Starting phenix.real_space_refine
on Fri Aug 22 22:18:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jxt_36712/08_2025/8jxt_36712_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jxt_36712/08_2025/8jxt_36712.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jxt_36712/08_2025/8jxt_36712.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jxt_36712/08_2025/8jxt_36712.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jxt_36712/08_2025/8jxt_36712_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jxt_36712/08_2025/8jxt_36712_neut.cif"
  }
  resolution = 3.07
  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=  -0.003 sd=   0.121
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
     P       1      5.49       5
     S      54      5.16       5
     C    5330      2.51       5
     N    1365      2.21       5
     O    1548      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8298
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1627
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 151
          Unresolved non-hydrogen dihedrals: 106
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 9, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 79
    Chain: "C"
      Number of atoms: 2489
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2489
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 7, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 75
    Chain: "D"
      Number of atoms: 336
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 336
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 39
    Chain: "E"
      Number of atoms: 1728
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1728
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 38
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "R"
      Number of atoms: 2105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2105
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 9, 'TRANS': 260}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 144
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 2, 'HIS:plan': 1, 'TRP:plan': 2, 'ARG:plan': 4, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 74
    Chain: "R"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 13
          Unusual residues: {'HSM': 1, 'PO4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.60, per 1000 atoms: 0.19
  Number of scatterers: 8298
  At special positions: 0
  Unit cell: (91.3, 124.3, 127.6, 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      54     16.00
     P       1     15.00
     O    1548      8.00
     N    1365      7.00
     C    5330      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 160 " - pdb=" SG  CYS E 230 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  87 " - pdb=" SG  CYS R 164 " 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: 0.50
  Conformation dependent library (CDL) restraints added in 417.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2076

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 12 sheets defined
      36.7% alpha, 22.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 30
    Processing helix  chain 'B' and resid 45 through 53
      removed outlier: 3.586A  pdb=" N   ILE B  49 " --> pdb=" O   GLY B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 216
      removed outlier: 3.673A  pdb=" N   CYS B 214 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 255
      removed outlier: 3.808A  pdb=" N   GLU B 245 " --> pdb=" O   ASN B 241 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ASN B 255 " --> pdb=" O   ASP B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 260
      removed outlier: 3.912A  pdb=" N   THR B 260 " --> pdb=" O   LYS B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 276
    Processing helix  chain 'B' and resid 282 through 286
    Processing helix  chain 'B' and resid 295 through 309
    Processing helix  chain 'B' and resid 329 through 351
      removed outlier: 3.789A  pdb=" N   GLN B 333 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   VAL B 335 " --> pdb=" O   ASN B 331 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   CYS B 351 " --> pdb=" O   ASN B 347 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 5 through 26
    Processing helix  chain 'C' and resid 29 through 37
      removed outlier: 4.363A  pdb=" N   THR C  34 " --> pdb=" O   SER C  31 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   ASN C  35 " --> pdb=" O   GLN C  32 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ASN C  36 " --> pdb=" O   ILE C  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 24
      removed outlier: 3.672A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.672A  pdb=" N   ALA D  33 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   HIS D  44 " --> pdb=" O   TYR D  40 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 56
      removed outlier: 4.359A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 15 through 43
      removed outlier: 4.064A  pdb=" N   VAL R  36 " --> pdb=" O   GLY R  32 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 48 through 78
      removed outlier: 3.805A  pdb=" N   GLY R  65 " --> pdb=" O   ASP R  61 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   VAL R  66 " --> pdb=" O   PHE R  62 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ILE R  67 " --> pdb=" O   PHE R  63 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER R  68 " --> pdb=" O   VAL R  64 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   ILE R  69 " --> pdb=" O   GLY R  65 " (cutoff:3.500A)
      Proline residue:  R  70  - end of helix
      Proline residue:  R  74  - end of helix
      removed outlier: 3.571A  pdb=" N   PHE R  78 " --> pdb=" O   PRO R  74 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 83 through 118
      removed outlier: 4.199A  pdb=" N   PHE R  89 " --> pdb=" O   GLU R  85 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   VAL R 116 " --> pdb=" O   ARG R 112 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ASN R 118 " --> pdb=" O   LEU R 114 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 119 through 124
    Processing helix  chain 'R' and resid 130 through 153
      removed outlier: 3.977A  pdb=" N   TRP R 140 " --> pdb=" O   MET R 136 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ASN R 147 " --> pdb=" O   ALA R 143 " (cutoff:3.500A)
      Proline residue:  R 149  - end of helix
    Processing helix  chain 'R' and resid 171 through 181
      removed outlier: 3.899A  pdb=" N   LEU R 175 " --> pdb=" O   GLU R 171 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   ILE R 177 " --> pdb=" O   TYR R 173 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 183 through 203
      removed outlier: 4.016A  pdb=" N   LYS R 203 " --> pdb=" O   TRP R 199 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 294 through 329
      removed outlier: 4.435A  pdb=" N   PHE R 312 " --> pdb=" O   LEU R 308 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
      removed outlier: 4.466A  pdb=" N   TYR R 329 " --> pdb=" O   VAL R 325 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 337 through 349
      removed outlier: 3.904A  pdb=" N   TRP R 345 " --> pdb=" O   ARG R 341 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLN R 347 " --> pdb=" O   ALA R 343 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   TRP R 348 " --> pdb=" O   PHE R 344 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   PHE R 349 " --> pdb=" O   TRP R 345 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 349 through 362
      removed outlier: 3.584A  pdb=" N   VAL R 353 " --> pdb=" O   PHE R 349 " (cutoff:3.500A)
      Proline residue:  R 355  - end of helix
      removed outlier: 3.548A  pdb=" N   TYR R 358 " --> pdb=" O   ASN R 354 " (cutoff:3.500A)
      Proline residue:  R 359  - end of helix
      removed outlier: 4.162A  pdb=" N   HIS R 362 " --> pdb=" O   TYR R 358 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 362 through 371
    Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191
      removed outlier: 6.923A  pdb=" N   LYS B  35 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   ILE B 222 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   CYS B 224 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   LEU B  39 " --> pdb=" O   CYS B 224 " (cutoff:3.500A)
      removed outlier: 9.030A  pdb=" N   ALA B 226 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 7.054A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 7.070A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 7.042A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153
      removed outlier: 7.109A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.374A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.069A  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: 6.747A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.169A  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: 6.745A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 277
      removed outlier: 6.566A  pdb=" N   GLY C 288 " --> pdb=" O   THR C 274 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   VAL C 276 " --> pdb=" O   LEU C 286 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   LEU C 286 " --> pdb=" O   VAL C 276 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
      removed outlier: 6.157A  pdb=" N   GLY E  16 " --> pdb=" O   SER E  85 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.264A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 142 through 143
      removed outlier: 3.567A  pdb=" N   THR E 142 " --> pdb=" O   ARG E 161 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ARG E 161 " --> pdb=" O   THR E 142 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149
      removed outlier: 3.554A  pdb=" N   GLU E 247 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LEU E 179 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   LEU E 188 " --> pdb=" O   LEU E 179 " (cutoff:3.500A)

    396 hydrogen bonds defined for protein.
    1116 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.84

  Time building geometry restraints manager: 0.72 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: 2636
        1.34 -     1.46: 2224
        1.46 -     1.59: 3550
        1.59 -     1.71: 0
        1.71 -     1.83: 77
  Bond restraints: 8487
  Sorted by residual:
  bond pdb=" O3  PO4 R 402 "
       pdb=" P   PO4 R 402 "
    ideal  model  delta    sigma   weight residual
    1.569  1.524  0.045 2.00e-02 2.50e+03 5.02e+00
  bond pdb=" CB  HSM R 401 "
       pdb=" CG  HSM R 401 "
    ideal  model  delta    sigma   weight residual
    1.496  1.452  0.044 2.00e-02 2.50e+03 4.88e+00
  bond pdb=" O2  PO4 R 402 "
       pdb=" P   PO4 R 402 "
    ideal  model  delta    sigma   weight residual
    1.567  1.523  0.044 2.00e-02 2.50e+03 4.76e+00
  bond pdb=" O4  PO4 R 402 "
       pdb=" P   PO4 R 402 "
    ideal  model  delta    sigma   weight residual
    1.568  1.525  0.043 2.00e-02 2.50e+03 4.60e+00
  bond pdb=" O1  PO4 R 402 "
       pdb=" P   PO4 R 402 "
    ideal  model  delta    sigma   weight residual
    1.565  1.524  0.041 2.00e-02 2.50e+03 4.27e+00
  ... (remaining 8482 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 11302
        1.85 -     3.71: 225
        3.71 -     5.56: 37
        5.56 -     7.41: 8
        7.41 -     9.27: 2
  Bond angle restraints: 11574
  Sorted by residual:
  angle pdb=" CA  MET E 193 "
        pdb=" CB  MET E 193 "
        pdb=" CG  MET E 193 "
      ideal   model   delta    sigma   weight residual
     114.10  120.62   -6.52 2.00e+00 2.50e-01 1.06e+01
  angle pdb=" CA  TRP C  82 "
        pdb=" CB  TRP C  82 "
        pdb=" CG  TRP C  82 "
      ideal   model   delta    sigma   weight residual
     113.60  119.78   -6.18 1.90e+00 2.77e-01 1.06e+01
  angle pdb=" CA  HSM R 401 "
        pdb=" CB  HSM R 401 "
        pdb=" CG  HSM R 401 "
      ideal   model   delta    sigma   weight residual
     114.47  105.20    9.27 3.00e+00 1.11e-01 9.54e+00
  angle pdb=" N   MET E 193 "
        pdb=" CA  MET E 193 "
        pdb=" CB  MET E 193 "
      ideal   model   delta    sigma   weight residual
     114.27  109.28    4.99 1.64e+00 3.72e-01 9.26e+00
  angle pdb=" CG  MET E 193 "
        pdb=" SD  MET E 193 "
        pdb=" CE  MET E 193 "
      ideal   model   delta    sigma   weight residual
     100.90  107.53   -6.63 2.20e+00 2.07e-01 9.09e+00
  ... (remaining 11569 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 4515
       17.57 -    35.14: 334
       35.14 -    52.70: 49
       52.70 -    70.27: 7
       70.27 -    87.84: 1
  Dihedral angle restraints: 4906
    sinusoidal: 1690
      harmonic: 3216
  Sorted by residual:
  dihedral pdb=" CB  CYS E 160 "
           pdb=" SG  CYS E 160 "
           pdb=" SG  CYS E 230 "
           pdb=" CB  CYS E 230 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.07  -43.07     1      1.00e+01 1.00e-02 2.59e+01
  dihedral pdb=" CA  ARG E 192 "
           pdb=" C   ARG E 192 "
           pdb=" N   MET E 193 "
           pdb=" CA  MET E 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.69   24.31     0      5.00e+00 4.00e-02 2.36e+01
  dihedral pdb=" CA  TRP C 339 "
           pdb=" C   TRP C 339 "
           pdb=" N   ASN C 340 "
           pdb=" CA  ASN C 340 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.10   18.90     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 4903 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 735
       0.030 -    0.059: 392
       0.059 -    0.089: 145
       0.089 -    0.119: 65
       0.119 -    0.148: 16
  Chirality restraints: 1353
  Sorted by residual:
  chirality pdb=" CA  PRO R 318 "
            pdb=" N   PRO R 318 "
            pdb=" C   PRO R 318 "
            pdb=" CB  PRO R 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.50e-01
  chirality pdb=" CA  ILE C  58 "
            pdb=" N   ILE C  58 "
            pdb=" C   ILE C  58 "
            pdb=" CB  ILE C  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.10e-01
  chirality pdb=" CA  ILE C 229 "
            pdb=" N   ILE C 229 "
            pdb=" C   ILE C 229 "
            pdb=" CB  ILE C 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.65e-01
  ... (remaining 1350 not shown)

  Planarity restraints: 1454
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU R 165 "    0.058 5.00e-02 4.00e+02   8.80e-02 1.24e+01
        pdb=" N   PRO R 166 "   -0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO R 166 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO R 166 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 235 "    0.045 5.00e-02 4.00e+02   6.83e-02 7.45e+00
        pdb=" N   PRO C 236 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO C 236 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C 236 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D  48 "    0.036 5.00e-02 4.00e+02   5.42e-02 4.71e+00
        pdb=" N   PRO D  49 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO D  49 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D  49 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1451 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1403
        2.76 -     3.30: 7407
        3.30 -     3.83: 12744
        3.83 -     4.37: 13796
        4.37 -     4.90: 25240
  Nonbonded interactions: 60590
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C  86 "
            pdb=" OD1 ASN C  88 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   GLY E 210 "
            pdb=" OG1 THR E 211 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OD1 ASP C 290 "
            pdb=" NE  ARG C 314 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" NH2 ARG E 203 "
            pdb=" OE2 GLU E 221 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" NH1 ARG E  38 "
            pdb=" OD1 ASP E  90 "
     model   vdw
     2.298 3.120
  ... (remaining 60585 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.810
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6597
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      :  0.005   0.045   8489  Z= 0.212
  Angle     :  0.685   9.267  11578  Z= 0.388
  Chirality :  0.045   0.148   1353
  Planarity :  0.005   0.088   1454
  Dihedral  : 12.498  87.839   2824
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.24 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.26), residues: 1089
  helix:  1.28 (0.28), residues: 357
  sheet:  0.34 (0.32), residues: 274
  loop : -1.83 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 304 
 TYR   0.017   0.002   TYR E  50 
 PHE   0.027   0.002   PHE C 199 
 TRP   0.030   0.002   TRP C  82 
 HIS   0.007   0.002   HIS R  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 8487)
  covalent geometry    : angle       0.68473 (11574)
  SS BOND              : bond        0.00897 (    2)
  SS BOND              : angle       0.83415 (    4)
  hydrogen bonds       : bond        0.13336 (  396)
  hydrogen bonds       : angle       5.14314 ( 1116)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 149
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: C  262 MET cc_start: 0.7771 (mmt) cc_final: 0.7513 (mpp)
REVERT: E  205 SER cc_start: 0.7476 (t) cc_final: 0.7198 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1006
  time to fit residues: 20.3468
Evaluate side-chains
  109 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0070
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.3980
   chunk 65 optimal weight:    0.0370
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.2980
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.3476

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

Flipped N/Q/H residues before XYZ refinement:
C 110 ASN
C 268 ASN
E 184 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.205834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.160425 restraints weight = 9144.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 3.62
r_work: 0.3693 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8489  Z= 0.117
  Angle     :  0.539   6.760  11578  Z= 0.289
  Chirality :  0.042   0.146   1353
  Planarity :  0.004   0.061   1454
  Dihedral  :  4.250  17.120   1178
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  7.20 %
    Favored  : 92.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.26), residues: 1089
  helix:  1.51 (0.29), residues: 370
  sheet:  0.30 (0.31), residues: 284
  loop : -1.63 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 304 
 TYR   0.011   0.001   TYR E  50 
 PHE   0.020   0.001   PHE R 144 
 TRP   0.024   0.002   TRP C  82 
 HIS   0.003   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 8487)
  covalent geometry    : angle       0.53905 (11574)
  SS BOND              : bond        0.00750 (    2)
  SS BOND              : angle       0.67332 (    4)
  hydrogen bonds       : bond        0.05101 (  396)
  hydrogen bonds       : angle       4.40298 ( 1116)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 118
  time to evaluate  : 0.241 
Fit side-chains
REVERT: C  280 LYS cc_start: 0.7831 (tttm) cc_final: 0.7544 (tttm)
REVERT: R  144 PHE cc_start: 0.8056 (t80) cc_final: 0.7788 (t80)
  outliers start: 4
  outliers final: 4
  residues processed: 119
  average time/residue: 0.1039
  time to fit residues: 16.7478
Evaluate side-chains
  102 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain E residue   64 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 72 optimal weight:    9.9990
   chunk 12 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 99 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   chunk 79 optimal weight:    9.9990
   chunk 108 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0370
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.9262

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

Flipped N/Q/H residues before XYZ refinement:
B 331 ASN
C 110 ASN
E 184 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.200874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.152917 restraints weight = 9067.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3884 rms_B_bonded: 3.91
r_work: 0.3569 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6994
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8489  Z= 0.138
  Angle     :  0.554   7.182  11578  Z= 0.294
  Chirality :  0.043   0.149   1353
  Planarity :  0.004   0.056   1454
  Dihedral  :  4.206  18.523   1178
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  9.92 %
    Favored  : 89.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.26), residues: 1089
  helix:  1.54 (0.28), residues: 372
  sheet:  0.44 (0.31), residues: 283
  loop : -1.66 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 304 
 TYR   0.018   0.001   TYR E  50 
 PHE   0.015   0.001   PHE C 199 
 TRP   0.026   0.002   TRP C 332 
 HIS   0.005   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8487)
  covalent geometry    : angle       0.55417 (11574)
  SS BOND              : bond        0.00513 (    2)
  SS BOND              : angle       0.40488 (    4)
  hydrogen bonds       : bond        0.05478 (  396)
  hydrogen bonds       : angle       4.26858 ( 1116)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.393 
Fit side-chains
REVERT: B  346 ASN cc_start: 0.7141 (m110) cc_final: 0.6765 (m-40)
REVERT: C  280 LYS cc_start: 0.7990 (tttm) cc_final: 0.7737 (tttm)
REVERT: C  301 LYS cc_start: 0.8256 (mttp) cc_final: 0.7811 (mmtm)
REVERT: E  205 SER cc_start: 0.6838 (t) cc_final: 0.6579 (m)
REVERT: R  144 PHE cc_start: 0.8139 (t80) cc_final: 0.7860 (t80)
  outliers start: 8
  outliers final: 6
  residues processed: 113
  average time/residue: 0.1002
  time to fit residues: 15.6111
Evaluate side-chains
  102 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  198 SER
Chi-restraints excluded: chain R residue  137 VAL
Chi-restraints excluded: chain R residue  360 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 75 optimal weight:    0.0570
   chunk 105 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0070
   chunk 79 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 104 optimal weight:    2.9990
   chunk 77 optimal weight:    0.4980
   chunk 96 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
B 331 ASN
E 184 GLN
R 196 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.202839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.156579 restraints weight = 9140.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3920 rms_B_bonded: 4.09
r_work: 0.3638 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8489  Z= 0.106
  Angle     :  0.503   6.369  11578  Z= 0.268
  Chirality :  0.041   0.145   1353
  Planarity :  0.004   0.053   1454
  Dihedral  :  4.021  17.456   1178
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 11.10 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.26), residues: 1089
  helix:  1.77 (0.29), residues: 372
  sheet:  0.42 (0.32), residues: 272
  loop : -1.52 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 304 
 TYR   0.022   0.001   TYR E 191 
 PHE   0.014   0.001   PHE B 189 
 TRP   0.034   0.002   TRP C 332 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 8487)
  covalent geometry    : angle       0.50249 (11574)
  SS BOND              : bond        0.00339 (    2)
  SS BOND              : angle       0.93403 (    4)
  hydrogen bonds       : bond        0.04603 (  396)
  hydrogen bonds       : angle       4.09425 ( 1116)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.312 
Fit side-chains
REVERT: B   33 GLU cc_start: 0.7984 (pt0) cc_final: 0.7730 (pt0)
REVERT: B  346 ASN cc_start: 0.7091 (m110) cc_final: 0.6725 (m-40)
REVERT: C  280 LYS cc_start: 0.7936 (tttm) cc_final: 0.7596 (tttm)
REVERT: C  301 LYS cc_start: 0.8132 (mttp) cc_final: 0.7796 (mmtm)
REVERT: C  332 TRP cc_start: 0.7842 (m-10) cc_final: 0.7530 (m-10)
REVERT: E  205 SER cc_start: 0.6942 (t) cc_final: 0.6665 (m)
REVERT: R  144 PHE cc_start: 0.8254 (t80) cc_final: 0.7979 (t80)
REVERT: R  195 MET cc_start: 0.6404 (mmp) cc_final: 0.5185 (ttm)
  outliers start: 7
  outliers final: 7
  residues processed: 111
  average time/residue: 0.1022
  time to fit residues: 15.6549
Evaluate side-chains
  108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  215 LEU
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  349 PHE
Chi-restraints excluded: chain R residue  360 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 54 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0020
   chunk 75 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    1.3994

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

Flipped N/Q/H residues before XYZ refinement:
B 188 HIS
B 331 ASN
E 184 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.196171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.149763 restraints weight = 9085.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 3.97
r_work: 0.3549 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7047
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8489  Z= 0.174
  Angle     :  0.589   8.592  11578  Z= 0.314
  Chirality :  0.044   0.143   1353
  Planarity :  0.004   0.054   1454
  Dihedral  :  4.330  19.191   1178
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 11.45 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.26), residues: 1089
  helix:  1.56 (0.28), residues: 374
  sheet:  0.34 (0.32), residues: 277
  loop : -1.53 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 304 
 TYR   0.023   0.002   TYR E  50 
 PHE   0.017   0.002   PHE C 199 
 TRP   0.030   0.002   TRP C 332 
 HIS   0.007   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 8487)
  covalent geometry    : angle       0.58922 (11574)
  SS BOND              : bond        0.00597 (    2)
  SS BOND              : angle       0.86280 (    4)
  hydrogen bonds       : bond        0.06027 (  396)
  hydrogen bonds       : angle       4.30066 ( 1116)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.319 
Fit side-chains
REVERT: B  346 ASN cc_start: 0.7208 (m110) cc_final: 0.7000 (m110)
REVERT: C   76 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.6853 (m-30)
REVERT: C  280 LYS cc_start: 0.8073 (tttm) cc_final: 0.7753 (tttm)
REVERT: C  301 LYS cc_start: 0.8080 (mttp) cc_final: 0.7731 (mmtm)
REVERT: C  332 TRP cc_start: 0.7844 (m-10) cc_final: 0.7536 (m-10)
  outliers start: 19
  outliers final: 13
  residues processed: 111
  average time/residue: 0.0926
  time to fit residues: 14.4175
Evaluate side-chains
  109 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  198 SER
Chi-restraints excluded: chain E residue  215 LEU
Chi-restraints excluded: chain R residue   42 VAL
Chi-restraints excluded: chain R residue  137 VAL
Chi-restraints excluded: chain R residue  360 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 102 optimal weight:    0.9980
   chunk 81 optimal weight:    7.9990
   chunk 84 optimal weight:    1.9990
   chunk 79 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 98 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   chunk 33 optimal weight:    0.6980
   chunk 107 optimal weight:    0.2980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B 331 ASN
E 184 GLN
R 196 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.197883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.151196 restraints weight = 9093.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 3.72
r_work: 0.3571 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8489  Z= 0.136
  Angle     :  0.546   7.572  11578  Z= 0.290
  Chirality :  0.042   0.140   1353
  Planarity :  0.004   0.054   1454
  Dihedral  :  4.223  20.826   1178
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.75 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.26), residues: 1089
  helix:  1.60 (0.28), residues: 373
  sheet:  0.39 (0.32), residues: 281
  loop : -1.50 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 304 
 TYR   0.017   0.001   TYR E  50 
 PHE   0.014   0.001   PHE B 189 
 TRP   0.026   0.002   TRP C 332 
 HIS   0.005   0.001   HIS E 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8487)
  covalent geometry    : angle       0.54568 (11574)
  SS BOND              : bond        0.00449 (    2)
  SS BOND              : angle       0.75918 (    4)
  hydrogen bonds       : bond        0.05311 (  396)
  hydrogen bonds       : angle       4.18192 ( 1116)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.342 
Fit side-chains
REVERT: B  346 ASN cc_start: 0.7163 (m110) cc_final: 0.6865 (m-40)
REVERT: C   76 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.6851 (m-30)
REVERT: C  280 LYS cc_start: 0.7998 (tttm) cc_final: 0.7616 (tttm)
REVERT: C  301 LYS cc_start: 0.8030 (mttp) cc_final: 0.7594 (mmtm)
REVERT: C  332 TRP cc_start: 0.7751 (m-10) cc_final: 0.7395 (m-10)
REVERT: R  144 PHE cc_start: 0.8148 (t80) cc_final: 0.7884 (t80)
  outliers start: 18
  outliers final: 13
  residues processed: 115
  average time/residue: 0.0931
  time to fit residues: 14.9748
Evaluate side-chains
  113 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  215 LEU
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  349 PHE
Chi-restraints excluded: chain R residue  360 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 46 optimal weight:    0.3980
   chunk 40 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0020
   chunk 6 optimal weight:    0.7980
   chunk 93 optimal weight:    5.9990
   chunk 98 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
B 331 ASN
R 196 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.198997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.153337 restraints weight = 9056.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 3.24
r_work: 0.3613 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8489  Z= 0.113
  Angle     :  0.520   6.485  11578  Z= 0.276
  Chirality :  0.041   0.142   1353
  Planarity :  0.004   0.052   1454
  Dihedral  :  4.088  21.731   1178
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.11 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.26), residues: 1089
  helix:  1.79 (0.29), residues: 373
  sheet:  0.45 (0.32), residues: 281
  loop : -1.45 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 304 
 TYR   0.012   0.001   TYR E  50 
 PHE   0.013   0.001   PHE B 189 
 TRP   0.023   0.002   TRP C 332 
 HIS   0.004   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8487)
  covalent geometry    : angle       0.52029 (11574)
  SS BOND              : bond        0.00352 (    2)
  SS BOND              : angle       0.67580 (    4)
  hydrogen bonds       : bond        0.04705 (  396)
  hydrogen bonds       : angle       4.06375 ( 1116)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.333 
Fit side-chains
REVERT: B   33 GLU cc_start: 0.8053 (pt0) cc_final: 0.7718 (pt0)
REVERT: C  280 LYS cc_start: 0.7943 (tttm) cc_final: 0.7495 (tttm)
REVERT: C  301 LYS cc_start: 0.7987 (mttp) cc_final: 0.7649 (mmtm)
REVERT: C  332 TRP cc_start: 0.7733 (m-10) cc_final: 0.7368 (m-10)
REVERT: R  144 PHE cc_start: 0.8128 (t80) cc_final: 0.7886 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 106
  average time/residue: 0.1021
  time to fit residues: 14.8695
Evaluate side-chains
  106 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  215 LEU
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  349 PHE
Chi-restraints excluded: chain R residue  360 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 108 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 55 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 105 optimal weight:    0.2980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B 331 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.195513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.149477 restraints weight = 9073.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 3.94
r_work: 0.3549 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7124
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8489  Z= 0.172
  Angle     :  0.591   8.702  11578  Z= 0.313
  Chirality :  0.044   0.143   1353
  Planarity :  0.004   0.054   1454
  Dihedral  :  4.350  29.211   1178
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.11 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.26), residues: 1089
  helix:  1.55 (0.28), residues: 375
  sheet:  0.39 (0.32), residues: 281
  loop : -1.54 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  67 
 TYR   0.023   0.002   TYR E  50 
 PHE   0.017   0.002   PHE C 199 
 TRP   0.027   0.002   TRP C 332 
 HIS   0.006   0.001   HIS E 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 8487)
  covalent geometry    : angle       0.59061 (11574)
  SS BOND              : bond        0.00544 (    2)
  SS BOND              : angle       0.81784 (    4)
  hydrogen bonds       : bond        0.05930 (  396)
  hydrogen bonds       : angle       4.26519 ( 1116)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.270 
Fit side-chains
REVERT: C   76 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6735 (m-30)
REVERT: C  280 LYS cc_start: 0.8053 (tttm) cc_final: 0.7660 (tttm)
REVERT: C  332 TRP cc_start: 0.7925 (m-10) cc_final: 0.7597 (m-10)
REVERT: R  144 PHE cc_start: 0.8193 (t80) cc_final: 0.7923 (t80)
  outliers start: 17
  outliers final: 13
  residues processed: 103
  average time/residue: 0.0753
  time to fit residues: 10.9462
Evaluate side-chains
  109 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  215 LEU
Chi-restraints excluded: chain R residue  172 TRP
Chi-restraints excluded: chain R residue  360 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   chunk 90 optimal weight:    0.8980
   chunk 85 optimal weight:    0.3980
   chunk 32 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 54 optimal weight:   30.0000
   chunk 68 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
B 331 ASN
R 196 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.197847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.153315 restraints weight = 9080.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 3.17
r_work: 0.3590 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8489  Z= 0.124
  Angle     :  0.531   7.247  11578  Z= 0.282
  Chirality :  0.042   0.139   1353
  Planarity :  0.004   0.053   1454
  Dihedral  :  4.196  33.746   1178
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.34 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.26), residues: 1089
  helix:  1.71 (0.28), residues: 373
  sheet:  0.43 (0.32), residues: 281
  loop : -1.50 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 304 
 TYR   0.014   0.001   TYR E  50 
 PHE   0.013   0.001   PHE C 199 
 TRP   0.024   0.002   TRP C 332 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8487)
  covalent geometry    : angle       0.53119 (11574)
  SS BOND              : bond        0.00415 (    2)
  SS BOND              : angle       0.61251 (    4)
  hydrogen bonds       : bond        0.04968 (  396)
  hydrogen bonds       : angle       4.11435 ( 1116)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.311 
Fit side-chains
REVERT: B   33 GLU cc_start: 0.8221 (pt0) cc_final: 0.7901 (pt0)
REVERT: C  268 ASN cc_start: 0.7977 (m110) cc_final: 0.7286 (t0)
REVERT: C  280 LYS cc_start: 0.7999 (tttm) cc_final: 0.7528 (tttm)
REVERT: C  332 TRP cc_start: 0.7869 (m-10) cc_final: 0.7580 (m-10)
REVERT: R  144 PHE cc_start: 0.8143 (t80) cc_final: 0.7901 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 102
  average time/residue: 0.0902
  time to fit residues: 12.9694
Evaluate side-chains
  107 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  215 LEU
Chi-restraints excluded: chain R residue  172 TRP
Chi-restraints excluded: chain R residue  360 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 105 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9980
   chunk 81 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 331 ASN
C 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.198090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.152639 restraints weight = 9036.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 3.66
r_work: 0.3595 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8489  Z= 0.118
  Angle     :  0.528   8.404  11578  Z= 0.278
  Chirality :  0.041   0.140   1353
  Planarity :  0.004   0.053   1454
  Dihedral  :  4.145  37.552   1178
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.81 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.26), residues: 1089
  helix:  1.94 (0.29), residues: 367
  sheet:  0.45 (0.32), residues: 281
  loop : -1.42 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 304 
 TYR   0.014   0.001   TYR E  50 
 PHE   0.034   0.001   PHE R 180 
 TRP   0.023   0.002   TRP C 332 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8487)
  covalent geometry    : angle       0.52763 (11574)
  SS BOND              : bond        0.00418 (    2)
  SS BOND              : angle       0.56338 (    4)
  hydrogen bonds       : bond        0.04757 (  396)
  hydrogen bonds       : angle       4.03976 ( 1116)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.327 
Fit side-chains
REVERT: B   33 GLU cc_start: 0.8153 (pt0) cc_final: 0.7826 (pt0)
REVERT: C  268 ASN cc_start: 0.7990 (m110) cc_final: 0.7324 (t0)
REVERT: C  280 LYS cc_start: 0.7879 (tttm) cc_final: 0.7428 (tttm)
REVERT: C  301 LYS cc_start: 0.8061 (mttp) cc_final: 0.7699 (mmtm)
REVERT: C  332 TRP cc_start: 0.7908 (m-10) cc_final: 0.7555 (m-10)
  outliers start: 13
  outliers final: 13
  residues processed: 104
  average time/residue: 0.0891
  time to fit residues: 13.0388
Evaluate side-chains
  108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  215 LEU
Chi-restraints excluded: chain R residue  172 TRP
Chi-restraints excluded: chain R residue  360 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 76 optimal weight:    0.2980
   chunk 14 optimal weight:    9.9990
   chunk 81 optimal weight:    0.1980
   chunk 103 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0770
   chunk 55 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
B 331 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.200369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.154986 restraints weight = 9059.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3920 rms_B_bonded: 3.27
r_work: 0.3633 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8489  Z= 0.103
  Angle     :  0.505   8.076  11578  Z= 0.266
  Chirality :  0.041   0.138   1353
  Planarity :  0.004   0.052   1454
  Dihedral  :  4.019  40.365   1178
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 14.76 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.26), residues: 1089
  helix:  2.18 (0.29), residues: 361
  sheet:  0.51 (0.32), residues: 282
  loop : -1.35 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 304 
 TYR   0.012   0.001   TYR E 191 
 PHE   0.032   0.001   PHE R 144 
 TRP   0.023   0.002   TRP C  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 8487)
  covalent geometry    : angle       0.50498 (11574)
  SS BOND              : bond        0.00352 (    2)
  SS BOND              : angle       0.46322 (    4)
  hydrogen bonds       : bond        0.04177 (  396)
  hydrogen bonds       : angle       3.92427 ( 1116)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2433.16 seconds
wall clock time: 42 minutes 16.54 seconds (2536.54 seconds total)