Starting phenix.real_space_refine
on Sun May 11 18:05:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jxt_36712/05_2025/8jxt_36712_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jxt_36712/05_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_36712/05_2025/8jxt_36712.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jxt_36712/05_2025/8jxt_36712.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jxt_36712/05_2025/8jxt_36712_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jxt_36712/05_2025/8jxt_36712_neut.cif"
  }
  resolution = 3.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 9, 'ARG:plan': 4}
          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, 'GLU:plan': 4, 'ARG:plan': 7}
          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, 'GLU:plan': 3, 'ARG:plan': 2, '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, 'GLU:plan': 2, 'ARG: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: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4}
          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: 5.25, per 1000 atoms: 0.63
  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: 2.12
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.96
  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: 2.34

  Time building geometry restraints manager: 2.50 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:             0.810
  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:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.690
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.120
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (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
 TRP   0.030   0.002   TRP C  82 
 HIS   0.007   0.002   HIS R  75 
 PHE   0.027   0.002   PHE C 199 
 TYR   0.017   0.002   TYR E  50 
 ARG   0.012   0.001   ARG C 304 

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

*********************** 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  : 0.891 
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: 0.2068
  time to fit residues: 42.1497
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  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0050
   chunk 45 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 55 optimal weight:    0.2980
   chunk 44 optimal weight:    0.3980
   chunk 85 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.4594

-------------------------------------------------------------------------------
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 = 0.4371 r_free = 0.4371 target = 0.203687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.158585 restraints weight = 8987.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 3.49
r_work: 0.3677 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.1422

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= 0.122
  Angle     :  0.548   6.713  11578  Z= 0.293
  Chirality :  0.042   0.142   1353
  Planarity :  0.004   0.063   1454
  Dihedral  :  4.285  17.466   1178
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  6.85 %
    Favored  : 92.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.26), residues: 1089
  helix:  1.46 (0.28), residues: 370
  sheet:  0.29 (0.31), residues: 284
  loop : -1.64 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C  82 
 HIS   0.003   0.001   HIS B 188 
 PHE   0.019   0.001   PHE R 144 
 TYR   0.012   0.001   TYR E  50 
 ARG   0.003   0.000   ARG C 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05416 (  396)
  hydrogen bonds       : angle       4.43364 ( 1116)
  SS BOND              : bond        0.00842 (    2)
  SS BOND              : angle       1.01526 (    4)
  covalent geometry    : bond        0.00248 ( 8487)
  covalent geometry    : angle       0.54780 (11574)

*********************** 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
  117 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 0.799 
Fit side-chains
REVERT: C  280 LYS cc_start: 0.7829 (tttm) cc_final: 0.7570 (tttm)
REVERT: R  144 PHE cc_start: 0.8086 (t80) cc_final: 0.7805 (t80)
  outliers start: 4
  outliers final: 4
  residues processed: 114
  average time/residue: 0.2083
  time to fit residues: 32.7230
Evaluate side-chains
  101 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
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 12 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.4317 r_free = 0.4317 target = 0.197682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.151425 restraints weight = 9160.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 4.04
r_work: 0.3563 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8489  Z= 0.170
  Angle     :  0.596   8.444  11578  Z= 0.319
  Chirality :  0.044   0.148   1353
  Planarity :  0.005   0.057   1454
  Dihedral  :  4.405  18.968   1178
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  9.21 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.26), residues: 1089
  helix:  1.39 (0.28), residues: 372
  sheet:  0.26 (0.31), residues: 287
  loop : -1.66 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C 332 
 HIS   0.005   0.001   HIS B 188 
 PHE   0.019   0.002   PHE C 199 
 TYR   0.022   0.002   TYR E  50 
 ARG   0.003   0.000   ARG C 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06161 (  396)
  hydrogen bonds       : angle       4.41218 ( 1116)
  SS BOND              : bond        0.00215 (    2)
  SS BOND              : angle       0.87006 (    4)
  covalent geometry    : bond        0.00391 ( 8487)
  covalent geometry    : angle       0.59618 (11574)

*********************** 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
  120 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.898 
Fit side-chains
REVERT: B   33 GLU cc_start: 0.8250 (pt0) cc_final: 0.8009 (pt0)
REVERT: B  346 ASN cc_start: 0.7193 (m110) cc_final: 0.6821 (m-40)
REVERT: C  204 CYS cc_start: 0.7792 (t) cc_final: 0.7549 (t)
REVERT: C  280 LYS cc_start: 0.8037 (tttm) cc_final: 0.7817 (tttm)
REVERT: C  301 LYS cc_start: 0.8097 (mttp) cc_final: 0.7629 (mmtm)
  outliers start: 11
  outliers final: 8
  residues processed: 114
  average time/residue: 0.1963
  time to fit residues: 31.1012
Evaluate side-chains
  103 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
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  198 MET
Chi-restraints excluded: chain C residue   76 ASP
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 8 optimal weight:    0.0000
   chunk 22 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 93 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0670
   chunk 40 optimal weight:    3.9990
   chunk 27 optimal weight:    0.2980
   chunk 74 optimal weight:    0.9980
   chunk 21 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.4122

-------------------------------------------------------------------------------
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 = 0.4357 r_free = 0.4357 target = 0.202206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.156287 restraints weight = 9054.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3920 rms_B_bonded: 3.30
r_work: 0.3634 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8489  Z= 0.102
  Angle     :  0.498   6.408  11578  Z= 0.267
  Chirality :  0.041   0.148   1353
  Planarity :  0.004   0.054   1454
  Dihedral  :  4.037  18.330   1178
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 10.86 %
    Favored  : 88.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.26), residues: 1089
  helix:  1.73 (0.29), residues: 372
  sheet:  0.40 (0.32), residues: 272
  loop : -1.53 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C 332 
 HIS   0.003   0.001   HIS E 233 
 PHE   0.014   0.001   PHE B 189 
 TYR   0.011   0.001   TYR E  50 
 ARG   0.003   0.000   ARG C 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04444 (  396)
  hydrogen bonds       : angle       4.08251 ( 1116)
  SS BOND              : bond        0.00353 (    2)
  SS BOND              : angle       0.95321 (    4)
  covalent geometry    : bond        0.00206 ( 8487)
  covalent geometry    : angle       0.49742 (11574)

*********************** 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
  116 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 0.899 
Fit side-chains
REVERT: B   33 GLU cc_start: 0.8123 (pt0) cc_final: 0.7730 (pt0)
REVERT: B  346 ASN cc_start: 0.7074 (m110) cc_final: 0.6769 (m-40)
REVERT: C  280 LYS cc_start: 0.7959 (tttm) cc_final: 0.7615 (tttm)
REVERT: C  301 LYS cc_start: 0.8100 (mttp) cc_final: 0.7739 (mmtm)
REVERT: R  144 PHE cc_start: 0.8123 (t80) cc_final: 0.7875 (t80)
REVERT: R  195 MET cc_start: 0.6313 (mmp) cc_final: 0.5099 (ttm)
  outliers start: 7
  outliers final: 7
  residues processed: 113
  average time/residue: 0.1984
  time to fit residues: 31.5326
Evaluate side-chains
  107 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  198 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 83 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 88 optimal weight:    0.0870
   chunk 61 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0970
   chunk 70 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 80 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.4349 r_free = 0.4349 target = 0.201088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.155010 restraints weight = 8979.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 3.55
r_work: 0.3614 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.2343

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= 0.109
  Angle     :  0.502   6.563  11578  Z= 0.267
  Chirality :  0.041   0.140   1353
  Planarity :  0.004   0.054   1454
  Dihedral  :  3.981  18.910   1178
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.40 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.26), residues: 1089
  helix:  1.78 (0.29), residues: 373
  sheet:  0.44 (0.32), residues: 277
  loop : -1.45 (0.27), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP C 332 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.014   0.001   PHE B 189 
 TYR   0.013   0.001   TYR E  50 
 ARG   0.009   0.000   ARG C 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04588 (  396)
  hydrogen bonds       : angle       4.00039 ( 1116)
  SS BOND              : bond        0.00381 (    2)
  SS BOND              : angle       0.71934 (    4)
  covalent geometry    : bond        0.00231 ( 8487)
  covalent geometry    : angle       0.50224 (11574)

*********************** 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
  115 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.821 
Fit side-chains
REVERT: B  346 ASN cc_start: 0.7081 (m110) cc_final: 0.6783 (m-40)
REVERT: C  280 LYS cc_start: 0.7913 (tttm) cc_final: 0.7517 (tttm)
REVERT: C  301 LYS cc_start: 0.8003 (mttp) cc_final: 0.7653 (mmtm)
REVERT: C  332 TRP cc_start: 0.7639 (m-10) cc_final: 0.7285 (m-10)
REVERT: R  144 PHE cc_start: 0.8203 (t80) cc_final: 0.7943 (t80)
  outliers start: 14
  outliers final: 11
  residues processed: 108
  average time/residue: 0.1939
  time to fit residues: 29.3432
Evaluate side-chains
  111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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  196 ASN
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 62 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 105 optimal weight:    0.3980
   chunk 31 optimal weight:    0.0670
   chunk 9 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.8322

-------------------------------------------------------------------------------
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 = 0.4333 r_free = 0.4333 target = 0.199214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.152134 restraints weight = 9110.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 3.59
r_work: 0.3591 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6983
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8489  Z= 0.124
  Angle     :  0.516   7.038  11578  Z= 0.275
  Chirality :  0.042   0.139   1353
  Planarity :  0.004   0.053   1454
  Dihedral  :  4.045  18.052   1178
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 12.87 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.26), residues: 1089
  helix:  1.81 (0.28), residues: 373
  sheet:  0.47 (0.32), residues: 281
  loop : -1.42 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP C 332 
 HIS   0.005   0.001   HIS E 233 
 PHE   0.014   0.001   PHE B 189 
 TYR   0.016   0.001   TYR E  50 
 ARG   0.003   0.000   ARG C 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04912 (  396)
  hydrogen bonds       : angle       4.02572 ( 1116)
  SS BOND              : bond        0.00380 (    2)
  SS BOND              : angle       0.72239 (    4)
  covalent geometry    : bond        0.00275 ( 8487)
  covalent geometry    : angle       0.51572 (11574)

*********************** 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
  121 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.809 
Fit side-chains
REVERT: B   33 GLU cc_start: 0.8008 (pt0) cc_final: 0.7735 (pt0)
REVERT: B  346 ASN cc_start: 0.7127 (m110) cc_final: 0.6838 (m-40)
REVERT: C  280 LYS cc_start: 0.7967 (tttm) cc_final: 0.7504 (tttm)
REVERT: C  301 LYS cc_start: 0.8003 (mttp) cc_final: 0.7655 (mmtm)
REVERT: R  144 PHE cc_start: 0.8152 (t80) cc_final: 0.7886 (t80)
  outliers start: 17
  outliers final: 11
  residues processed: 113
  average time/residue: 0.1912
  time to fit residues: 29.9629
Evaluate side-chains
  110 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  182 THR
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    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 85 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0970
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 52 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.4331 r_free = 0.4331 target = 0.198421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.152106 restraints weight = 9074.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3884 rms_B_bonded: 3.71
r_work: 0.3593 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8489  Z= 0.137
  Angle     :  0.537   7.605  11578  Z= 0.287
  Chirality :  0.042   0.136   1353
  Planarity :  0.004   0.053   1454
  Dihedral  :  4.139  22.915   1178
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.46 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.26), residues: 1089
  helix:  1.73 (0.28), residues: 373
  sheet:  0.46 (0.32), residues: 281
  loop : -1.44 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP C 332 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.028   0.001   PHE R 180 
 TYR   0.018   0.001   TYR E  50 
 ARG   0.004   0.000   ARG C 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05191 (  396)
  hydrogen bonds       : angle       4.09180 ( 1116)
  SS BOND              : bond        0.00427 (    2)
  SS BOND              : angle       0.75787 (    4)
  covalent geometry    : bond        0.00310 ( 8487)
  covalent geometry    : angle       0.53734 (11574)

*********************** 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
  123 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.828 
Fit side-chains
REVERT: B  346 ASN cc_start: 0.7261 (m110) cc_final: 0.6956 (m-40)
REVERT: C   76 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6817 (m-30)
REVERT: C  280 LYS cc_start: 0.7989 (tttm) cc_final: 0.7546 (tttm)
REVERT: C  301 LYS cc_start: 0.8010 (mttp) cc_final: 0.7646 (mmtm)
REVERT: R  144 PHE cc_start: 0.8190 (t80) cc_final: 0.7912 (t80)
  outliers start: 19
  outliers final: 12
  residues processed: 112
  average time/residue: 0.1955
  time to fit residues: 30.5025
Evaluate side-chains
  110 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
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    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  196 ASN
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 0 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 90 optimal weight:    0.7980
   chunk 94 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 108 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0270
   chunk 22 optimal weight:    6.9990
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.6638

-------------------------------------------------------------------------------
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 = 0.4336 r_free = 0.4336 target = 0.199014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.152906 restraints weight = 9042.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 3.61
r_work: 0.3609 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.2691

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     :  0.515   6.645  11578  Z= 0.274
  Chirality :  0.041   0.138   1353
  Planarity :  0.004   0.052   1454
  Dihedral  :  4.045  25.234   1178
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.17 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.26), residues: 1089
  helix:  1.87 (0.28), residues: 373
  sheet:  0.49 (0.32), residues: 281
  loop : -1.39 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP C 332 
 HIS   0.005   0.001   HIS C 225 
 PHE   0.027   0.001   PHE R 180 
 TYR   0.013   0.001   TYR E  50 
 ARG   0.004   0.000   ARG C 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04658 (  396)
  hydrogen bonds       : angle       3.99475 ( 1116)
  SS BOND              : bond        0.00342 (    2)
  SS BOND              : angle       0.64692 (    4)
  covalent geometry    : bond        0.00245 ( 8487)
  covalent geometry    : angle       0.51534 (11574)

*********************** 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
  116 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.809 
Fit side-chains
REVERT: B   33 GLU cc_start: 0.7972 (pt0) cc_final: 0.7719 (pt0)
REVERT: C  268 ASN cc_start: 0.7995 (m110) cc_final: 0.7309 (t0)
REVERT: C  280 LYS cc_start: 0.7952 (tttm) cc_final: 0.7478 (tttm)
REVERT: C  301 LYS cc_start: 0.7997 (mttp) cc_final: 0.7661 (mmtm)
REVERT: R  144 PHE cc_start: 0.8189 (t80) cc_final: 0.7951 (t80)
  outliers start: 14
  outliers final: 13
  residues processed: 110
  average time/residue: 0.1998
  time to fit residues: 30.5628
Evaluate side-chains
  110 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
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  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  196 ASN
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 61 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 106 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4336 r_free = 0.4336 target = 0.199020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.152102 restraints weight = 9178.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 3.94
r_work: 0.3596 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8489  Z= 0.125
  Angle     :  0.528   7.097  11578  Z= 0.280
  Chirality :  0.042   0.152   1353
  Planarity :  0.004   0.053   1454
  Dihedral  :  4.102  29.614   1178
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.93 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.26), residues: 1089
  helix:  2.01 (0.28), residues: 367
  sheet:  0.52 (0.32), residues: 281
  loop : -1.35 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP C 332 
 HIS   0.004   0.001   HIS E 233 
 PHE   0.027   0.001   PHE R 180 
 TYR   0.016   0.001   TYR E 191 
 ARG   0.005   0.000   ARG C 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04908 (  396)
  hydrogen bonds       : angle       4.01639 ( 1116)
  SS BOND              : bond        0.00402 (    2)
  SS BOND              : angle       0.65452 (    4)
  covalent geometry    : bond        0.00280 ( 8487)
  covalent geometry    : angle       0.52779 (11574)

*********************** 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
  113 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.823 
Fit side-chains
REVERT: B   33 GLU cc_start: 0.8130 (pt0) cc_final: 0.7833 (pt0)
REVERT: C   76 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6806 (m-30)
REVERT: C  268 ASN cc_start: 0.7911 (m110) cc_final: 0.7253 (t0)
REVERT: C  280 LYS cc_start: 0.7902 (tttm) cc_final: 0.7425 (tttm)
REVERT: C  301 LYS cc_start: 0.8054 (mttp) cc_final: 0.7698 (mmtm)
REVERT: R  144 PHE cc_start: 0.8170 (t80) cc_final: 0.7935 (t80)
  outliers start: 16
  outliers final: 13
  residues processed: 104
  average time/residue: 0.2019
  time to fit residues: 29.3198
Evaluate side-chains
  108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
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  172 TRP
Chi-restraints excluded: chain R residue  196 ASN
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 41 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0770
   chunk 12 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 90 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 93 optimal weight:    0.0060
   chunk 3 optimal weight:    0.0670
   overall best weight:    0.3292

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

Flipped N/Q/H residues before XYZ refinement:
B 331 ASN
C 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.202891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.158413 restraints weight = 8992.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3953 rms_B_bonded: 2.88
r_work: 0.3667 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8489  Z= 0.094
  Angle     :  0.488   7.129  11578  Z= 0.257
  Chirality :  0.040   0.139   1353
  Planarity :  0.004   0.051   1454
  Dihedral  :  3.872  28.406   1178
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 14.52 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.26), residues: 1089
  helix:  2.36 (0.29), residues: 358
  sheet:  0.67 (0.32), residues: 280
  loop : -1.23 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP C 332 
 HIS   0.003   0.001   HIS C 225 
 PHE   0.029   0.001   PHE R 180 
 TYR   0.011   0.001   TYR E 191 
 ARG   0.004   0.000   ARG C 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03795 (  396)
  hydrogen bonds       : angle       3.82621 ( 1116)
  SS BOND              : bond        0.00313 (    2)
  SS BOND              : angle       0.44305 (    4)
  covalent geometry    : bond        0.00192 ( 8487)
  covalent geometry    : angle       0.48782 (11574)

********************** 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
  113 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.881 
Fit side-chains
REVERT: C  268 ASN cc_start: 0.7865 (m110) cc_final: 0.7281 (t0)
REVERT: C  280 LYS cc_start: 0.7787 (tttm) cc_final: 0.7384 (tttm)
REVERT: C  301 LYS cc_start: 0.7976 (mttp) cc_final: 0.7681 (mmtm)
REVERT: R  195 MET cc_start: 0.6088 (mmp) cc_final: 0.4933 (ttm)
  outliers start: 12
  outliers final: 11
  residues processed: 107
  average time/residue: 0.2025
  time to fit residues: 30.4807
Evaluate side-chains
  108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
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  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   93 MET
Chi-restraints excluded: chain E residue  215 LEU
Chi-restraints excluded: chain R residue  172 TRP
Chi-restraints excluded: chain R residue  196 ASN
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 62 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0870
   chunk 45 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.1964

-------------------------------------------------------------------------------
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 = 0.4320 r_free = 0.4320 target = 0.196995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.152569 restraints weight = 9160.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 3.22
r_work: 0.3576 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.2860

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= 0.152
  Angle     :  0.560   8.116  11578  Z= 0.297
  Chirality :  0.043   0.141   1353
  Planarity :  0.004   0.053   1454
  Dihedral  :  4.174  35.880   1178
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 14.99 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.26), residues: 1089
  helix:  2.03 (0.28), residues: 365
  sheet:  0.64 (0.32), residues: 280
  loop : -1.33 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP C 332 
 HIS   0.006   0.001   HIS B 188 
 PHE   0.031   0.002   PHE R 144 
 TYR   0.019   0.002   TYR E  50 
 ARG   0.003   0.000   ARG C 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05308 (  396)
  hydrogen bonds       : angle       4.09409 ( 1116)
  SS BOND              : bond        0.00491 (    2)
  SS BOND              : angle       0.67762 (    4)
  covalent geometry    : bond        0.00353 ( 8487)
  covalent geometry    : angle       0.56003 (11574)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4701.70 seconds
wall clock time: 81 minutes 50.63 seconds (4910.63 seconds total)