Starting phenix.real_space_refine
on Thu Jul  2 10:41:30 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7s8o_24899/07_2026/7s8o_24899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s8o_24899/07_2026/7s8o_24899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s8o_24899/07_2026/7s8o_24899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s8o_24899/07_2026/7s8o_24899.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7s8o_24899/07_2026/7s8o_24899.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7s8o_24899/07_2026/7s8o_24899.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s8o_24899/07_2026/7s8o_24899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s8o_24899/07_2026/7s8o_24899.map"
  }
  resolution = 2.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.027
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    5332      2.51       5
     N    1407      2.21       5
     O    1530      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8331
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 1893
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 1893
          Classifications: {'peptide': 257}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 8, 'TRANS': 248}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 160
          Unresolved non-hydrogen angles: 203
          Unresolved non-hydrogen dihedrals: 144
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 9, 'TRP:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 104
    Chain: "B"
      Number of atoms: 1707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1707
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "C"
      Number of atoms: 2564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2564
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 34
    Chain: "D"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 401
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "E"
      Number of atoms: 1743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1743
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "R"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'8IU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.53, per 1000 atoms: 0.18
  Number of scatterers: 8331
  At special positions: 0
  Unit cell: (91.91, 125.58, 121.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      62     16.00
     O    1530      8.00
     N    1407      7.00
     C    5332      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 168 " - pdb=" SG  CYS R 180 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 368.7 milliseconds
  

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2048

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 13 sheets defined
      36.7% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'R' and resid 30 through 57
      removed outlier: 3.967A  pdb=" N   VAL R  34 " --> pdb=" O   THR R  30 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   PHE R  35 " --> pdb=" O   LEU R  31 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL R  43 " --> pdb=" O   PHE R  39 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLY R  44 " --> pdb=" O   ILE R  40 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU R  45 " --> pdb=" O   ALA R  41 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   VAL R  46 " --> pdb=" O   LEU R  42 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLY R  47 " --> pdb=" O   VAL R  43 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 64 through 95
      removed outlier: 3.889A  pdb=" N   VAL R  68 " --> pdb=" O   PHE R  64 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 133
      removed outlier: 4.371A  pdb=" N   THR R 106 " --> pdb=" O   PRO R 102 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   THR R 107 " --> pdb=" O   SER R 103 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   LEU R 120 " --> pdb=" O   GLY R 116 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   SER R 121 " --> pdb=" O   LEU R 117 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 133 through 139
    Processing helix  chain 'R' and resid 144 through 167
      removed outlier: 3.715A  pdb=" N   PHE R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 212
      removed outlier: 3.645A  pdb=" N   GLY R 212 " --> pdb=" O   ARG R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 236
      removed outlier: 3.637A  pdb=" N   LEU R 221 " --> pdb=" O   PRO R 217 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 236 through 250
      removed outlier: 4.496A  pdb=" N   GLY R 240 " --> pdb=" O   GLY R 236 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   LEU R 247 " --> pdb=" O   TRP R 243 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   TRP R 248 " --> pdb=" O   PHE R 244 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 254 through 259
      removed outlier: 4.184A  pdb=" N   CYS R 258 " --> pdb=" O   ASP R 254 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 260 through 281
      Proline residue:  R 276  - end of helix
    Processing helix  chain 'B' and resid 6 through 31
    Processing helix  chain 'B' and resid 46 through 53
    Processing helix  chain 'B' and resid 207 through 216
      removed outlier: 3.546A  pdb=" N   LYS B 210 " --> pdb=" O   GLU B 207 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TRP B 211 " --> pdb=" O   ARG B 208 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   ILE B 212 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 5.437A  pdb=" N   HIS B 213 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE B 215 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 255
    Processing helix  chain 'B' and resid 270 through 278
      removed outlier: 3.544A  pdb=" N   PHE B 274 " --> pdb=" O   LYS B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 286
      removed outlier: 3.609A  pdb=" N   ILE B 285 " --> pdb=" O   PRO B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 309
    Processing helix  chain 'B' and resid 330 through 350
      removed outlier: 3.944A  pdb=" N   ASP B 341 " --> pdb=" O   ASP B 337 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL B 342 " --> pdb=" O   ALA B 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 24
      removed outlier: 3.510A  pdb=" N   LEU C  14 " --> pdb=" O   GLU C  10 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LYS C  15 " --> pdb=" O   ALA C  11 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASN C  16 " --> pdb=" O   GLU C  12 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLN C  17 " --> pdb=" O   GLN C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'D' and resid 9 through 23
    Processing helix  chain 'D' and resid 29 through 43
    Processing helix  chain 'D' and resid 55 through 59
      removed outlier: 3.876A  pdb=" N   ASN D  59 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.554A  pdb=" N   SER E  31 " --> pdb=" O   ALA E  28 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.828A  pdb=" N   ASP E  90 " --> pdb=" O   ARG E  87 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 87 through 91'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 190
      removed outlier: 6.914A  pdb=" N   LYS B  35 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
      removed outlier: 8.010A  pdb=" N   ILE B 222 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   CYS B 224 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   LEU B  39 " --> pdb=" O   CYS B 224 " (cutoff:3.500A)
      removed outlier: 8.810A  pdb=" N   ALA B 226 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ILE B 221 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   PHE B 267 " --> pdb=" O   ILE B 221 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   PHE B 223 " --> pdb=" O   PHE B 267 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   ASN B 269 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   VAL B 225 " --> pdb=" O   ASN B 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51
      removed outlier: 3.954A  pdb=" N   ARG C  46 " --> pdb=" O   ASN C 340 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   CYS C 317 " --> pdb=" O   GLY C 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 7.033A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.435A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASN C  88 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.990A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.206A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.938A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.935A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE C 199 " --> pdb=" O   TRP C 211 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.581A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.771A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLY C 306 " --> pdb=" O   VAL C 296 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.138A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.138A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129
    Processing sheet with id=AB4, first strand: chain 'E' and resid 135 through 136
      removed outlier: 6.773A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)

    409 hydrogen bonds defined for protein.
    1155 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: 1.30

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2664
        1.34 -     1.46: 1953
        1.46 -     1.58: 3804
        1.58 -     1.70: 1
        1.70 -     1.81: 86
  Bond restraints: 8508
  Sorted by residual:
  bond pdb=" C03 8IU R 401 "
       pdb=" C04 8IU R 401 "
    ideal  model  delta    sigma   weight residual
    1.528  1.320  0.208 2.00e-02 2.50e+03 1.09e+02
  bond pdb=" C04 8IU R 401 "
       pdb=" N05 8IU R 401 "
    ideal  model  delta    sigma   weight residual
    1.457  1.647 -0.190 2.00e-02 2.50e+03 9.07e+01
  bond pdb=" C21 8IU R 401 "
       pdb=" N05 8IU R 401 "
    ideal  model  delta    sigma   weight residual
    1.470  1.326  0.144 2.00e-02 2.50e+03 5.20e+01
  bond pdb=" C03 8IU R 401 "
       pdb=" N02 8IU R 401 "
    ideal  model  delta    sigma   weight residual
    1.448  1.557 -0.109 2.00e-02 2.50e+03 2.98e+01
  bond pdb=" N19 8IU R 401 "
       pdb=" N20 8IU R 401 "
    ideal  model  delta    sigma   weight residual
    1.341  1.444 -0.103 2.00e-02 2.50e+03 2.63e+01
  ... (remaining 8503 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 11344
        2.15 -     4.30: 180
        4.30 -     6.46: 32
        6.46 -     8.61: 4
        8.61 -    10.76: 1
  Bond angle restraints: 11561
  Sorted by residual:
  angle pdb=" CA  LEU R 163 "
        pdb=" C   LEU R 163 "
        pdb=" N   GLU R 164 "
      ideal   model   delta    sigma   weight residual
     118.14  122.91   -4.77 1.31e+00 5.83e-01 1.32e+01
  angle pdb=" N   LEU R 237 "
        pdb=" CA  LEU R 237 "
        pdb=" C   LEU R 237 "
      ideal   model   delta    sigma   weight residual
     109.81  117.45   -7.64 2.21e+00 2.05e-01 1.19e+01
  angle pdb=" N   PRO E 224 "
        pdb=" CA  PRO E 224 "
        pdb=" C   PRO E 224 "
      ideal   model   delta    sigma   weight residual
     112.10  120.22   -8.12 2.60e+00 1.48e-01 9.74e+00
  angle pdb=" CA  TYR E 178 "
        pdb=" CB  TYR E 178 "
        pdb=" CG  TYR E 178 "
      ideal   model   delta    sigma   weight residual
     113.90  119.47   -5.57 1.80e+00 3.09e-01 9.56e+00
  angle pdb=" CA  LEU B 227 "
        pdb=" CB  LEU B 227 "
        pdb=" CG  LEU B 227 "
      ideal   model   delta    sigma   weight residual
     116.30  127.06  -10.76 3.50e+00 8.16e-02 9.45e+00
  ... (remaining 11556 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.88: 4517
       16.88 -    33.76: 364
       33.76 -    50.64: 76
       50.64 -    67.51: 12
       67.51 -    84.39: 5
  Dihedral angle restraints: 4974
    sinusoidal: 1799
      harmonic: 3175
  Sorted by residual:
  dihedral pdb=" CA  ARG E 206 "
           pdb=" C   ARG E 206 "
           pdb=" N   LEU E 207 "
           pdb=" CA  LEU E 207 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.85  -22.15     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  ASN B 347 "
           pdb=" C   ASN B 347 "
           pdb=" N   LEU B 348 "
           pdb=" CA  LEU B 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.06   21.94     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  CYS R  95 "
           pdb=" C   CYS R  95 "
           pdb=" N   SER R  96 "
           pdb=" CA  SER R  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.44  -21.56     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 4971 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 863
       0.038 -    0.076: 352
       0.076 -    0.113: 96
       0.113 -    0.151: 29
       0.151 -    0.189: 3
  Chirality restraints: 1343
  Sorted by residual:
  chirality pdb=" CA  PRO E 224 "
            pdb=" N   PRO E 224 "
            pdb=" C   PRO E 224 "
            pdb=" CB  PRO E 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.93e-01
  chirality pdb=" CA  LEU R 237 "
            pdb=" N   LEU R 237 "
            pdb=" C   LEU R 237 "
            pdb=" CB  LEU R 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.52e-01
  chirality pdb=" CA  ASN B 347 "
            pdb=" N   ASN B 347 "
            pdb=" C   ASN B 347 "
            pdb=" CB  ASN B 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.15e-01
  ... (remaining 1340 not shown)

  Planarity restraints: 1449
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E 135 "    0.044 5.00e-02 4.00e+02   6.75e-02 7.29e+00
        pdb=" N   PRO E 136 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO E 136 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO E 136 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN R 242 "    0.010 2.00e-02 2.50e+03   1.98e-02 3.94e+00
        pdb=" C   GLN R 242 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   GLN R 242 "    0.013 2.00e-02 2.50e+03
        pdb=" N   TRP R 243 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 123 "    0.010 2.00e-02 2.50e+03   1.94e-02 3.76e+00
        pdb=" C   VAL R 123 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   VAL R 123 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER R 124 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1446 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 67
        2.66 -     3.22: 7178
        3.22 -     3.78: 11683
        3.78 -     4.34: 15805
        4.34 -     4.90: 28160
  Nonbonded interactions: 62893
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP R  75 "
            pdb=" OG  SER R 272 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" OG1 THR C 128 "
            pdb=" O   GLU C 130 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OH  TYR R 113 "
            pdb=" O   GLY R 236 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   ASP C 333 "
            pdb=" OG  SER C 334 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" O   SER E 106 "
            pdb=" OG  SER E 106 "
     model   vdw
     2.334 3.040
  ... (remaining 62888 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:             1.110
  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:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.040
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:8.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
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      :  0.007   0.208   8509  Z= 0.309
  Angle     :  0.718  10.761  11563  Z= 0.386
  Chirality :  0.046   0.189   1343
  Planarity :  0.005   0.068   1449
  Dihedral  : 13.182  84.393   2923
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.26), residues: 1083
  helix:  2.11 (0.28), residues: 359
  sheet:  0.95 (0.31), residues: 292
  loop : -2.12 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 206 
 TYR   0.029   0.002   TYR E 178 
 PHE   0.020   0.002   PHE R 232 
 TRP   0.016   0.002   TRP C  82 
 HIS   0.005   0.001   HIS C  91 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00678 /  0.31 ( 8508)
  covalent geometry    : angle       0.71802 /  0.39 (11561)
  SS BOND              : bond        0.00267 /  0.17 (    1)
  SS BOND              : angle       1.88583 /  0.87 (    2)
  hydrogen bonds       : bond        0.15049 / 10.47 (  405)
  hydrogen bonds       : angle       5.79503 /  4.46 ( 1155)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.345 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.5238
  time to fit residues: 90.1996
Evaluate side-chains
  148 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    0.0060
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7596

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  75 GLN
C 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.118810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.101858 restraints weight = 11657.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.70
r_work: 0.3250 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8509  Z= 0.148
  Angle     :  0.588   7.179  11563  Z= 0.312
  Chirality :  0.042   0.171   1343
  Planarity :  0.004   0.051   1449
  Dihedral  :  4.940  57.357   1181
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.27 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.26), residues: 1083
  helix:  2.77 (0.28), residues: 362
  sheet:  1.26 (0.32), residues: 268
  loop : -2.02 (0.25), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 206 
 TYR   0.020   0.002   TYR E 178 
 PHE   0.014   0.001   PHE R 232 
 TRP   0.019   0.002   TRP R 248 
 HIS   0.003   0.001   HIS C  91 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 ( 8508)
  covalent geometry    : angle       0.58817 /  0.31 (11561)
  SS BOND              : bond        0.00128 /  0.08 (    1)
  SS BOND              : angle       0.88818 /  0.38 (    2)
  hydrogen bonds       : bond        0.05772 /  3.93 (  405)
  hydrogen bonds       : angle       4.37069 /  3.28 ( 1155)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.257 
Fit side-chains
REVERT: C   23 LYS cc_start: 0.8169 (tmmt) cc_final: 0.7750 (ttmt)
REVERT: C   57 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8216 (ptmt)
  outliers start: 15
  outliers final: 5
  residues processed: 153
  average time/residue: 0.5099
  time to fit residues: 83.2586
Evaluate side-chains
  147 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 141
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   77 LEU
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain R residue  249 ILE
Chi-restraints excluded: chain C residue   57 LYS
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain E residue  115 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0070
   chunk 96 optimal weight:    0.0030
   chunk 30 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 69 optimal weight:    0.0670
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.2746

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  48 ASN
B 255 ASN
C 132 ASN
C 142 HIS
C 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.122451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.105639 restraints weight = 11770.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.70
r_work: 0.3309 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8509  Z= 0.094
  Angle     :  0.487   6.149  11563  Z= 0.258
  Chirality :  0.039   0.134   1343
  Planarity :  0.003   0.037   1449
  Dihedral  :  4.579  58.241   1181
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.80 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.26), residues: 1083
  helix:  3.17 (0.28), residues: 361
  sheet:  1.26 (0.31), residues: 273
  loop : -1.85 (0.26), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 140 
 TYR   0.014   0.001   TYR R 222 
 PHE   0.010   0.001   PHE B 189 
 TRP   0.015   0.001   TRP R 248 
 HIS   0.002   0.001   HIS B 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00187 /  0.09 ( 8508)
  covalent geometry    : angle       0.48702 /  0.26 (11561)
  SS BOND              : bond        0.00076 /  0.05 (    1)
  SS BOND              : angle       0.66422 /  0.30 (    2)
  hydrogen bonds       : bond        0.04072 /  2.77 (  405)
  hydrogen bonds       : angle       3.91790 /  2.94 ( 1155)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 155
  time to evaluate  : 0.315 
Fit side-chains
REVERT: B  252 SER cc_start: 0.8413 (t) cc_final: 0.8083 (p)
  outliers start: 17
  outliers final: 3
  residues processed: 160
  average time/residue: 0.4896
  time to fit residues: 83.7290
Evaluate side-chains
  161 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 158
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  350 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0980
   chunk 51 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 98 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0970
   overall best weight:    0.4778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  48 ASN
C  75 GLN
C 132 ASN
C 142 HIS
C 340 ASN
E 130 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.120007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.103222 restraints weight = 11853.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 1.70
r_work: 0.3276 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8509  Z= 0.110
  Angle     :  0.510   5.736  11563  Z= 0.270
  Chirality :  0.040   0.149   1343
  Planarity :  0.003   0.037   1449
  Dihedral  :  4.549  56.311   1181
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.88 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.26), residues: 1083
  helix:  3.28 (0.28), residues: 361
  sheet:  1.34 (0.31), residues: 267
  loop : -1.84 (0.25), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  19 
 TYR   0.017   0.001   TYR E 178 
 PHE   0.011   0.001   PHE B 189 
 TRP   0.014   0.001   TRP R 248 
 HIS   0.003   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 8508)
  covalent geometry    : angle       0.50975 /  0.27 (11561)
  SS BOND              : bond        0.00049 /  0.03 (    1)
  SS BOND              : angle       0.89707 /  0.39 (    2)
  hydrogen bonds       : bond        0.04645 /  3.16 (  405)
  hydrogen bonds       : angle       3.89697 /  2.93 ( 1155)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 154
  time to evaluate  : 0.261 
Fit side-chains
REVERT: B  252 SER cc_start: 0.8384 (t) cc_final: 0.8084 (p)
  outliers start: 17
  outliers final: 7
  residues processed: 158
  average time/residue: 0.4670
  time to fit residues: 78.6771
Evaluate side-chains
  155 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 148
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   77 LEU
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  207 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 28 optimal weight:    0.0670
   chunk 93 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0060
   chunk 84 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 92 optimal weight:    0.6980
   chunk 98 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.4334

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  48 ASN
C  75 GLN
C 132 ASN
C 142 HIS
C 340 ASN
E 130 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.120755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.103948 restraints weight = 11822.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 1.72
r_work: 0.3283 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8509  Z= 0.103
  Angle     :  0.497   6.498  11563  Z= 0.263
  Chirality :  0.040   0.146   1343
  Planarity :  0.003   0.036   1449
  Dihedral  :  4.419  52.706   1181
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 2.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 16.61 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.26), residues: 1083
  helix:  3.34 (0.28), residues: 361
  sheet:  1.37 (0.31), residues: 267
  loop : -1.81 (0.25), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 137 
 TYR   0.016   0.001   TYR E 178 
 PHE   0.011   0.001   PHE B 189 
 TRP   0.017   0.001   TRP R 248 
 HIS   0.003   0.001   HIS E 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00217 /  0.10 ( 8508)
  covalent geometry    : angle       0.49728 /  0.26 (11561)
  SS BOND              : bond        0.00036 /  0.02 (    1)
  SS BOND              : angle       0.81212 /  0.35 (    2)
  hydrogen bonds       : bond        0.04425 /  3.00 (  405)
  hydrogen bonds       : angle       3.84530 /  2.88 ( 1155)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.240 
Fit side-chains
REVERT: B  252 SER cc_start: 0.8366 (t) cc_final: 0.8046 (p)
REVERT: C  129 ARG cc_start: 0.7647 (mmm160) cc_final: 0.7380 (mmm160)
REVERT: C  164 THR cc_start: 0.7979 (m) cc_final: 0.7637 (p)
REVERT: C  220 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8155 (mt0)
  outliers start: 18
  outliers final: 8
  residues processed: 165
  average time/residue: 0.4422
  time to fit residues: 78.3289
Evaluate side-chains
  162 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 153
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  220 GLN
Chi-restraints excluded: chain E residue  115 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  48 ASN
C  75 GLN
C 132 ASN
C 142 HIS
C 340 ASN
E 130 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.116726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.100149 restraints weight = 11611.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 1.68
r_work: 0.3226 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8509  Z= 0.165
  Angle     :  0.594   7.610  11563  Z= 0.312
  Chirality :  0.043   0.187   1343
  Planarity :  0.004   0.038   1449
  Dihedral  :  4.751  51.098   1181
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.76 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.26), residues: 1083
  helix:  3.16 (0.28), residues: 363
  sheet:  1.34 (0.31), residues: 264
  loop : -1.79 (0.25), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  19 
 TYR   0.026   0.002   TYR E 178 
 PHE   0.017   0.002   PHE R 232 
 TRP   0.020   0.002   TRP R 248 
 HIS   0.005   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00388 /  0.17 ( 8508)
  covalent geometry    : angle       0.59363 /  0.31 (11561)
  SS BOND              : bond        0.00116 /  0.07 (    1)
  SS BOND              : angle       1.56015 /  0.67 (    2)
  hydrogen bonds       : bond        0.06216 /  4.22 (  405)
  hydrogen bonds       : angle       4.12683 /  3.08 ( 1155)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 161
  time to evaluate  : 0.330 
Fit side-chains
REVERT: B  243 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7990 (mmt)
REVERT: B  252 SER cc_start: 0.8374 (t) cc_final: 0.8090 (p)
REVERT: C  164 THR cc_start: 0.8097 (m) cc_final: 0.7811 (p)
  outliers start: 17
  outliers final: 12
  residues processed: 169
  average time/residue: 0.5375
  time to fit residues: 96.6285
Evaluate side-chains
  175 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 162
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 VAL
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue  243 MET
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain E residue  115 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 104 optimal weight:    4.9990
   chunk 57 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 86 optimal weight:    3.9990
   chunk 98 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 99 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  48 ASN
C  75 GLN
C 132 ASN
C 340 ASN
E 167 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.117725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.101032 restraints weight = 11828.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 1.72
r_work: 0.3238 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8509  Z= 0.140
  Angle     :  0.558   7.524  11563  Z= 0.295
  Chirality :  0.042   0.170   1343
  Planarity :  0.004   0.038   1449
  Dihedral  :  4.550  43.577   1181
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 17.76 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.26), residues: 1083
  helix:  3.16 (0.28), residues: 363
  sheet:  1.39 (0.31), residues: 263
  loop : -1.84 (0.25), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  19 
 TYR   0.020   0.002   TYR E 178 
 PHE   0.013   0.001   PHE C 151 
 TRP   0.016   0.002   TRP R 248 
 HIS   0.004   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.14 ( 8508)
  covalent geometry    : angle       0.55743 /  0.29 (11561)
  SS BOND              : bond        0.00042 /  0.03 (    1)
  SS BOND              : angle       1.14348 /  0.50 (    2)
  hydrogen bonds       : bond        0.05560 /  3.77 (  405)
  hydrogen bonds       : angle       4.01496 /  2.99 ( 1155)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.314 
Fit side-chains
REVERT: R   68 VAL cc_start: 0.7265 (OUTLIER) cc_final: 0.7059 (t)
REVERT: B  252 SER cc_start: 0.8404 (t) cc_final: 0.8125 (p)
REVERT: C  164 THR cc_start: 0.8088 (m) cc_final: 0.7788 (p)
REVERT: C  220 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8325 (mt0)
REVERT: C  258 ASP cc_start: 0.8260 (t70) cc_final: 0.7970 (t70)
  outliers start: 24
  outliers final: 14
  residues processed: 162
  average time/residue: 0.5626
  time to fit residues: 96.9343
Evaluate side-chains
  168 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 VAL
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  309 ASP
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  220 GLN
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  115 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  48 ASN
C  75 GLN
C 132 ASN
C 259 GLN
C 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.115954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.099442 restraints weight = 11654.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.68
r_work: 0.3214 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8509  Z= 0.184
  Angle     :  0.616   7.957  11563  Z= 0.325
  Chirality :  0.044   0.197   1343
  Planarity :  0.004   0.040   1449
  Dihedral  :  4.503  21.871   1181
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 2.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 18.92 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.26), residues: 1083
  helix:  3.06 (0.28), residues: 362
  sheet:  1.38 (0.31), residues: 258
  loop : -1.85 (0.25), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  19 
 TYR   0.027   0.002   TYR E 178 
 PHE   0.018   0.002   PHE R 232 
 TRP   0.017   0.002   TRP R 248 
 HIS   0.005   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00442 /  0.18 ( 8508)
  covalent geometry    : angle       0.61589 /  0.32 (11561)
  SS BOND              : bond        0.00093 /  0.06 (    1)
  SS BOND              : angle       1.60691 /  0.70 (    2)
  hydrogen bonds       : bond        0.06599 /  4.49 (  405)
  hydrogen bonds       : angle       4.18355 /  3.12 ( 1155)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 159
  time to evaluate  : 0.328 
Fit side-chains
REVERT: B  252 SER cc_start: 0.8373 (t) cc_final: 0.8105 (p)
REVERT: C  164 THR cc_start: 0.8156 (m) cc_final: 0.7869 (p)
REVERT: C  220 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8418 (mt0)
REVERT: E  128 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8654 (mmm)
  outliers start: 23
  outliers final: 15
  residues processed: 168
  average time/residue: 0.5515
  time to fit residues: 98.7225
Evaluate side-chains
  174 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 VAL
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  309 ASP
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  220 GLN
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  128 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 62 optimal weight:    0.4980
   chunk 4 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  48 ASN
B 294 ASN
C  75 GLN
C 132 ASN
C 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.117675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.101024 restraints weight = 11759.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.71
r_work: 0.3239 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8509  Z= 0.136
  Angle     :  0.555   7.408  11563  Z= 0.294
  Chirality :  0.041   0.172   1343
  Planarity :  0.004   0.038   1449
  Dihedral  :  4.252  19.329   1181
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.61 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.26), residues: 1083
  helix:  3.16 (0.28), residues: 362
  sheet:  1.36 (0.31), residues: 262
  loop : -1.87 (0.25), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  19 
 TYR   0.020   0.002   TYR E 178 
 PHE   0.013   0.001   PHE B 189 
 TRP   0.015   0.002   TRP R 248 
 HIS   0.004   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.14 ( 8508)
  covalent geometry    : angle       0.55452 /  0.29 (11561)
  SS BOND              : bond        0.00008 /  0.01 (    1)
  SS BOND              : angle       1.10563 /  0.49 (    2)
  hydrogen bonds       : bond        0.05533 /  3.76 (  405)
  hydrogen bonds       : angle       4.01097 /  2.98 ( 1155)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 151
  time to evaluate  : 0.288 
Fit side-chains
REVERT: B  252 SER cc_start: 0.8366 (t) cc_final: 0.8066 (p)
REVERT: C  164 THR cc_start: 0.8093 (m) cc_final: 0.7793 (p)
REVERT: C  220 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8360 (mt0)
REVERT: E  128 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8652 (mmm)
  outliers start: 22
  outliers final: 16
  residues processed: 161
  average time/residue: 0.5381
  time to fit residues: 92.4258
Evaluate side-chains
  169 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   54 LEU
Chi-restraints excluded: chain R residue   68 VAL
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  309 ASP
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  220 GLN
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  128 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0570
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    5.9990
   chunk 98 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0670
   chunk 7 optimal weight:    9.9990
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.5036

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  48 ASN
C  75 GLN
C 132 ASN
C 142 HIS
C 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.119401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.102769 restraints weight = 11765.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.70
r_work: 0.3265 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8509  Z= 0.112
  Angle     :  0.516   7.055  11563  Z= 0.275
  Chirality :  0.040   0.154   1343
  Planarity :  0.004   0.038   1449
  Dihedral  :  4.028  19.071   1181
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 20.42 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.26), residues: 1083
  helix:  3.29 (0.28), residues: 363
  sheet:  1.39 (0.31), residues: 262
  loop : -1.84 (0.25), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  19 
 TYR   0.015   0.001   TYR E 178 
 PHE   0.012   0.001   PHE B 189 
 TRP   0.013   0.001   TRP R 243 
 HIS   0.002   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.11 ( 8508)
  covalent geometry    : angle       0.51599 /  0.27 (11561)
  SS BOND              : bond        0.00053 /  0.03 (    1)
  SS BOND              : angle       0.93188 /  0.41 (    2)
  hydrogen bonds       : bond        0.04712 /  3.20 (  405)
  hydrogen bonds       : angle       3.84542 /  2.86 ( 1155)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.317 
Fit side-chains
REVERT: B  252 SER cc_start: 0.8377 (t) cc_final: 0.8072 (p)
REVERT: C   22 ARG cc_start: 0.8276 (mtm180) cc_final: 0.7884 (mtt180)
REVERT: C  164 THR cc_start: 0.8044 (m) cc_final: 0.7747 (p)
REVERT: C  220 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8275 (mt0)
REVERT: E  128 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8647 (mmm)
  outliers start: 19
  outliers final: 14
  residues processed: 165
  average time/residue: 0.5292
  time to fit residues: 93.2772
Evaluate side-chains
  169 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 VAL
Chi-restraints excluded: chain R residue  226 LEU
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  309 ASP
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  220 GLN
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  128 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0060
   chunk 97 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.7196

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  48 ASN
C  75 GLN
C 132 ASN
C 142 HIS
C 340 ASN
E 130 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.117826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.101235 restraints weight = 11752.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.69
r_work: 0.3243 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8509  Z= 0.135
  Angle     :  0.551   6.976  11563  Z= 0.292
  Chirality :  0.041   0.170   1343
  Planarity :  0.004   0.038   1449
  Dihedral  :  4.153  19.446   1181
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 20.42 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.26), residues: 1083
  helix:  3.32 (0.28), residues: 363
  sheet:  1.45 (0.31), residues: 252
  loop : -1.80 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  19 
 TYR   0.020   0.002   TYR E 178 
 PHE   0.013   0.001   PHE R 232 
 TRP   0.013   0.001   TRP R 243 
 HIS   0.003   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.13 ( 8508)
  covalent geometry    : angle       0.55084 /  0.29 (11561)
  SS BOND              : bond        0.00005 /  0.00 (    1)
  SS BOND              : angle       1.22125 /  0.53 (    2)
  hydrogen bonds       : bond        0.05412 /  3.68 (  405)
  hydrogen bonds       : angle       3.93102 /  2.93 ( 1155)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3557.16 seconds
wall clock time: 61 minutes 13.13 seconds (3673.13 seconds total)