Starting phenix.real_space_refine
on Thu Jun 12 16:05:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fcx_28998/06_2025/8fcx_28998.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fcx_28998/06_2025/8fcx_28998.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fcx_28998/06_2025/8fcx_28998.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fcx_28998/06_2025/8fcx_28998.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fcx_28998/06_2025/8fcx_28998.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fcx_28998/06_2025/8fcx_28998.cif"
  }
  resolution = 3.04
  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=   0.002 sd=   0.016
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: 6
    Type Number    sf(0)   Gaussians
     P      15      5.49       5
     Mg      5      5.21       5
     S      40      5.16       5
     C    8835      2.51       5
     N    2440      2.21       5
     O    2605      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13940
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "R"
      Number of atoms: 2756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2756
          Classifications: {'peptide': 343}
          Link IDs: {'PTRANS': 13, 'TRANS': 329}
    Chain: "S"
      Number of atoms: 2756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2756
          Classifications: {'peptide': 343}
          Link IDs: {'PTRANS': 13, 'TRANS': 329}
    Chain: "T"
      Number of atoms: 2756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2756
          Classifications: {'peptide': 343}
          Link IDs: {'PTRANS': 13, 'TRANS': 329}
    Chain: "U"
      Number of atoms: 2756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2756
          Classifications: {'peptide': 343}
          Link IDs: {'PTRANS': 13, 'TRANS': 329}
    Chain: "V"
      Number of atoms: 2756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2756
          Classifications: {'peptide': 343}
          Link IDs: {'PTRANS': 13, 'TRANS': 329}
    Chain: "R"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "S"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "T"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "U"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "V"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 8.64, per 1000 atoms: 0.62
  Number of scatterers: 13940
  At special positions: 0
  Unit cell: (77.996, 124.372, 151.776, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      40     16.00
     P      15     15.00
     Mg      5     11.99
     O    2605      8.00
     N    2440      7.00
     C    8835      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 3.42
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3240

  Finding SS restraints...
    Secondary structure from input PDB file:
      82 helices and 10 sheets defined
      63.5% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.51
  Creating SS restraints...
    Processing helix  chain 'R' and resid 8 through 13
      removed outlier: 3.595A  pdb=" N   LEU R  11 " --> pdb=" O   PRO R   8 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 15 through 26
      removed outlier: 3.505A  pdb=" N   ARG R  19 " --> pdb=" O   PRO R  15 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 46
      removed outlier: 3.560A  pdb=" N   GLU R  46 " --> pdb=" O   ARG R  42 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 85
      Proline residue:  R  80  - end of helix
      removed outlier: 3.634A  pdb=" N   SER R  84 " --> pdb=" O   PRO R  80 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 105 through 118
    Processing helix  chain 'R' and resid 148 through 164
    Processing helix  chain 'R' and resid 172 through 178
      removed outlier: 3.509A  pdb=" N   LYS R 178 " --> pdb=" O   HIS R 175 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 183 through 200
      removed outlier: 3.527A  pdb=" N   ASP R 187 " --> pdb=" O   TYR R 183 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   MET R 198 " --> pdb=" O   SER R 194 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   THR R 199 " --> pdb=" O   LEU R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 215
    Processing helix  chain 'R' and resid 218 through 224
    Processing helix  chain 'R' and resid 237 through 254
      removed outlier: 3.533A  pdb=" N   VAL R 241 " --> pdb=" O   SER R 237 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 266 through 275
    Processing helix  chain 'R' and resid 277 through 296
    Processing helix  chain 'R' and resid 301 through 308
      removed outlier: 3.507A  pdb=" N   LEU R 305 " --> pdb=" O   THR R 301 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ARG R 308 " --> pdb=" O   ASP R 304 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 311 through 329
      removed outlier: 3.849A  pdb=" N   GLN R 328 " --> pdb=" O   GLU R 324 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 333 through 343
      removed outlier: 3.727A  pdb=" N   ASN R 338 " --> pdb=" O   ALA R 334 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU R 339 " --> pdb=" O   ASP R 335 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 8 through 14
      removed outlier: 3.661A  pdb=" N   LEU S  12 " --> pdb=" O   LEU S   9 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 15 through 26
      removed outlier: 3.503A  pdb=" N   ARG S  19 " --> pdb=" O   PRO S  15 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 30 through 46
      removed outlier: 3.609A  pdb=" N   GLU S  46 " --> pdb=" O   ARG S  42 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 62 through 83
      Proline residue:  S  80  - end of helix
    Processing helix  chain 'S' and resid 105 through 118
    Processing helix  chain 'S' and resid 148 through 164
    Processing helix  chain 'S' and resid 172 through 178
      removed outlier: 3.567A  pdb=" N   LYS S 178 " --> pdb=" O   HIS S 175 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 183 through 200
      removed outlier: 3.833A  pdb=" N   ASP S 187 " --> pdb=" O   TYR S 183 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   MET S 198 " --> pdb=" O   SER S 194 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   THR S 199 " --> pdb=" O   LEU S 195 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 208 through 215
    Processing helix  chain 'S' and resid 218 through 224
      removed outlier: 3.734A  pdb=" N   ARG S 224 " --> pdb=" O   GLN S 220 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 237 through 254
    Processing helix  chain 'S' and resid 266 through 275
    Processing helix  chain 'S' and resid 277 through 295
      removed outlier: 3.540A  pdb=" N   LEU S 281 " --> pdb=" O   CYS S 277 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 301 through 309
      removed outlier: 3.611A  pdb=" N   ARG S 308 " --> pdb=" O   ASP S 304 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 311 through 329
    Processing helix  chain 'S' and resid 332 through 343
      removed outlier: 3.658A  pdb=" N   VAL S 336 " --> pdb=" O   THR S 332 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 8 through 13
      removed outlier: 3.512A  pdb=" N   LEU T  12 " --> pdb=" O   LEU T   9 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 15 through 26
      removed outlier: 3.736A  pdb=" N   ARG T  19 " --> pdb=" O   PRO T  15 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 30 through 46
    Processing helix  chain 'T' and resid 62 through 85
      Proline residue:  T  80  - end of helix
      removed outlier: 4.017A  pdb=" N   SER T  84 " --> pdb=" O   PRO T  80 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 105 through 118
      removed outlier: 4.097A  pdb=" N   TYR T 109 " --> pdb=" O   ASN T 105 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 148 through 164
    Processing helix  chain 'T' and resid 172 through 178
      removed outlier: 3.512A  pdb=" N   LYS T 178 " --> pdb=" O   HIS T 175 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 181 through 200
      removed outlier: 3.520A  pdb=" N   LEU T 185 " --> pdb=" O   SER T 181 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   GLN T 186 " --> pdb=" O   GLY T 182 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU T 189 " --> pdb=" O   LEU T 185 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 208 through 215
      removed outlier: 3.507A  pdb=" N   THR T 213 " --> pdb=" O   GLU T 210 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 218 through 224
    Processing helix  chain 'T' and resid 237 through 254
    Processing helix  chain 'T' and resid 266 through 275
    Processing helix  chain 'T' and resid 277 through 296
    Processing helix  chain 'T' and resid 301 through 308
      removed outlier: 3.550A  pdb=" N   ARG T 308 " --> pdb=" O   ASP T 304 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 311 through 329
    Processing helix  chain 'T' and resid 332 through 343
      removed outlier: 3.632A  pdb=" N   VAL T 336 " --> pdb=" O   THR T 332 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 8 through 13
      removed outlier: 3.574A  pdb=" N   LEU U  11 " --> pdb=" O   PRO U   8 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 15 through 26
      removed outlier: 3.582A  pdb=" N   ARG U  19 " --> pdb=" O   PRO U  15 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 30 through 46
      removed outlier: 3.590A  pdb=" N   GLU U  46 " --> pdb=" O   ARG U  42 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 62 through 84
      Proline residue:  U  80  - end of helix
    Processing helix  chain 'U' and resid 105 through 118
    Processing helix  chain 'U' and resid 148 through 164
    Processing helix  chain 'U' and resid 172 through 178
    Processing helix  chain 'U' and resid 183 through 200
      removed outlier: 3.726A  pdb=" N   ASP U 187 " --> pdb=" O   TYR U 183 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   MET U 198 " --> pdb=" O   SER U 194 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   THR U 199 " --> pdb=" O   LEU U 195 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 208 through 215
    Processing helix  chain 'U' and resid 218 through 224
    Processing helix  chain 'U' and resid 237 through 254
    Processing helix  chain 'U' and resid 263 through 265
      No H-bonds generated for 'chain 'U' and resid 263 through 265'
    Processing helix  chain 'U' and resid 266 through 275
      removed outlier: 3.551A  pdb=" N   PHE U 270 " --> pdb=" O   HIS U 266 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 277 through 296
    Processing helix  chain 'U' and resid 301 through 308
      removed outlier: 3.716A  pdb=" N   ARG U 308 " --> pdb=" O   ASP U 304 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 311 through 329
    Processing helix  chain 'U' and resid 332 through 344
      removed outlier: 3.751A  pdb=" N   VAL U 336 " --> pdb=" O   THR U 332 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 8 through 13
      removed outlier: 3.545A  pdb=" N   LEU V  11 " --> pdb=" O   PRO V   8 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 15 through 26
    Processing helix  chain 'V' and resid 30 through 46
      removed outlier: 4.118A  pdb=" N   GLU V  46 " --> pdb=" O   ARG V  42 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 62 through 78
    Processing helix  chain 'V' and resid 78 through 85
    Processing helix  chain 'V' and resid 105 through 118
    Processing helix  chain 'V' and resid 148 through 164
    Processing helix  chain 'V' and resid 173 through 178
      removed outlier: 3.754A  pdb=" N   LYS V 178 " --> pdb=" O   HIS V 175 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 183 through 200
      removed outlier: 4.014A  pdb=" N   LEU V 189 " --> pdb=" O   LEU V 185 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 208 through 215
    Processing helix  chain 'V' and resid 217 through 224
      removed outlier: 4.009A  pdb=" N   LEU V 221 " --> pdb=" O   LEU V 217 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 237 through 254
    Processing helix  chain 'V' and resid 266 through 275
    Processing helix  chain 'V' and resid 277 through 295
      removed outlier: 3.622A  pdb=" N   ARG V 295 " --> pdb=" O   ASP V 291 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 301 through 308
      removed outlier: 3.605A  pdb=" N   ARG V 308 " --> pdb=" O   ASP V 304 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 311 through 329
      removed outlier: 3.846A  pdb=" N   LYS V 317 " --> pdb=" O   ALA V 313 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   PHE V 319 " --> pdb=" O   CYS V 315 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 332 through 344
    Processing sheet with id=AA1, first strand: chain 'R' and resid 91 through 95
      removed outlier: 3.572A  pdb=" N   VAL R  92 " --> pdb=" O   VAL R 167 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   PHE R 168 " --> pdb=" O   CYS R 204 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   LEU R 206 " --> pdb=" O   PHE R 168 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   VAL R 170 " --> pdb=" O   LEU R 206 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   PHE R  52 " --> pdb=" O   VAL R 226 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   ILE R 228 " --> pdb=" O   PHE R  52 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   PHE R  54 " --> pdb=" O   ILE R 228 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   PHE R 230 " --> pdb=" O   PHE R  54 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   TYR R  56 " --> pdb=" O   PHE R 230 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'R' and resid 133 through 134
      removed outlier: 3.791A  pdb=" N   SER R 134 " --> pdb=" O   ASN R 142 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'S' and resid 91 through 95
      removed outlier: 6.660A  pdb=" N   VAL S  92 " --> pdb=" O   PHE S 169 " (cutoff:3.500A)
      removed outlier: 7.561A  pdb=" N   ASP S 171 " --> pdb=" O   VAL S  92 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ILE S  94 " --> pdb=" O   ASP S 171 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ILE S  53 " --> pdb=" O   LEU S 205 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   GLY S 207 " --> pdb=" O   ILE S  53 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   VAL S  55 " --> pdb=" O   GLY S 207 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   PHE S  52 " --> pdb=" O   VAL S 226 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   ILE S 228 " --> pdb=" O   PHE S  52 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   PHE S  54 " --> pdb=" O   ILE S 228 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   PHE S 230 " --> pdb=" O   PHE S  54 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   TYR S  56 " --> pdb=" O   PHE S 230 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'S' and resid 133 through 134
      removed outlier: 3.550A  pdb=" N   SER S 134 " --> pdb=" O   ASN S 142 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'T' and resid 91 through 95
      removed outlier: 6.792A  pdb=" N   PHE T  52 " --> pdb=" O   VAL T 226 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   ILE T 228 " --> pdb=" O   PHE T  52 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   PHE T  54 " --> pdb=" O   ILE T 228 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   PHE T 230 " --> pdb=" O   PHE T  54 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   TYR T  56 " --> pdb=" O   PHE T 230 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'T' and resid 133 through 134
    Processing sheet with id=AA7, first strand: chain 'U' and resid 91 through 95
      removed outlier: 6.951A  pdb=" N   VAL U  92 " --> pdb=" O   PHE U 169 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   ASP U 171 " --> pdb=" O   VAL U  92 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   ILE U  94 " --> pdb=" O   ASP U 171 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   ILE U  53 " --> pdb=" O   LEU U 205 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'U' and resid 133 through 134
    Processing sheet with id=AA9, first strand: chain 'V' and resid 92 through 95
      removed outlier: 7.137A  pdb=" N   VAL V  92 " --> pdb=" O   PHE V 169 " (cutoff:3.500A)
      removed outlier: 8.278A  pdb=" N   ASP V 171 " --> pdb=" O   VAL V  92 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ILE V  94 " --> pdb=" O   ASP V 171 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ILE V  53 " --> pdb=" O   LEU V 205 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   GLY V 207 " --> pdb=" O   ILE V  53 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   VAL V  55 " --> pdb=" O   GLY V 207 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   PHE V  52 " --> pdb=" O   VAL V 226 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   ILE V 228 " --> pdb=" O   PHE V  52 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   PHE V  54 " --> pdb=" O   ILE V 228 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   PHE V 230 " --> pdb=" O   PHE V  54 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   TYR V  56 " --> pdb=" O   PHE V 230 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'V' and resid 133 through 134
      removed outlier: 3.836A  pdb=" N   SER V 134 " --> pdb=" O   ASN V 142 " (cutoff:3.500A)

    753 hydrogen bonds defined for protein.
    2094 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: 4.01

  Time building geometry restraints manager: 4.05 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: 4581
        1.34 -     1.46: 1901
        1.46 -     1.57: 7663
        1.57 -     1.69: 25
        1.69 -     1.81: 55
  Bond restraints: 14225
  Sorted by residual:
  bond pdb=" N   SER V  59 "
       pdb=" CA  SER V  59 "
    ideal  model  delta    sigma   weight residual
    1.463  1.437  0.027 1.29e-02 6.01e+03 4.23e+00
  bond pdb=" CA  SER V  59 "
       pdb=" C   SER V  59 "
    ideal  model  delta    sigma   weight residual
    1.530  1.514  0.015 1.10e-02 8.26e+03 1.94e+00
  bond pdb=" CA  ASP V 127 "
       pdb=" CB  ASP V 127 "
    ideal  model  delta    sigma   weight residual
    1.527  1.549 -0.022 1.61e-02 3.86e+03 1.93e+00
  bond pdb=" CA  LEU U  82 "
       pdb=" C   LEU U  82 "
    ideal  model  delta    sigma   weight residual
    1.524  1.508  0.017 1.28e-02 6.10e+03 1.75e+00
  bond pdb=" CG  ASP V 187 "
       pdb=" OD1 ASP V 187 "
    ideal  model  delta    sigma   weight residual
    1.249  1.224  0.025 1.90e-02 2.77e+03 1.73e+00
  ... (remaining 14220 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 18844
        1.69 -     3.38: 361
        3.38 -     5.07: 55
        5.07 -     6.76: 15
        6.76 -     8.45: 10
  Bond angle restraints: 19285
  Sorted by residual:
  angle pdb=" N   THR V 299 "
        pdb=" CA  THR V 299 "
        pdb=" C   THR V 299 "
      ideal   model   delta    sigma   weight residual
     108.38  115.75   -7.37 1.35e+00 5.49e-01 2.98e+01
  angle pdb=" N   THR U 299 "
        pdb=" CA  THR U 299 "
        pdb=" C   THR U 299 "
      ideal   model   delta    sigma   weight residual
     108.74  115.57   -6.83 1.38e+00 5.25e-01 2.45e+01
  angle pdb=" C   VAL S  61 "
        pdb=" N   GLY S  62 "
        pdb=" CA  GLY S  62 "
      ideal   model   delta    sigma   weight residual
     122.26  116.29    5.97 1.34e+00 5.57e-01 1.99e+01
  angle pdb=" N   SER U  59 "
        pdb=" CA  SER U  59 "
        pdb=" C   SER U  59 "
      ideal   model   delta    sigma   weight residual
     109.24  102.68    6.56 1.63e+00 3.76e-01 1.62e+01
  angle pdb=" N   VAL U  61 "
        pdb=" CA  VAL U  61 "
        pdb=" C   VAL U  61 "
      ideal   model   delta    sigma   weight residual
     109.34  117.63   -8.29 2.08e+00 2.31e-01 1.59e+01
  ... (remaining 19280 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 7282
       17.65 -    35.30: 1026
       35.30 -    52.95: 297
       52.95 -    70.60: 59
       70.60 -    88.25: 11
  Dihedral angle restraints: 8675
    sinusoidal: 3660
      harmonic: 5015
  Sorted by residual:
  dihedral pdb=" CA  ASP V 187 "
           pdb=" C   ASP V 187 "
           pdb=" N   GLN V 188 "
           pdb=" CA  GLN V 188 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.01   16.99     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  ASP U 127 "
           pdb=" C   ASP U 127 "
           pdb=" N   TYR U 128 "
           pdb=" CA  TYR U 128 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.33  -16.67     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  LEU V 121 "
           pdb=" C   LEU V 121 "
           pdb=" N   ILE V 122 "
           pdb=" CA  ILE V 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.51  -16.49     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 8672 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1496
       0.033 -    0.067: 454
       0.067 -    0.100: 132
       0.100 -    0.134: 71
       0.134 -    0.167: 7
  Chirality restraints: 2160
  Sorted by residual:
  chirality pdb=" CA  ASP V 127 "
            pdb=" N   ASP V 127 "
            pdb=" C   ASP V 127 "
            pdb=" CB  ASP V 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.96e-01
  chirality pdb=" CA  ASP T 127 "
            pdb=" N   ASP T 127 "
            pdb=" C   ASP T 127 "
            pdb=" CB  ASP T 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.70e-01
  chirality pdb=" CA  ILE S  94 "
            pdb=" N   ILE S  94 "
            pdb=" C   ILE S  94 "
            pdb=" CB  ILE S  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.35e-01
  ... (remaining 2157 not shown)

  Planarity restraints: 2455
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE V 126 "   -0.013 2.00e-02 2.50e+03   2.13e-02 7.93e+00
        pdb=" CG  PHE V 126 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 PHE V 126 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE V 126 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE V 126 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE V 126 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE V 126 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA U 297 "   -0.011 2.00e-02 2.50e+03   2.26e-02 5.09e+00
        pdb=" C   ALA U 297 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA U 297 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   THR U 298 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU S  79 "    0.036 5.00e-02 4.00e+02   5.45e-02 4.75e+00
        pdb=" N   PRO S  80 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO S  80 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO S  80 "    0.031 5.00e-02 4.00e+02
  ... (remaining 2452 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.57: 152
        2.57 -     3.15: 11796
        3.15 -     3.73: 22939
        3.73 -     4.32: 30355
        4.32 -     4.90: 50514
  Nonbonded interactions: 115756
  Sorted by model distance:
  nonbonded pdb=" O3A ATP V 600 "
            pdb="MG    MG V 601 "
     model   vdw
     1.984 2.170
  nonbonded pdb=" O3B ATP T 600 "
            pdb="MG    MG T 601 "
     model   vdw
     1.995 2.170
  nonbonded pdb=" O3B ATP U 600 "
            pdb="MG    MG U 601 "
     model   vdw
     2.000 2.170
  nonbonded pdb=" O3B ATP S 600 "
            pdb="MG    MG S 601 "
     model   vdw
     2.005 2.170
  nonbonded pdb=" O3A ATP U 600 "
            pdb="MG    MG U 601 "
     model   vdw
     2.026 2.170
  ... (remaining 115751 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'R'
  selection = chain 'S'
  selection = chain 'T'
  selection = chain 'U'
  selection = chain 'V'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.300
  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:          0.540
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     32.890
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.090
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14225  Z= 0.142
  Angle     :  0.599   8.446  19285  Z= 0.328
  Chirality :  0.040   0.167   2160
  Planarity :  0.004   0.054   2455
  Dihedral  : 17.789  88.249   5435
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  :  3.93 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 27.03 %
    Favored  : 72.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.34 (0.22), residues: 1705
  helix:  0.97 (0.17), residues: 1040
  sheet: -0.54 (0.48), residues: 140
  loop : -0.94 (0.29), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP S 267 
 HIS   0.006   0.001   HIS S 124 
 PHE   0.047   0.001   PHE V 126 
 TYR   0.014   0.001   TYR T 128 
 ARG   0.011   0.000   ARG V 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18484 (  753)
  hydrogen bonds       : angle       5.88902 ( 2094)
  covalent geometry    : bond        0.00266 (14225)
  covalent geometry    : angle       0.59899 (19285)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 254
  time to evaluate  : 1.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  156 LEU cc_start: 0.9236 (tp) cc_final: 0.8871 (tp)
REVERT: R  190 ASP cc_start: 0.8941 (m-30) cc_final: 0.8691 (m-30)
REVERT: S   56 TYR cc_start: 0.8152 (m-80) cc_final: 0.7225 (m-10)
REVERT: S  318 MET cc_start: 0.8866 (mtm) cc_final: 0.8345 (mtt)
REVERT: S  333 GLU cc_start: 0.8828 (tp30) cc_final: 0.8559 (tm-30)
REVERT: T  244 PHE cc_start: 0.9532 (t80) cc_final: 0.9245 (t80)
REVERT: T  277 CYS cc_start: 0.8974 (m) cc_final: 0.8420 (m)
REVERT: T  333 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8698 (tp30)
REVERT: U  172 GLU cc_start: 0.9175 (pt0) cc_final: 0.8756 (pm20)
REVERT: U  210 GLU cc_start: 0.9000 (tt0) cc_final: 0.8783 (tt0)
REVERT: V   30 HIS cc_start: 0.7327 (p90) cc_final: 0.6806 (p-80)
REVERT: V  190 ASP cc_start: 0.9234 (m-30) cc_final: 0.8841 (m-30)
REVERT: V  277 CYS cc_start: 0.8892 (m) cc_final: 0.8378 (m)
REVERT: V  278 ILE cc_start: 0.8329 (mm) cc_final: 0.8010 (tt)
REVERT: V  281 LEU cc_start: 0.8850 (tp) cc_final: 0.8625 (tt)
REVERT: V  315 CYS cc_start: 0.7785 (t) cc_final: 0.7281 (p)
  outliers start: 9
  outliers final: 4
  residues processed: 261
  average time/residue: 0.2758
  time to fit residues: 103.2643
Evaluate side-chains
  143 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 139
  time to evaluate  : 1.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  272 GLU
Chi-restraints excluded: chain R residue  301 THR
Chi-restraints excluded: chain V residue   59 SER
Chi-restraints excluded: chain V residue  301 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 143 optimal weight:    6.9990
   chunk 128 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   chunk 133 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 81 optimal weight:    6.9990
   chunk 99 optimal weight:    4.9990
   chunk 154 optimal weight:    0.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 314 GLN
R 323 GLN
S 252 GLN
T  25 ASN
** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
V 158 ASN
V 164 HIS
V 220 GLN
** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.066979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.049946 restraints weight = 62110.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 5.63
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14225  Z= 0.142
  Angle     :  0.594   8.284  19285  Z= 0.308
  Chirality :  0.042   0.185   2160
  Planarity :  0.004   0.041   2455
  Dihedral  :  9.907  82.608   2081
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  3.81 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 25.00 %
    Favored  : 72.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.63 (0.22), residues: 1705
  helix:  1.24 (0.17), residues: 1065
  sheet: -0.55 (0.47), residues: 140
  loop : -0.98 (0.29), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP V 267 
 HIS   0.004   0.001   HIS V  30 
 PHE   0.014   0.001   PHE U 126 
 TYR   0.017   0.001   TYR T 103 
 ARG   0.006   0.000   ARG S  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04085 (  753)
  hydrogen bonds       : angle       4.34172 ( 2094)
  covalent geometry    : bond        0.00309 (14225)
  covalent geometry    : angle       0.59365 (19285)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 145
  time to evaluate  : 1.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  105 ASN cc_start: 0.9051 (t0) cc_final: 0.8784 (t0)
REVERT: R  307 LYS cc_start: 0.9475 (mttt) cc_final: 0.9140 (tttm)
REVERT: S  318 MET cc_start: 0.8954 (mtm) cc_final: 0.8731 (mtt)
REVERT: T   81 LYS cc_start: 0.9585 (mppt) cc_final: 0.9378 (pttt)
REVERT: T  164 HIS cc_start: 0.9024 (t-90) cc_final: 0.8793 (t-90)
REVERT: T  193 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.9151 (ptmm)
REVERT: T  277 CYS cc_start: 0.8717 (m) cc_final: 0.8439 (m)
REVERT: U  164 HIS cc_start: 0.9052 (t-90) cc_final: 0.8842 (t-90)
REVERT: U  172 GLU cc_start: 0.9258 (pt0) cc_final: 0.8950 (pm20)
REVERT: U  252 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8748 (tt0)
REVERT: U  318 MET cc_start: 0.9448 (mtp) cc_final: 0.9220 (mtm)
REVERT: U  328 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.9032 (mt0)
REVERT: U  338 ASN cc_start: 0.9338 (m110) cc_final: 0.9100 (m110)
REVERT: V   30 HIS cc_start: 0.7680 (p90) cc_final: 0.7105 (p-80)
REVERT: V  172 GLU cc_start: 0.9285 (tp30) cc_final: 0.8991 (tp30)
REVERT: V  190 ASP cc_start: 0.9259 (m-30) cc_final: 0.8841 (m-30)
REVERT: V  220 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7925 (tp40)
REVERT: V  277 CYS cc_start: 0.9144 (m) cc_final: 0.8829 (m)
REVERT: V  278 ILE cc_start: 0.8241 (mm) cc_final: 0.7912 (tt)
REVERT: V  315 CYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7267 (m)
  outliers start: 40
  outliers final: 11
  residues processed: 177
  average time/residue: 0.3345
  time to fit residues: 89.8675
Evaluate side-chains
  131 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 2.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   95 GLU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  301 THR
Chi-restraints excluded: chain S residue   94 ILE
Chi-restraints excluded: chain T residue   27 THR
Chi-restraints excluded: chain T residue  189 LEU
Chi-restraints excluded: chain T residue  193 LYS
Chi-restraints excluded: chain U residue   94 ILE
Chi-restraints excluded: chain U residue  137 ASN
Chi-restraints excluded: chain U residue  252 GLN
Chi-restraints excluded: chain U residue  328 GLN
Chi-restraints excluded: chain V residue   26 TYR
Chi-restraints excluded: chain V residue  220 GLN
Chi-restraints excluded: chain V residue  264 VAL
Chi-restraints excluded: chain V residue  284 TRP
Chi-restraints excluded: chain V residue  315 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 164 optimal weight:    5.9990
   chunk 163 optimal weight:    0.9980
   chunk 130 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 85 optimal weight:    1.9990
   chunk 165 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 131 optimal weight:    2.9990
   chunk 101 optimal weight:    0.4980
   chunk 112 optimal weight:    3.9990
   chunk 141 optimal weight:    7.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
R 158 ASN
** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
U 158 ASN
** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 164 HIS
** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.064271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.047630 restraints weight = 65045.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 5.49
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14225  Z= 0.168
  Angle     :  0.579   8.078  19285  Z= 0.300
  Chirality :  0.041   0.179   2160
  Planarity :  0.004   0.042   2455
  Dihedral  :  9.189  86.404   2076
  Min Nonbonded Distance : 1.816

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  3.46 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 24.26 %
    Favored  : 72.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.77 (0.21), residues: 1705
  helix:  1.31 (0.17), residues: 1070
  sheet: -0.62 (0.48), residues: 140
  loop : -0.82 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP V 267 
 HIS   0.004   0.001   HIS R  30 
 PHE   0.018   0.001   PHE U 126 
 TYR   0.026   0.002   TYR V 109 
 ARG   0.006   0.000   ARG R 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03949 (  753)
  hydrogen bonds       : angle       4.08902 ( 2094)
  covalent geometry    : bond        0.00366 (14225)
  covalent geometry    : angle       0.57851 (19285)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 127
  time to evaluate  : 1.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  105 ASN cc_start: 0.9168 (t0) cc_final: 0.8950 (t0)
REVERT: R  117 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8838 (mp)
REVERT: R  277 CYS cc_start: 0.7961 (m) cc_final: 0.7725 (m)
REVERT: R  307 LYS cc_start: 0.9516 (mttt) cc_final: 0.9070 (tmtt)
REVERT: S  172 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8720 (mm-30)
REVERT: S  283 ASP cc_start: 0.9079 (m-30) cc_final: 0.8846 (m-30)
REVERT: T   81 LYS cc_start: 0.9588 (mppt) cc_final: 0.9308 (pttt)
REVERT: T  164 HIS cc_start: 0.9071 (t-90) cc_final: 0.8551 (t-90)
REVERT: T  193 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9084 (ptmm)
REVERT: T  277 CYS cc_start: 0.9066 (m) cc_final: 0.8723 (m)
REVERT: U  164 HIS cc_start: 0.9030 (t-90) cc_final: 0.8544 (t-90)
REVERT: U  172 GLU cc_start: 0.9177 (pt0) cc_final: 0.8664 (pm20)
REVERT: U  328 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.9025 (mt0)
REVERT: V   30 HIS cc_start: 0.8159 (p90) cc_final: 0.7784 (p90)
REVERT: V   81 LYS cc_start: 0.9356 (mmtm) cc_final: 0.9081 (tptp)
REVERT: V   82 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8263 (mm)
REVERT: V  172 GLU cc_start: 0.9270 (tp30) cc_final: 0.8930 (tp30)
REVERT: V  190 ASP cc_start: 0.9215 (m-30) cc_final: 0.8797 (m-30)
REVERT: V  251 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8436 (t80)
REVERT: V  278 ILE cc_start: 0.8296 (mm) cc_final: 0.8018 (tt)
  outliers start: 52
  outliers final: 26
  residues processed: 167
  average time/residue: 0.2346
  time to fit residues: 59.3897
Evaluate side-chains
  134 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 103
  time to evaluate  : 1.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   41 MET
Chi-restraints excluded: chain R residue   64 THR
Chi-restraints excluded: chain R residue   95 GLU
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  203 HIS
Chi-restraints excluded: chain R residue  272 GLU
Chi-restraints excluded: chain R residue  301 THR
Chi-restraints excluded: chain S residue   17 THR
Chi-restraints excluded: chain S residue   36 VAL
Chi-restraints excluded: chain S residue  114 LEU
Chi-restraints excluded: chain S residue  128 TYR
Chi-restraints excluded: chain S residue  183 TYR
Chi-restraints excluded: chain S residue  208 THR
Chi-restraints excluded: chain T residue   27 THR
Chi-restraints excluded: chain T residue  145 SER
Chi-restraints excluded: chain T residue  192 LEU
Chi-restraints excluded: chain T residue  193 LYS
Chi-restraints excluded: chain T residue  266 HIS
Chi-restraints excluded: chain T residue  332 THR
Chi-restraints excluded: chain U residue   94 ILE
Chi-restraints excluded: chain U residue  128 TYR
Chi-restraints excluded: chain U residue  137 ASN
Chi-restraints excluded: chain U residue  143 VAL
Chi-restraints excluded: chain U residue  328 GLN
Chi-restraints excluded: chain V residue   82 LEU
Chi-restraints excluded: chain V residue  124 HIS
Chi-restraints excluded: chain V residue  251 PHE
Chi-restraints excluded: chain V residue  264 VAL
Chi-restraints excluded: chain V residue  284 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 130 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 160 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 115 optimal weight:    7.9990
   chunk 85 optimal weight:    5.9990
   chunk 109 optimal weight:   10.0000
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** R  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T 197 ASN
** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
V 164 HIS
V 197 ASN
V 253 GLN
** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.062641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.046056 restraints weight = 65046.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 5.44
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  14225  Z= 0.189
  Angle     :  0.590  12.651  19285  Z= 0.302
  Chirality :  0.041   0.192   2160
  Planarity :  0.004   0.043   2455
  Dihedral  :  9.159  87.711   2076
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  3.81 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 24.39 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.82 (0.22), residues: 1705
  helix:  1.36 (0.17), residues: 1060
  sheet: -0.65 (0.48), residues: 140
  loop : -0.77 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP V 267 
 HIS   0.004   0.001   HIS T  30 
 PHE   0.020   0.002   PHE U 126 
 TYR   0.019   0.002   TYR T 128 
 ARG   0.005   0.000   ARG S 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03828 (  753)
  hydrogen bonds       : angle       4.02921 ( 2094)
  covalent geometry    : bond        0.00412 (14225)
  covalent geometry    : angle       0.58998 (19285)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 113
  time to evaluate  : 1.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  117 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8885 (mp)
REVERT: R  277 CYS cc_start: 0.8036 (m) cc_final: 0.7733 (m)
REVERT: S  172 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8639 (mm-30)
REVERT: S  198 MET cc_start: 0.8916 (mpp) cc_final: 0.8595 (mpp)
REVERT: S  283 ASP cc_start: 0.9118 (m-30) cc_final: 0.8867 (m-30)
REVERT: S  293 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9406 (mt)
REVERT: T   41 MET cc_start: 0.9068 (mmt) cc_final: 0.8804 (mmm)
REVERT: T  164 HIS cc_start: 0.9145 (t-90) cc_final: 0.8591 (t-90)
REVERT: T  277 CYS cc_start: 0.9144 (m) cc_final: 0.8769 (m)
REVERT: U   19 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8598 (mtt90)
REVERT: U  164 HIS cc_start: 0.9128 (t-90) cc_final: 0.8818 (t70)
REVERT: U  172 GLU cc_start: 0.9169 (pt0) cc_final: 0.8882 (pm20)
REVERT: V  172 GLU cc_start: 0.9285 (tp30) cc_final: 0.8935 (tp30)
REVERT: V  190 ASP cc_start: 0.9233 (m-30) cc_final: 0.8822 (m-30)
REVERT: V  251 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8522 (t80)
REVERT: V  294 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7333 (m-30)
  outliers start: 52
  outliers final: 21
  residues processed: 157
  average time/residue: 0.2609
  time to fit residues: 63.2290
Evaluate side-chains
  124 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 1.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   64 THR
Chi-restraints excluded: chain R residue   66 LEU
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  214 PHE
Chi-restraints excluded: chain S residue   17 THR
Chi-restraints excluded: chain S residue   36 VAL
Chi-restraints excluded: chain S residue  114 LEU
Chi-restraints excluded: chain S residue  128 TYR
Chi-restraints excluded: chain S residue  183 TYR
Chi-restraints excluded: chain S residue  208 THR
Chi-restraints excluded: chain S residue  293 LEU
Chi-restraints excluded: chain T residue   27 THR
Chi-restraints excluded: chain T residue  138 PHE
Chi-restraints excluded: chain T residue  145 SER
Chi-restraints excluded: chain T residue  192 LEU
Chi-restraints excluded: chain T residue  305 LEU
Chi-restraints excluded: chain T residue  332 THR
Chi-restraints excluded: chain U residue   19 ARG
Chi-restraints excluded: chain U residue   94 ILE
Chi-restraints excluded: chain U residue  128 TYR
Chi-restraints excluded: chain U residue  143 VAL
Chi-restraints excluded: chain V residue  164 HIS
Chi-restraints excluded: chain V residue  251 PHE
Chi-restraints excluded: chain V residue  264 VAL
Chi-restraints excluded: chain V residue  294 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 90 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 129 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 126 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 169 optimal weight:   10.0000
   chunk 106 optimal weight:    0.8980
   chunk 157 optimal weight:    7.9990
   chunk 23 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** R  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 188 GLN
** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.063461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.046930 restraints weight = 64931.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 5.47
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.4233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14225  Z= 0.124
  Angle     :  0.558   8.614  19285  Z= 0.282
  Chirality :  0.041   0.220   2160
  Planarity :  0.004   0.043   2455
  Dihedral  :  8.840  88.416   2075
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  3.23 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 25.54 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.95 (0.22), residues: 1705
  helix:  1.47 (0.17), residues: 1060
  sheet: -0.63 (0.47), residues: 140
  loop : -0.70 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP V 267 
 HIS   0.004   0.001   HIS R  30 
 PHE   0.018   0.001   PHE S 214 
 TYR   0.025   0.001   TYR T 183 
 ARG   0.005   0.000   ARG S 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03572 (  753)
  hydrogen bonds       : angle       3.93821 ( 2094)
  covalent geometry    : bond        0.00274 (14225)
  covalent geometry    : angle       0.55776 (19285)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 114
  time to evaluate  : 1.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  117 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8941 (mp)
REVERT: R  277 CYS cc_start: 0.7980 (m) cc_final: 0.7687 (m)
REVERT: S  172 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8616 (mm-30)
REVERT: S  283 ASP cc_start: 0.9066 (m-30) cc_final: 0.8783 (m-30)
REVERT: S  293 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9397 (mt)
REVERT: T   41 MET cc_start: 0.9108 (mmt) cc_final: 0.8838 (mmm)
REVERT: T   81 LYS cc_start: 0.9603 (mppt) cc_final: 0.9340 (pttt)
REVERT: T  164 HIS cc_start: 0.9135 (t-90) cc_final: 0.8708 (t-90)
REVERT: T  277 CYS cc_start: 0.9051 (m) cc_final: 0.8750 (m)
REVERT: U   19 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8658 (mtt90)
REVERT: U  164 HIS cc_start: 0.9151 (t-90) cc_final: 0.8809 (t70)
REVERT: V   12 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7332 (mm)
REVERT: V   30 HIS cc_start: 0.8278 (p90) cc_final: 0.8031 (p90)
REVERT: V  172 GLU cc_start: 0.9270 (tp30) cc_final: 0.8924 (tp30)
REVERT: V  190 ASP cc_start: 0.9155 (m-30) cc_final: 0.8765 (m-30)
REVERT: V  251 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8474 (t80)
  outliers start: 35
  outliers final: 20
  residues processed: 142
  average time/residue: 0.2910
  time to fit residues: 64.1816
Evaluate side-chains
  126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 1.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   18 GLU
Chi-restraints excluded: chain R residue   64 THR
Chi-restraints excluded: chain R residue   66 LEU
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  203 HIS
Chi-restraints excluded: chain R residue  214 PHE
Chi-restraints excluded: chain R residue  272 GLU
Chi-restraints excluded: chain S residue  128 TYR
Chi-restraints excluded: chain S residue  183 TYR
Chi-restraints excluded: chain S residue  293 LEU
Chi-restraints excluded: chain T residue   27 THR
Chi-restraints excluded: chain T residue  145 SER
Chi-restraints excluded: chain T residue  192 LEU
Chi-restraints excluded: chain T residue  305 LEU
Chi-restraints excluded: chain U residue   19 ARG
Chi-restraints excluded: chain U residue   94 ILE
Chi-restraints excluded: chain U residue  128 TYR
Chi-restraints excluded: chain U residue  143 VAL
Chi-restraints excluded: chain V residue   12 LEU
Chi-restraints excluded: chain V residue   26 TYR
Chi-restraints excluded: chain V residue  164 HIS
Chi-restraints excluded: chain V residue  251 PHE
Chi-restraints excluded: chain V residue  264 VAL
Chi-restraints excluded: chain V residue  308 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 121 optimal weight:    4.9990
   chunk 103 optimal weight:    7.9990
   chunk 140 optimal weight:    0.4980
   chunk 97 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 114 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 164 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   chunk 150 optimal weight:    7.9990
   overall best weight:    3.2986

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

Flipped N/Q/H residues before XYZ refinement:
** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
U 254 HIS
V 164 HIS
** V 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.060799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.044529 restraints weight = 66382.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 5.34
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.4813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  14225  Z= 0.231
  Angle     :  0.617   7.964  19285  Z= 0.321
  Chirality :  0.043   0.201   2160
  Planarity :  0.004   0.043   2455
  Dihedral  :  9.438  86.765   2075
  Min Nonbonded Distance : 1.818

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.40 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 25.14 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.75 (0.21), residues: 1705
  helix:  1.26 (0.17), residues: 1060
  sheet: -0.67 (0.48), residues: 140
  loop : -0.66 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP S 267 
 HIS   0.005   0.001   HIS S 124 
 PHE   0.032   0.002   PHE T 138 
 TYR   0.020   0.002   TYR S 109 
 ARG   0.003   0.000   ARG S 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04011 (  753)
  hydrogen bonds       : angle       4.08160 ( 2094)
  covalent geometry    : bond        0.00502 (14225)
  covalent geometry    : angle       0.61705 (19285)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 101
  time to evaluate  : 1.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  117 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8962 (mp)
REVERT: R  277 CYS cc_start: 0.8400 (m) cc_final: 0.8148 (m)
REVERT: S  172 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8661 (mm-30)
REVERT: S  283 ASP cc_start: 0.9113 (m-30) cc_final: 0.8841 (m-30)
REVERT: S  333 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8495 (tm-30)
REVERT: T   41 MET cc_start: 0.9173 (mmt) cc_final: 0.8890 (mmm)
REVERT: T  164 HIS cc_start: 0.9148 (t-90) cc_final: 0.8527 (t-90)
REVERT: T  172 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8924 (mm-30)
REVERT: T  277 CYS cc_start: 0.9186 (m) cc_final: 0.8831 (m)
REVERT: U  164 HIS cc_start: 0.9126 (t-90) cc_final: 0.8631 (t70)
REVERT: U  172 GLU cc_start: 0.8926 (pm20) cc_final: 0.8594 (pm20)
REVERT: V  172 GLU cc_start: 0.9264 (tp30) cc_final: 0.8941 (tp30)
REVERT: V  190 ASP cc_start: 0.9257 (m-30) cc_final: 0.8821 (m-30)
REVERT: V  251 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8561 (t80)
REVERT: V  294 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7745 (m-30)
  outliers start: 45
  outliers final: 23
  residues processed: 139
  average time/residue: 0.2129
  time to fit residues: 47.9925
Evaluate side-chains
  121 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 1.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   64 THR
Chi-restraints excluded: chain R residue   66 LEU
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  203 HIS
Chi-restraints excluded: chain R residue  214 PHE
Chi-restraints excluded: chain R residue  272 GLU
Chi-restraints excluded: chain S residue  208 THR
Chi-restraints excluded: chain S residue  333 GLU
Chi-restraints excluded: chain T residue   27 THR
Chi-restraints excluded: chain T residue   68 LEU
Chi-restraints excluded: chain T residue  145 SER
Chi-restraints excluded: chain T residue  192 LEU
Chi-restraints excluded: chain T residue  266 HIS
Chi-restraints excluded: chain T residue  305 LEU
Chi-restraints excluded: chain T residue  332 THR
Chi-restraints excluded: chain U residue  128 TYR
Chi-restraints excluded: chain U residue  143 VAL
Chi-restraints excluded: chain U residue  192 LEU
Chi-restraints excluded: chain V residue  158 ASN
Chi-restraints excluded: chain V residue  226 VAL
Chi-restraints excluded: chain V residue  251 PHE
Chi-restraints excluded: chain V residue  264 VAL
Chi-restraints excluded: chain V residue  294 ASP
Chi-restraints excluded: chain V residue  308 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 159 optimal weight:    8.9990
   chunk 163 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0020
   chunk 126 optimal weight:    0.0670
   chunk 143 optimal weight:    7.9990
   chunk 127 optimal weight:    0.4980
   chunk 132 optimal weight:    5.9990
   chunk 151 optimal weight:    5.9990
   chunk 160 optimal weight:    0.6980
   overall best weight:    0.4528

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

Flipped N/Q/H residues before XYZ refinement:
** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** V 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 164 HIS
** V 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.063448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.047137 restraints weight = 64175.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 5.34
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.4824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  14225  Z= 0.114
  Angle     :  0.565   9.179  19285  Z= 0.285
  Chirality :  0.041   0.212   2160
  Planarity :  0.004   0.042   2455
  Dihedral  :  8.636  83.288   2075
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  3.17 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 26.01 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.04 (0.22), residues: 1705
  helix:  1.51 (0.17), residues: 1045
  sheet: -0.44 (0.48), residues: 140
  loop : -0.59 (0.29), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP V 267 
 HIS   0.004   0.001   HIS S  30 
 PHE   0.028   0.001   PHE T 138 
 TYR   0.024   0.001   TYR T 183 
 ARG   0.004   0.000   ARG S 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03448 (  753)
  hydrogen bonds       : angle       3.85349 ( 2094)
  covalent geometry    : bond        0.00240 (14225)
  covalent geometry    : angle       0.56468 (19285)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 2.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   18 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8291 (mp0)
REVERT: R  103 TYR cc_start: 0.7726 (m-10) cc_final: 0.7351 (m-80)
REVERT: R  117 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8969 (mp)
REVERT: R  277 CYS cc_start: 0.7980 (m) cc_final: 0.7690 (m)
REVERT: R  283 ASP cc_start: 0.8994 (m-30) cc_final: 0.8772 (t0)
REVERT: S  172 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8594 (mm-30)
REVERT: S  283 ASP cc_start: 0.9078 (m-30) cc_final: 0.8748 (m-30)
REVERT: T   41 MET cc_start: 0.9116 (mmt) cc_final: 0.8808 (mmm)
REVERT: T  164 HIS cc_start: 0.9149 (t-90) cc_final: 0.8615 (t-90)
REVERT: T  277 CYS cc_start: 0.8931 (m) cc_final: 0.8660 (m)
REVERT: T  318 MET cc_start: 0.9082 (mmt) cc_final: 0.8876 (mmt)
REVERT: U   19 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8526 (mtm-85)
REVERT: U  172 GLU cc_start: 0.8736 (pm20) cc_final: 0.8391 (pm20)
REVERT: V   12 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6785 (mm)
REVERT: V   30 HIS cc_start: 0.8348 (p90) cc_final: 0.8108 (p90)
REVERT: V  105 ASN cc_start: 0.8734 (p0) cc_final: 0.8523 (p0)
REVERT: V  108 GLU cc_start: 0.8767 (tp30) cc_final: 0.8350 (tp30)
REVERT: V  172 GLU cc_start: 0.9217 (tp30) cc_final: 0.8883 (tp30)
REVERT: V  190 ASP cc_start: 0.9187 (m-30) cc_final: 0.8758 (m-30)
REVERT: V  251 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8529 (t80)
  outliers start: 28
  outliers final: 16
  residues processed: 133
  average time/residue: 0.2134
  time to fit residues: 45.5468
Evaluate side-chains
  123 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 1.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   18 GLU
Chi-restraints excluded: chain R residue   41 MET
Chi-restraints excluded: chain R residue   66 LEU
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  203 HIS
Chi-restraints excluded: chain R residue  214 PHE
Chi-restraints excluded: chain R residue  272 GLU
Chi-restraints excluded: chain T residue   27 THR
Chi-restraints excluded: chain T residue  305 LEU
Chi-restraints excluded: chain T residue  332 THR
Chi-restraints excluded: chain U residue   19 ARG
Chi-restraints excluded: chain U residue   94 ILE
Chi-restraints excluded: chain U residue  128 TYR
Chi-restraints excluded: chain U residue  143 VAL
Chi-restraints excluded: chain V residue   12 LEU
Chi-restraints excluded: chain V residue   26 TYR
Chi-restraints excluded: chain V residue  164 HIS
Chi-restraints excluded: chain V residue  251 PHE
Chi-restraints excluded: chain V residue  264 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 151 optimal weight:    0.8980
   chunk 154 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 106 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 42 optimal weight:   10.0000
   chunk 90 optimal weight:    2.9990
   chunk 167 optimal weight:    8.9990
   chunk 96 optimal weight:    0.7980
   chunk 139 optimal weight:    8.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
U 164 HIS
V 105 ASN
V 164 HIS
V 197 ASN
V 252 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.063086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.046799 restraints weight = 64104.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 5.38
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.4911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14225  Z= 0.118
  Angle     :  0.567  10.753  19285  Z= 0.288
  Chirality :  0.041   0.218   2160
  Planarity :  0.004   0.072   2455
  Dihedral  :  8.619  82.398   2075
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  3.52 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 26.62 %
    Favored  : 71.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.13 (0.22), residues: 1705
  helix:  1.59 (0.17), residues: 1045
  sheet: -0.44 (0.48), residues: 140
  loop : -0.55 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP V 267 
 HIS   0.005   0.001   HIS V 164 
 PHE   0.023   0.001   PHE T 138 
 TYR   0.027   0.001   TYR S 109 
 ARG   0.006   0.000   ARG V 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03389 (  753)
  hydrogen bonds       : angle       3.81474 ( 2094)
  covalent geometry    : bond        0.00258 (14225)
  covalent geometry    : angle       0.56668 (19285)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 1.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  117 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8965 (mp)
REVERT: R  172 GLU cc_start: 0.8854 (pm20) cc_final: 0.8593 (pm20)
REVERT: R  277 CYS cc_start: 0.8180 (m) cc_final: 0.7920 (m)
REVERT: R  283 ASP cc_start: 0.8977 (m-30) cc_final: 0.8748 (t0)
REVERT: S  172 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8591 (mm-30)
REVERT: S  283 ASP cc_start: 0.9088 (m-30) cc_final: 0.8758 (m-30)
REVERT: T   41 MET cc_start: 0.9114 (mmt) cc_final: 0.8816 (mmm)
REVERT: T  164 HIS cc_start: 0.9139 (t-90) cc_final: 0.8583 (t-90)
REVERT: T  277 CYS cc_start: 0.8928 (m) cc_final: 0.8693 (m)
REVERT: U   19 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8689 (mtt90)
REVERT: U  164 HIS cc_start: 0.9075 (t-170) cc_final: 0.8694 (t-90)
REVERT: U  172 GLU cc_start: 0.8779 (pm20) cc_final: 0.8561 (pm20)
REVERT: V   12 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6747 (mm)
REVERT: V  105 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.7954 (p0)
REVERT: V  172 GLU cc_start: 0.9209 (tp30) cc_final: 0.8880 (tp30)
REVERT: V  190 ASP cc_start: 0.9183 (m-30) cc_final: 0.8752 (m-30)
REVERT: V  198 MET cc_start: 0.8559 (mtm) cc_final: 0.8306 (mtm)
REVERT: V  251 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8457 (t80)
  outliers start: 29
  outliers final: 17
  residues processed: 128
  average time/residue: 0.2176
  time to fit residues: 43.5927
Evaluate side-chains
  123 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 1.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   18 GLU
Chi-restraints excluded: chain R residue   66 LEU
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  203 HIS
Chi-restraints excluded: chain R residue  214 PHE
Chi-restraints excluded: chain R residue  272 GLU
Chi-restraints excluded: chain T residue   27 THR
Chi-restraints excluded: chain T residue  305 LEU
Chi-restraints excluded: chain T residue  332 THR
Chi-restraints excluded: chain U residue   19 ARG
Chi-restraints excluded: chain U residue   94 ILE
Chi-restraints excluded: chain U residue  128 TYR
Chi-restraints excluded: chain U residue  143 VAL
Chi-restraints excluded: chain V residue   12 LEU
Chi-restraints excluded: chain V residue  105 ASN
Chi-restraints excluded: chain V residue  158 ASN
Chi-restraints excluded: chain V residue  164 HIS
Chi-restraints excluded: chain V residue  226 VAL
Chi-restraints excluded: chain V residue  251 PHE
Chi-restraints excluded: chain V residue  264 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 8 optimal weight:    0.0270
   chunk 117 optimal weight:    6.9990
   chunk 144 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 162 optimal weight:    0.9990
   chunk 102 optimal weight:   10.0000
   chunk 69 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 96 optimal weight:    0.9990
   overall best weight:    0.7642

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

Flipped N/Q/H residues before XYZ refinement:
** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** V 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.063340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.046972 restraints weight = 63955.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 5.41
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.4990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14225  Z= 0.116
  Angle     :  0.578   9.640  19285  Z= 0.292
  Chirality :  0.042   0.284   2160
  Planarity :  0.004   0.044   2455
  Dihedral  :  8.551  84.587   2075
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  3.52 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 26.62 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.19 (0.22), residues: 1705
  helix:  1.61 (0.17), residues: 1045
  sheet: -0.37 (0.48), residues: 140
  loop : -0.48 (0.29), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP V 267 
 HIS   0.009   0.001   HIS V 164 
 PHE   0.020   0.001   PHE T 138 
 TYR   0.028   0.001   TYR S 109 
 ARG   0.003   0.000   ARG S 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03344 (  753)
  hydrogen bonds       : angle       3.80648 ( 2094)
  covalent geometry    : bond        0.00251 (14225)
  covalent geometry    : angle       0.57836 (19285)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 1.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  117 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8958 (mp)
REVERT: R  172 GLU cc_start: 0.8955 (pm20) cc_final: 0.8718 (pm20)
REVERT: R  277 CYS cc_start: 0.8169 (m) cc_final: 0.7885 (m)
REVERT: R  283 ASP cc_start: 0.9014 (m-30) cc_final: 0.8791 (t0)
REVERT: S  172 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8577 (mm-30)
REVERT: S  283 ASP cc_start: 0.9084 (m-30) cc_final: 0.8742 (m-30)
REVERT: T   41 MET cc_start: 0.9109 (mmt) cc_final: 0.8815 (mmm)
REVERT: T  164 HIS cc_start: 0.9159 (t-90) cc_final: 0.8608 (t-90)
REVERT: T  277 CYS cc_start: 0.8917 (m) cc_final: 0.8690 (m)
REVERT: U   19 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8688 (mtt90)
REVERT: U  164 HIS cc_start: 0.9094 (t-170) cc_final: 0.8699 (t-90)
REVERT: U  172 GLU cc_start: 0.8765 (pm20) cc_final: 0.8523 (pm20)
REVERT: V   12 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6712 (mm)
REVERT: V   30 HIS cc_start: 0.8373 (p90) cc_final: 0.8099 (p90)
REVERT: V  105 ASN cc_start: 0.8496 (p0) cc_final: 0.8272 (p0)
REVERT: V  172 GLU cc_start: 0.9097 (tp30) cc_final: 0.8890 (tp30)
REVERT: V  190 ASP cc_start: 0.9158 (m-30) cc_final: 0.8751 (m-30)
REVERT: V  198 MET cc_start: 0.8598 (mtm) cc_final: 0.8332 (mtm)
REVERT: V  251 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8612 (t80)
REVERT: V  281 LEU cc_start: 0.9017 (mt) cc_final: 0.8359 (tt)
  outliers start: 22
  outliers final: 15
  residues processed: 123
  average time/residue: 0.2158
  time to fit residues: 42.4331
Evaluate side-chains
  124 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 1.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   18 GLU
Chi-restraints excluded: chain R residue   30 HIS
Chi-restraints excluded: chain R residue   66 LEU
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  203 HIS
Chi-restraints excluded: chain R residue  214 PHE
Chi-restraints excluded: chain T residue   27 THR
Chi-restraints excluded: chain T residue  305 LEU
Chi-restraints excluded: chain T residue  332 THR
Chi-restraints excluded: chain U residue   19 ARG
Chi-restraints excluded: chain U residue   94 ILE
Chi-restraints excluded: chain U residue  128 TYR
Chi-restraints excluded: chain V residue   12 LEU
Chi-restraints excluded: chain V residue   26 TYR
Chi-restraints excluded: chain V residue  226 VAL
Chi-restraints excluded: chain V residue  251 PHE
Chi-restraints excluded: chain V residue  264 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9990
   chunk 151 optimal weight:    8.9990
   chunk 162 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 150 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 105 ASN
** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 328 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.062452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.046107 restraints weight = 64526.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 5.38
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.5173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14225  Z= 0.133
  Angle     :  0.578  10.043  19285  Z= 0.292
  Chirality :  0.041   0.281   2160
  Planarity :  0.004   0.043   2455
  Dihedral  :  8.746  86.932   2075
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  3.70 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 26.62 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.45 (0.22), residues: 1705
  helix:  1.88 (0.17), residues: 1010
  sheet: -0.47 (0.48), residues: 140
  loop : -0.31 (0.28), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP V 267 
 HIS   0.003   0.001   HIS S 254 
 PHE   0.019   0.001   PHE T 138 
 TYR   0.030   0.001   TYR S 109 
 ARG   0.003   0.000   ARG S 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03415 (  753)
  hydrogen bonds       : angle       3.82756 ( 2094)
  covalent geometry    : bond        0.00294 (14225)
  covalent geometry    : angle       0.57843 (19285)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 1.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   18 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8334 (mp0)
REVERT: R  117 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8916 (mp)
REVERT: R  277 CYS cc_start: 0.8236 (m) cc_final: 0.7979 (m)
REVERT: R  283 ASP cc_start: 0.9021 (m-30) cc_final: 0.8812 (t0)
REVERT: S  172 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8644 (mm-30)
REVERT: S  283 ASP cc_start: 0.9084 (m-30) cc_final: 0.8749 (m-30)
REVERT: T   41 MET cc_start: 0.9111 (mmt) cc_final: 0.8812 (mmm)
REVERT: T  164 HIS cc_start: 0.9157 (t-90) cc_final: 0.8544 (t-90)
REVERT: T  277 CYS cc_start: 0.9025 (m) cc_final: 0.8737 (m)
REVERT: U   19 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8675 (mtt90)
REVERT: U  164 HIS cc_start: 0.9060 (t-170) cc_final: 0.8676 (t-90)
REVERT: U  172 GLU cc_start: 0.8770 (pm20) cc_final: 0.8522 (pm20)
REVERT: V  190 ASP cc_start: 0.9201 (m-30) cc_final: 0.8752 (m-30)
REVERT: V  251 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8458 (t80)
  outliers start: 23
  outliers final: 14
  residues processed: 120
  average time/residue: 0.2447
  time to fit residues: 47.9569
Evaluate side-chains
  116 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 1.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   18 GLU
Chi-restraints excluded: chain R residue   66 LEU
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  203 HIS
Chi-restraints excluded: chain R residue  214 PHE
Chi-restraints excluded: chain T residue   27 THR
Chi-restraints excluded: chain T residue  305 LEU
Chi-restraints excluded: chain T residue  332 THR
Chi-restraints excluded: chain U residue   19 ARG
Chi-restraints excluded: chain U residue   94 ILE
Chi-restraints excluded: chain U residue  114 LEU
Chi-restraints excluded: chain U residue  128 TYR
Chi-restraints excluded: chain U residue  278 ILE
Chi-restraints excluded: chain V residue  226 VAL
Chi-restraints excluded: chain V residue  251 PHE
Chi-restraints excluded: chain V residue  264 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 149 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 78 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 135 optimal weight:    3.9990
   chunk 134 optimal weight:    9.9990
   chunk 145 optimal weight:    8.9990
   chunk 18 optimal weight:    0.6980
   chunk 10 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    2.8786

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

Flipped N/Q/H residues before XYZ refinement:
** R 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T 197 ASN
T 253 GLN
V 164 HIS
** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.060791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.044552 restraints weight = 65847.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 5.28
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.5383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  14225  Z= 0.204
  Angle     :  0.631  10.944  19285  Z= 0.323
  Chirality :  0.043   0.274   2160
  Planarity :  0.004   0.042   2455
  Dihedral  :  9.297  89.506   2075
  Min Nonbonded Distance : 1.822

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  3.93 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 26.89 %
    Favored  : 71.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.27 (0.22), residues: 1705
  helix:  1.73 (0.17), residues: 1010
  sheet: -0.53 (0.49), residues: 140
  loop : -0.37 (0.28), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP V 267 
 HIS   0.008   0.001   HIS V 175 
 PHE   0.022   0.002   PHE U 126 
 TYR   0.030   0.002   TYR S 109 
 ARG   0.004   0.000   ARG V 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03792 (  753)
  hydrogen bonds       : angle       3.99752 ( 2094)
  covalent geometry    : bond        0.00445 (14225)
  covalent geometry    : angle       0.63053 (19285)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7009.84 seconds
wall clock time: 124 minutes 17.97 seconds (7457.97 seconds total)