: 0.5539 (mtt90)
REVERT: B   59 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8530 (t80)
REVERT: B  175 GLN cc_start: 0.7968 (mm110) cc_final: 0.7553 (mt0)
REVERT: B  259 GLN cc_start: 0.7772 (tt0) cc_final: 0.7458 (mt0)
REVERT: B  284 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7994 (mp)
REVERT: B  318 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8802 (tt)
REVERT: N   98 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8347 (ppt170)
REVERT: R  115 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8114 (mtt180)
REVERT: R  123 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7078 (mt)
  outliers start: 35
  outliers final: 21
  residues processed: 107
  average time/residue: 2.7078
  time to fit residues: 308.2074
Evaluate side-chains
  103 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 73
  time to evaluate  : 1.309 
-------------------------------------------------------------------------------
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  309 GLU
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  189 SER
Chi-restraints excluded: chain B residue  275 SER
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
Chi-restraints excluded: chain R residue  246 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 68 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0020
   chunk 90 optimal weight:    9.9990
   chunk 86 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 75 optimal weight:    9.9990
   chunk 58 optimal weight:    9.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
N  39 GLN
R 100 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.174828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.134381 restraints weight = 26214.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 2.05
r_work: 0.3455 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8512  Z= 0.098
  Angle     :  0.478   5.027  11540  Z= 0.260
  Chirality :  0.040   0.138   1274
  Planarity :  0.003   0.047   1486
  Dihedral  :  5.194  56.312   1167
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 18.29 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.27), residues: 1044
  helix:  2.41 (0.27), residues: 407
  sheet: -0.26 (0.34), residues: 220
  loop : -1.38 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 297 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.024   0.001   PHE R  19 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.007   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04595 (  401)
  hydrogen bonds       : angle       4.08537 ( 1146)
  SS BOND              : bond        0.00208 (    4)
  SS BOND              : angle       1.22047 (    8)
  covalent geometry    : bond        0.00205 ( 8508)
  covalent geometry    : angle       0.47668 (11532)

*********************** 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
  102 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 73
  time to evaluate  : 1.431 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.6485 (mp0)
REVERT: A  229 ASP cc_start: 0.7582 (m-30) cc_final: 0.7306 (p0)
REVERT: A  344 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7555 (mm-30)
REVERT: B   22 ARG cc_start: 0.5593 (mtt180) cc_final: 0.5373 (mtt90)
REVERT: B   59 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8374 (t80)
REVERT: B  146 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8514 (mm)
REVERT: B  175 GLN cc_start: 0.7812 (mm110) cc_final: 0.7341 (mt0)
REVERT: B  259 GLN cc_start: 0.7665 (tt0) cc_final: 0.7342 (mt0)
REVERT: B  318 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8603 (tt)
REVERT: N   98 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8457 (ppt90)
REVERT: R  115 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7707 (mtt180)
REVERT: R  123 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6771 (mt)
REVERT: R  181 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6054 (tmm)
  outliers start: 29
  outliers final: 15
  residues processed: 100
  average time/residue: 2.6035
  time to fit residues: 277.1881
Evaluate side-chains
  96 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
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  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  189 SER
Chi-restraints excluded: chain B residue  275 SER
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   90 CYS
Chi-restraints excluded: chain R residue  100 ASN
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
Chi-restraints excluded: chain R residue  246 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0370
   chunk 33 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 71 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.5458

-------------------------------------------------------------------------------
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 = 0.3995 r_free = 0.3995 target = 0.175055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.135110 restraints weight = 26357.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 2.20
r_work: 0.3461 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3359 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8512  Z= 0.097
  Angle     :  0.475   4.953  11540  Z= 0.257
  Chirality :  0.040   0.141   1274
  Planarity :  0.003   0.046   1486
  Dihedral  :  5.131  56.273   1167
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 1.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.74 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1044
  helix:  2.47 (0.27), residues: 407
  sheet: -0.22 (0.34), residues: 208
  loop : -1.35 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 297 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.027   0.001   PHE R  19 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.006   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04523 (  401)
  hydrogen bonds       : angle       4.06121 ( 1146)
  SS BOND              : bond        0.00213 (    4)
  SS BOND              : angle       1.15873 (    8)
  covalent geometry    : bond        0.00201 ( 8508)
  covalent geometry    : angle       0.47373 (11532)

********************** 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
  100 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 1.449 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6373 (mp0)
REVERT: A  229 ASP cc_start: 0.7563 (m-30) cc_final: 0.7289 (p0)
REVERT: A  344 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7605 (mm-30)
REVERT: B   22 ARG cc_start: 0.5585 (mtt180) cc_final: 0.5375 (mtt90)
REVERT: B   59 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8355 (t80)
REVERT: B  117 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8467 (mt)
REVERT: B  146 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8498 (mm)
REVERT: B  175 GLN cc_start: 0.7795 (mm110) cc_final: 0.7341 (mt0)
REVERT: B  259 GLN cc_start: 0.7620 (tt0) cc_final: 0.7264 (mt0)
REVERT: B  318 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8561 (tt)
REVERT: N   98 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8327 (ppt170)
REVERT: R  115 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7942 (mtt180)
REVERT: R  123 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6753 (mt)
REVERT: R  181 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6032 (tmm)
  outliers start: 25
  outliers final: 14
  residues processed: 97
  average time/residue: 2.6711
  time to fit residues: 275.4328
Evaluate side-chains
  97 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
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  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  117 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  275 SER
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   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 21 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 75 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
N  39 GLN
R  85 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.174016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.132086 restraints weight = 26237.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.97
r_work: 0.3427 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8512  Z= 0.110
  Angle     :  0.492   5.006  11540  Z= 0.268
  Chirality :  0.040   0.140   1274
  Planarity :  0.003   0.046   1486
  Dihedral  :  5.209  56.298   1167
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.63 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.26), residues: 1044
  helix:  2.45 (0.27), residues: 407
  sheet: -0.21 (0.35), residues: 208
  loop : -1.37 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.010   0.001   PHE R 159 
 TYR   0.013   0.001   TYR N  95 
 ARG   0.006   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04918 (  401)
  hydrogen bonds       : angle       4.10415 ( 1146)
  SS BOND              : bond        0.00274 (    4)
  SS BOND              : angle       1.24386 (    8)
  covalent geometry    : bond        0.00235 ( 8508)
  covalent geometry    : angle       0.49150 (11532)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10945.90 seconds
wall clock time: 187 minutes 22.11 seconds (11242.11 seconds total)