Starting phenix.real_space_refine
on Wed Mar  4 08:28:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k21_22639/03_2026/7k21_22639.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k21_22639/03_2026/7k21_22639.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k21_22639/03_2026/7k21_22639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k21_22639/03_2026/7k21_22639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k21_22639/03_2026/7k21_22639.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k21_22639/03_2026/7k21_22639.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      12      5.49       5
     Mg      4      5.21       5
     S      84      5.16       5
     C    7480      2.51       5
     N    1984      2.21       5
     O    2284      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11848
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 2909
          Classifications: {'peptide': 372}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 352}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 2909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 2909
          Classifications: {'peptide': 372}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 352}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 2909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 2909
          Classifications: {'peptide': 372}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 352}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 2909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 2909
          Classifications: {'peptide': 372}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 352}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 53
          Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1, 'PO4': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 53
          Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1, 'PO4': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 53
          Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1, 'PO4': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "D"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 53
          Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1, 'PO4': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 2.89, per 1000 atoms: 0.24
  Number of scatterers: 11848
  At special positions: 0
  Unit cell: (100.32, 76.285, 164.065, 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      84     16.00
     P      12     15.00
     Mg      4     11.99
     O    2284      8.00
     N    1984      7.00
     C    7480      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 543.8 milliseconds
  

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2752

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 24 sheets defined
      43.8% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 61
    Processing helix  chain 'A' and resid 78 through 93
      removed outlier: 3.530A  pdb=" N   GLU A  83 " --> pdb=" O   TRP A  79 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LYS A  84 " --> pdb=" O   ASP A  80 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   TYR A  91 " --> pdb=" O   HIS A  87 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLU A  93 " --> pdb=" O   THR A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 126
      removed outlier: 3.843A  pdb=" N   ARG A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 145
      removed outlier: 3.522A  pdb=" N   SER A 145 " --> pdb=" O   SER A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 175
      removed outlier: 3.793A  pdb=" N   ILE A 175 " --> pdb=" O   PRO A 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 172 through 175'
    Processing helix  chain 'A' and resid 181 through 193
    Processing helix  chain 'A' and resid 194 through 197
    Processing helix  chain 'A' and resid 205 through 217
      removed outlier: 3.684A  pdb=" N   LYS A 215 " --> pdb=" O   ASP A 211 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   CYS A 217 " --> pdb=" O   LYS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 230
      removed outlier: 3.552A  pdb=" N   ALA A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 257
      removed outlier: 4.151A  pdb=" N   CYS A 257 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 262
    Processing helix  chain 'A' and resid 263 through 267
      removed outlier: 3.543A  pdb=" N   PHE A 266 " --> pdb=" O   GLN A 263 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE A 267 " --> pdb=" O   PRO A 264 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 263 through 267'
    Processing helix  chain 'A' and resid 273 through 284
    Processing helix  chain 'A' and resid 289 through 294
    Processing helix  chain 'A' and resid 302 through 306
      removed outlier: 3.906A  pdb=" N   TYR A 306 " --> pdb=" O   THR A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 318
    Processing helix  chain 'A' and resid 337 through 348
    Processing helix  chain 'A' and resid 359 through 366
      removed outlier: 4.230A  pdb=" N   GLU A 364 " --> pdb=" O   GLN A 360 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ALA A 365 " --> pdb=" O   GLU A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 370
      removed outlier: 3.547A  pdb=" N   VAL A 370 " --> pdb=" O   PRO A 367 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 367 through 370'
    Processing helix  chain 'B' and resid 55 through 61
    Processing helix  chain 'B' and resid 78 through 93
      removed outlier: 3.542A  pdb=" N   GLU B  83 " --> pdb=" O   TRP B  79 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LYS B  84 " --> pdb=" O   ASP B  80 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE B  85 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TYR B  91 " --> pdb=" O   HIS B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 126
      removed outlier: 3.849A  pdb=" N   ARG B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 145
    Processing helix  chain 'B' and resid 172 through 175
      removed outlier: 3.791A  pdb=" N   ILE B 175 " --> pdb=" O   PRO B 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 172 through 175'
    Processing helix  chain 'B' and resid 181 through 193
    Processing helix  chain 'B' and resid 194 through 197
    Processing helix  chain 'B' and resid 205 through 217
      removed outlier: 3.693A  pdb=" N   LYS B 215 " --> pdb=" O   ASP B 211 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   CYS B 217 " --> pdb=" O   LYS B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 230
    Processing helix  chain 'B' and resid 252 through 257
      removed outlier: 4.095A  pdb=" N   CYS B 257 " --> pdb=" O   GLU B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 262
    Processing helix  chain 'B' and resid 263 through 268
      removed outlier: 3.569A  pdb=" N   ILE B 267 " --> pdb=" O   PRO B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 283
    Processing helix  chain 'B' and resid 286 through 288
      No H-bonds generated for 'chain 'B' and resid 286 through 288'
    Processing helix  chain 'B' and resid 289 through 294
    Processing helix  chain 'B' and resid 302 through 306
      removed outlier: 3.946A  pdb=" N   TYR B 306 " --> pdb=" O   THR B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 318
    Processing helix  chain 'B' and resid 337 through 348
    Processing helix  chain 'B' and resid 359 through 366
      removed outlier: 4.160A  pdb=" N   GLU B 364 " --> pdb=" O   GLN B 360 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ALA B 365 " --> pdb=" O   GLU B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 370
      removed outlier: 3.592A  pdb=" N   VAL B 370 " --> pdb=" O   PRO B 367 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 367 through 370'
    Processing helix  chain 'C' and resid 55 through 61
    Processing helix  chain 'C' and resid 78 through 93
      removed outlier: 3.540A  pdb=" N   GLU C  83 " --> pdb=" O   TRP C  79 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LYS C  84 " --> pdb=" O   ASP C  80 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   TYR C  91 " --> pdb=" O   HIS C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 126
      removed outlier: 3.864A  pdb=" N   ARG C 116 " --> pdb=" O   PRO C 112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 145
    Processing helix  chain 'C' and resid 172 through 175
      removed outlier: 3.849A  pdb=" N   ILE C 175 " --> pdb=" O   PRO C 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 172 through 175'
    Processing helix  chain 'C' and resid 181 through 193
    Processing helix  chain 'C' and resid 194 through 197
    Processing helix  chain 'C' and resid 205 through 217
      removed outlier: 3.631A  pdb=" N   LYS C 215 " --> pdb=" O   ASP C 211 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   CYS C 217 " --> pdb=" O   LYS C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 230
    Processing helix  chain 'C' and resid 252 through 257
      removed outlier: 4.119A  pdb=" N   CYS C 257 " --> pdb=" O   GLU C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 258 through 262
    Processing helix  chain 'C' and resid 263 through 268
      removed outlier: 3.615A  pdb=" N   ILE C 267 " --> pdb=" O   PRO C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 283
    Processing helix  chain 'C' and resid 289 through 294
    Processing helix  chain 'C' and resid 302 through 306
      removed outlier: 3.975A  pdb=" N   TYR C 306 " --> pdb=" O   THR C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 318
    Processing helix  chain 'C' and resid 337 through 347
    Processing helix  chain 'C' and resid 359 through 366
      removed outlier: 4.248A  pdb=" N   GLU C 364 " --> pdb=" O   GLN C 360 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA C 365 " --> pdb=" O   GLU C 361 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 367 through 370
      removed outlier: 3.540A  pdb=" N   VAL C 370 " --> pdb=" O   PRO C 367 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 367 through 370'
    Processing helix  chain 'D' and resid 55 through 61
    Processing helix  chain 'D' and resid 78 through 92
      removed outlier: 3.514A  pdb=" N   GLU D  83 " --> pdb=" O   TRP D  79 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   LYS D  84 " --> pdb=" O   ASP D  80 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   TYR D  91 " --> pdb=" O   HIS D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 112 through 126
      removed outlier: 3.865A  pdb=" N   ARG D 116 " --> pdb=" O   PRO D 112 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 145
      removed outlier: 3.553A  pdb=" N   SER D 145 " --> pdb=" O   SER D 141 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 181 through 193
    Processing helix  chain 'D' and resid 194 through 197
    Processing helix  chain 'D' and resid 205 through 217
      removed outlier: 3.652A  pdb=" N   LYS D 215 " --> pdb=" O   ASP D 211 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   CYS D 217 " --> pdb=" O   LYS D 213 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 230
    Processing helix  chain 'D' and resid 252 through 257
      removed outlier: 4.121A  pdb=" N   CYS D 257 " --> pdb=" O   GLU D 253 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 258 through 262
    Processing helix  chain 'D' and resid 263 through 267
      removed outlier: 3.597A  pdb=" N   ILE D 267 " --> pdb=" O   PRO D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 273 through 283
    Processing helix  chain 'D' and resid 289 through 294
    Processing helix  chain 'D' and resid 302 through 306
      removed outlier: 3.890A  pdb=" N   TYR D 306 " --> pdb=" O   THR D 303 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 308 through 318
    Processing helix  chain 'D' and resid 337 through 348
      removed outlier: 3.531A  pdb=" N   SER D 348 " --> pdb=" O   SER D 344 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 359 through 366
      removed outlier: 4.117A  pdb=" N   GLU D 364 " --> pdb=" O   GLN D 360 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ALA D 365 " --> pdb=" O   GLU D 361 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 367 through 370
      removed outlier: 3.526A  pdb=" N   VAL D 370 " --> pdb=" O   PRO D 367 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 367 through 370'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32
      removed outlier: 3.838A  pdb=" N   THR A 106 " --> pdb=" O   CYS A  10 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   ASN A  12 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   THR A 103 " --> pdb=" O   TYR A 133 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   ALA A 135 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   LEU A 105 " --> pdb=" O   ALA A 135 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54
      removed outlier: 3.733A  pdb=" N   LYS A  68 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ARG A  37 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72
    Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170
    Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170
      removed outlier: 3.532A  pdb=" N   SER A 155 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   ASN A 297 " --> pdb=" O   ILE A 330 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241
    Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32
      removed outlier: 3.875A  pdb=" N   THR B 106 " --> pdb=" O   CYS B  10 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   ASN B  12 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   THR B 103 " --> pdb=" O   TYR B 133 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   ALA B 135 " --> pdb=" O   THR B 103 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   LEU B 105 " --> pdb=" O   ALA B 135 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54
      removed outlier: 3.565A  pdb=" N   ARG B  37 " --> pdb=" O   THR B  66 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72
    Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170
    Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170
      removed outlier: 3.567A  pdb=" N   SER B 155 " --> pdb=" O   SER B 300 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   ASN B 297 " --> pdb=" O   ILE B 330 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241
    Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32
      removed outlier: 3.845A  pdb=" N   THR C 106 " --> pdb=" O   CYS C  10 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   ASN C  12 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   THR C 103 " --> pdb=" O   TYR C 133 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   ALA C 135 " --> pdb=" O   THR C 103 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   LEU C 105 " --> pdb=" O   ALA C 135 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54
      removed outlier: 3.626A  pdb=" N   LYS C  68 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG C  37 " --> pdb=" O   THR C  66 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170
    Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170
      removed outlier: 3.567A  pdb=" N   SER C 155 " --> pdb=" O   SER C 300 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   ASN C 297 " --> pdb=" O   ILE C 330 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241
    Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32
      removed outlier: 3.824A  pdb=" N   THR D 106 " --> pdb=" O   CYS D  10 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   ASN D  12 " --> pdb=" O   THR D 106 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   THR D 103 " --> pdb=" O   TYR D 133 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   ALA D 135 " --> pdb=" O   THR D 103 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   LEU D 105 " --> pdb=" O   ALA D 135 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54
      removed outlier: 3.538A  pdb=" N   LYS D  68 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG D  37 " --> pdb=" O   THR D  66 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72
    Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170
    Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170
      removed outlier: 3.637A  pdb=" N   SER D 155 " --> pdb=" O   SER D 300 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   ASN D 297 " --> pdb=" O   ILE D 330 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241

    467 hydrogen bonds defined for protein.
    1206 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.15

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3637
        1.33 -     1.45: 1782
        1.45 -     1.57: 6533
        1.57 -     1.69: 12
        1.69 -     1.80: 148
  Bond restraints: 12112
  Sorted by residual:
  bond pdb=" O4  PO4 A 803 "
       pdb=" P   PO4 A 803 "
    ideal  model  delta    sigma   weight residual
    1.568  1.500  0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" O4  PO4 B 803 "
       pdb=" P   PO4 B 803 "
    ideal  model  delta    sigma   weight residual
    1.568  1.500  0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" O4  PO4 D 803 "
       pdb=" P   PO4 D 803 "
    ideal  model  delta    sigma   weight residual
    1.568  1.501  0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" O4  PO4 C 803 "
       pdb=" P   PO4 C 803 "
    ideal  model  delta    sigma   weight residual
    1.568  1.501  0.067 2.00e-02 2.50e+03 1.12e+01
  bond pdb=" O3  PO4 B 803 "
       pdb=" P   PO4 B 803 "
    ideal  model  delta    sigma   weight residual
    1.569  1.502  0.067 2.00e-02 2.50e+03 1.11e+01
  ... (remaining 12107 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 15953
        2.15 -     4.31: 409
        4.31 -     6.46: 66
        6.46 -     8.61: 20
        8.61 -    10.77: 4
  Bond angle restraints: 16452
  Sorted by residual:
  angle pdb=" N   HIC B  73 "
        pdb=" CA  HIC B  73 "
        pdb=" CB  HIC B  73 "
      ideal   model   delta    sigma   weight residual
     110.50  116.68   -6.18 1.70e+00 3.46e-01 1.32e+01
  angle pdb=" C19 1T4 B 804 "
        pdb=" C17 1T4 B 804 "
        pdb=" N1  1T4 B 804 "
      ideal   model   delta    sigma   weight residual
     114.67  125.44  -10.77 3.00e+00 1.11e-01 1.29e+01
  angle pdb=" N   HIC C  73 "
        pdb=" CA  HIC C  73 "
        pdb=" CB  HIC C  73 "
      ideal   model   delta    sigma   weight residual
     110.50  116.51   -6.01 1.70e+00 3.46e-01 1.25e+01
  angle pdb=" C19 1T4 D 804 "
        pdb=" C17 1T4 D 804 "
        pdb=" N1  1T4 D 804 "
      ideal   model   delta    sigma   weight residual
     114.67  125.18  -10.51 3.00e+00 1.11e-01 1.23e+01
  angle pdb=" C19 1T4 C 804 "
        pdb=" C17 1T4 C 804 "
        pdb=" N1  1T4 C 804 "
      ideal   model   delta    sigma   weight residual
     114.67  125.01  -10.34 3.00e+00 1.11e-01 1.19e+01
  ... (remaining 16447 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.95: 6992
       20.95 -    41.89: 205
       41.89 -    62.84: 9
       62.84 -    83.78: 10
       83.78 -   104.73: 4
  Dihedral angle restraints: 7220
    sinusoidal: 2920
      harmonic: 4300
  Sorted by residual:
  dihedral pdb=" O1B ADP A 802 "
           pdb=" O3A ADP A 802 "
           pdb=" PB  ADP A 802 "
           pdb=" PA  ADP A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -164.73  104.73     1      2.00e+01 2.50e-03 3.01e+01
  dihedral pdb=" O1B ADP D 802 "
           pdb=" O3A ADP D 802 "
           pdb=" PB  ADP D 802 "
           pdb=" PA  ADP D 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -159.76   99.76     1      2.00e+01 2.50e-03 2.81e+01
  dihedral pdb=" O1B ADP C 802 "
           pdb=" O3A ADP C 802 "
           pdb=" PB  ADP C 802 "
           pdb=" PA  ADP C 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -157.82   97.82     1      2.00e+01 2.50e-03 2.73e+01
  ... (remaining 7217 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1288
       0.057 -    0.115: 451
       0.115 -    0.172: 56
       0.172 -    0.229: 5
       0.229 -    0.287: 8
  Chirality restraints: 1808
  Sorted by residual:
  chirality pdb=" CB  ILE C 151 "
            pdb=" CA  ILE C 151 "
            pdb=" CG1 ILE C 151 "
            pdb=" CG2 ILE C 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" CB  ILE D 151 "
            pdb=" CA  ILE D 151 "
            pdb=" CG1 ILE D 151 "
            pdb=" CG2 ILE D 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CB  ILE A 151 "
            pdb=" CA  ILE A 151 "
            pdb=" CG1 ILE A 151 "
            pdb=" CG2 ILE A 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.75e+00
  ... (remaining 1805 not shown)

  Planarity restraints: 2092
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 163 "    0.035 5.00e-02 4.00e+02   5.31e-02 4.50e+00
        pdb=" N   PRO A 164 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 164 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 164 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 340 "   -0.019 2.00e-02 2.50e+03   1.34e-02 4.48e+00
        pdb=" CG  TRP D 340 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 340 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 340 "    0.008 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 340 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 340 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 340 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 340 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 340 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 340 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 340 "   -0.019 2.00e-02 2.50e+03   1.31e-02 4.29e+00
        pdb=" CG  TRP A 340 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 340 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 340 "    0.008 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 340 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 340 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 340 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 340 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 340 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 340 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 2089 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 160
        2.63 -     3.20: 9964
        3.20 -     3.77: 18163
        3.77 -     4.33: 27392
        4.33 -     4.90: 43761
  Nonbonded interactions: 99440
  Sorted by model distance:
  nonbonded pdb="MG    MG B 801 "
            pdb=" O1B ADP B 802 "
     model   vdw
     2.066 2.170
  nonbonded pdb="MG    MG D 801 "
            pdb=" O1B ADP D 802 "
     model   vdw
     2.070 2.170
  nonbonded pdb="MG    MG C 801 "
            pdb=" O1B ADP C 802 "
     model   vdw
     2.075 2.170
  nonbonded pdb="MG    MG A 801 "
            pdb=" O1B ADP A 802 "
     model   vdw
     2.076 2.170
  nonbonded pdb=" OG1 THR A 202 "
            pdb=" OE1 GLU A 205 "
     model   vdw
     2.223 3.040
  ... (remaining 99435 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             2.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     12.160
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  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:7.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
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      :  0.008   0.231  12116  Z= 0.499
  Angle     :  0.866  10.768  16452  Z= 0.436
  Chirality :  0.057   0.287   1808
  Planarity :  0.007   0.053   2092
  Dihedral  : 10.390 104.727   4468
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.23 (0.17), residues: 1468
  helix: -4.24 (0.09), residues: 592
  sheet: -1.26 (0.41), residues: 136
  loop : -1.73 (0.19), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG D  39 
 TYR   0.030   0.003   TYR C  69 
 PHE   0.021   0.003   PHE A 124 
 TRP   0.034   0.004   TRP D 340 
 HIS   0.011   0.003   HIS C  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00743 (12112)
  covalent geometry    : angle       0.86564 (16452)
  hydrogen bonds       : bond        0.28042 (  457)
  hydrogen bonds       : angle       9.87074 ( 1206)
  Misc. bond           : bond        0.21086 (    4)

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

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

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  299 MET cc_start: 0.8549 (mtm) cc_final: 0.8223 (mtm)
  outliers start: 0
  outliers final: 1
  residues processed: 125
  average time/residue: 0.6390
  time to fit residues: 86.0949
Evaluate side-chains
  89 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  40 HIS
A  87 HIS
A  88 HIS
A 161 HIS
B  40 HIS
B  88 HIS
B 161 HIS
C  88 HIS
C 161 HIS
C 296 ASN
D  88 HIS
** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.078659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.064787 restraints weight = 23416.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 2.38
r_work: 0.2780 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2622 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12116  Z= 0.157
  Angle     :  0.610   6.701  16452  Z= 0.303
  Chirality :  0.046   0.146   1808
  Planarity :  0.005   0.049   2092
  Dihedral  :  8.656  86.698   1674
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  6.45 %
    Favored  : 92.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.06 (0.20), residues: 1468
  helix: -2.21 (0.17), residues: 568
  sheet: -1.06 (0.31), residues: 248
  loop : -0.41 (0.25), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  39 
 TYR   0.008   0.001   TYR A  69 
 PHE   0.011   0.002   PHE D 262 
 TRP   0.017   0.002   TRP D 340 
 HIS   0.004   0.001   HIS D  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (12112)
  covalent geometry    : angle       0.60990 (16452)
  hydrogen bonds       : bond        0.04095 (  457)
  hydrogen bonds       : angle       5.44583 ( 1206)
  Misc. bond           : bond        0.00063 (    4)

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

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

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A   12 ASN cc_start: 0.8684 (p0) cc_final: 0.8468 (p0)
REVERT: B  299 MET cc_start: 0.9166 (mtm) cc_final: 0.8888 (mtm)
REVERT: C  325 MET cc_start: 0.8010 (ptp) cc_final: 0.7767 (ptm)
REVERT: D  184 ASP cc_start: 0.9017 (m-30) cc_final: 0.8815 (m-30)
REVERT: D  205 GLU cc_start: 0.8866 (mp0) cc_final: 0.8540 (mt-10)
  outliers start: 9
  outliers final: 0
  residues processed: 100
  average time/residue: 0.5715
  time to fit residues: 62.2384
Evaluate side-chains
  86 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 108 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 134 optimal weight:    3.9990
   chunk 142 optimal weight:    3.9990
   chunk 140 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
B  59 GLN
C 353 GLN
D 353 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.077013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.063160 restraints weight = 23645.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 2.38
r_work: 0.2741 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2581 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8740
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  12116  Z= 0.202
  Angle     :  0.601   6.555  16452  Z= 0.294
  Chirality :  0.047   0.156   1808
  Planarity :  0.004   0.045   2092
  Dihedral  :  8.009  82.424   1672
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  7.32 %
    Favored  : 91.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.85 (0.22), residues: 1468
  helix: -0.71 (0.21), residues: 556
  sheet: -1.03 (0.30), residues: 268
  loop :  0.06 (0.26), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  39 
 TYR   0.014   0.001   TYR D  69 
 PHE   0.011   0.001   PHE D 262 
 TRP   0.014   0.002   TRP C 340 
 HIS   0.005   0.001   HIS C  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (12112)
  covalent geometry    : angle       0.60053 (16452)
  hydrogen bonds       : bond        0.03644 (  457)
  hydrogen bonds       : angle       4.82660 ( 1206)
  Misc. bond           : bond        0.00023 (    4)

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

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

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A   12 ASN cc_start: 0.8725 (p0) cc_final: 0.8517 (p0)
REVERT: B  205 GLU cc_start: 0.8796 (mp0) cc_final: 0.8506 (mp0)
REVERT: B  299 MET cc_start: 0.9267 (mtm) cc_final: 0.9041 (mtm)
REVERT: D  184 ASP cc_start: 0.8993 (m-30) cc_final: 0.8769 (m-30)
REVERT: D  205 GLU cc_start: 0.8848 (mp0) cc_final: 0.8505 (mt-10)
  outliers start: 11
  outliers final: 2
  residues processed: 96
  average time/residue: 0.5293
  time to fit residues: 55.5617
Evaluate side-chains
  89 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain C residue   34 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 119 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 101 optimal weight:    0.6980
   chunk 132 optimal weight:    2.9990
   chunk 147 optimal weight:    0.2980
   chunk 71 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
D  12 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.078112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.064362 restraints weight = 23314.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 2.36
r_work: 0.2767 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2609 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  12116  Z= 0.128
  Angle     :  0.550   6.629  16452  Z= 0.263
  Chirality :  0.045   0.142   1808
  Planarity :  0.004   0.043   2092
  Dihedral  :  7.698  85.293   1672
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  7.80 %
    Favored  : 90.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.23), residues: 1468
  helix: -0.12 (0.23), residues: 560
  sheet: -0.80 (0.31), residues: 268
  loop :  0.34 (0.26), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  39 
 TYR   0.007   0.001   TYR A  69 
 PHE   0.007   0.001   PHE C  31 
 TRP   0.011   0.001   TRP D 340 
 HIS   0.003   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (12112)
  covalent geometry    : angle       0.55030 (16452)
  hydrogen bonds       : bond        0.03060 (  457)
  hydrogen bonds       : angle       4.56909 ( 1206)
  Misc. bond           : bond        0.00017 (    4)

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

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

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.483 
Fit side-chains
REVERT: A  205 GLU cc_start: 0.8649 (mp0) cc_final: 0.8066 (mp0)
REVERT: B  205 GLU cc_start: 0.8801 (mp0) cc_final: 0.8264 (mt-10)
REVERT: D  184 ASP cc_start: 0.8972 (m-30) cc_final: 0.8753 (m-30)
REVERT: D  205 GLU cc_start: 0.8845 (mp0) cc_final: 0.8404 (mt-10)
  outliers start: 16
  outliers final: 2
  residues processed: 98
  average time/residue: 0.5952
  time to fit residues: 63.4033
Evaluate side-chains
  88 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 MET
Chi-restraints excluded: chain A residue  201 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 131 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 110 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 112 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
C  12 ASN
C  59 GLN
D  12 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.077782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.063908 restraints weight = 23417.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 2.37
r_work: 0.2759 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2599 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12116  Z= 0.146
  Angle     :  0.557   6.866  16452  Z= 0.265
  Chirality :  0.046   0.148   1808
  Planarity :  0.003   0.043   2092
  Dihedral  :  7.625  85.801   1672
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  8.84 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.23), residues: 1468
  helix:  0.18 (0.23), residues: 560
  sheet: -0.61 (0.32), residues: 268
  loop :  0.48 (0.27), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  39 
 TYR   0.009   0.001   TYR A  69 
 PHE   0.007   0.001   PHE C  31 
 TRP   0.010   0.001   TRP D 340 
 HIS   0.004   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (12112)
  covalent geometry    : angle       0.55651 (16452)
  hydrogen bonds       : bond        0.02999 (  457)
  hydrogen bonds       : angle       4.42242 ( 1206)
  Misc. bond           : bond        0.00015 (    4)

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

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

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A  205 GLU cc_start: 0.8634 (mp0) cc_final: 0.7922 (mp0)
REVERT: B  205 GLU cc_start: 0.8799 (mp0) cc_final: 0.8521 (mp0)
REVERT: D  184 ASP cc_start: 0.8985 (m-30) cc_final: 0.8773 (m-30)
REVERT: D  205 GLU cc_start: 0.8870 (mp0) cc_final: 0.8436 (mt-10)
  outliers start: 12
  outliers final: 3
  residues processed: 92
  average time/residue: 0.5994
  time to fit residues: 59.9627
Evaluate side-chains
  94 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  355 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   chunk 147 optimal weight:    0.0000
   chunk 141 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
A  12 ASN
C  12 ASN
D  12 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.078537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.064853 restraints weight = 23299.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 2.32
r_work: 0.2779 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2621 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12116  Z= 0.118
  Angle     :  0.539   6.975  16452  Z= 0.255
  Chirality :  0.045   0.140   1808
  Planarity :  0.003   0.042   2092
  Dihedral  :  7.466  87.453   1672
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  9.16 %
    Favored  : 89.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.23), residues: 1468
  helix:  0.40 (0.23), residues: 560
  sheet: -0.43 (0.32), residues: 268
  loop :  0.61 (0.27), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 312 
 TYR   0.009   0.001   TYR A  69 
 PHE   0.007   0.001   PHE C  31 
 TRP   0.009   0.001   TRP D 340 
 HIS   0.003   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (12112)
  covalent geometry    : angle       0.53877 (16452)
  hydrogen bonds       : bond        0.02826 (  457)
  hydrogen bonds       : angle       4.31955 ( 1206)
  Misc. bond           : bond        0.00012 (    4)

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

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

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A  205 GLU cc_start: 0.8581 (mp0) cc_final: 0.7942 (mp0)
REVERT: B  205 GLU cc_start: 0.8783 (mp0) cc_final: 0.8287 (mt-10)
REVERT: C   41 GLN cc_start: 0.8868 (mm110) cc_final: 0.8146 (mm-40)
REVERT: D  184 ASP cc_start: 0.8936 (m-30) cc_final: 0.8732 (m-30)
  outliers start: 15
  outliers final: 3
  residues processed: 101
  average time/residue: 0.6203
  time to fit residues: 67.9038
Evaluate side-chains
  93 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain C residue  305 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 142 optimal weight:    0.3980
   chunk 132 optimal weight:    3.9990
   chunk 106 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 118 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 136 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C  12 ASN
C  49 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.078285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.064460 restraints weight = 23358.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 2.36
r_work: 0.2771 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2611 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12116  Z= 0.128
  Angle     :  0.551   6.504  16452  Z= 0.262
  Chirality :  0.045   0.141   1808
  Planarity :  0.003   0.040   2092
  Dihedral  :  7.406  87.178   1672
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  9.87 %
    Favored  : 88.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.23), residues: 1468
  helix:  0.53 (0.23), residues: 560
  sheet: -0.31 (0.32), residues: 268
  loop :  0.69 (0.27), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 183 
 TYR   0.009   0.001   TYR A  69 
 PHE   0.007   0.001   PHE C  31 
 TRP   0.009   0.001   TRP D 340 
 HIS   0.003   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (12112)
  covalent geometry    : angle       0.55089 (16452)
  hydrogen bonds       : bond        0.02791 (  457)
  hydrogen bonds       : angle       4.25052 ( 1206)
  Misc. bond           : bond        0.00013 (    4)

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

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

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   12 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8494 (p0)
REVERT: A  205 GLU cc_start: 0.8610 (mp0) cc_final: 0.7917 (mp0)
REVERT: B  205 GLU cc_start: 0.8873 (mp0) cc_final: 0.8387 (mp0)
REVERT: C   41 GLN cc_start: 0.8889 (mm110) cc_final: 0.8144 (mm-40)
REVERT: C  360 GLN cc_start: 0.8616 (pm20) cc_final: 0.8408 (pm20)
REVERT: D  184 ASP cc_start: 0.8952 (m-30) cc_final: 0.8741 (m-30)
  outliers start: 16
  outliers final: 4
  residues processed: 98
  average time/residue: 0.6088
  time to fit residues: 64.7917
Evaluate side-chains
  94 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain C residue  305 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 147 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
C  12 ASN
C  49 GLN
D  59 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.076146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.062374 restraints weight = 23611.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 2.32
r_work: 0.2724 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2565 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072  12116  Z= 0.232
  Angle     :  0.601   6.512  16452  Z= 0.290
  Chirality :  0.048   0.153   1808
  Planarity :  0.004   0.041   2092
  Dihedral  :  7.662  83.282   1672
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 10.43 %
    Favored  : 88.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.23), residues: 1468
  helix:  0.41 (0.23), residues: 560
  sheet: -0.39 (0.32), residues: 268
  loop :  0.69 (0.27), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  39 
 TYR   0.012   0.001   TYR A 306 
 PHE   0.008   0.001   PHE A 127 
 TRP   0.011   0.002   TRP B  79 
 HIS   0.005   0.001   HIS C  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 (12112)
  covalent geometry    : angle       0.60117 (16452)
  hydrogen bonds       : bond        0.03148 (  457)
  hydrogen bonds       : angle       4.34086 ( 1206)
  Misc. bond           : bond        0.00026 (    4)

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

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

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8590 (p0)
REVERT: B  205 GLU cc_start: 0.8795 (mp0) cc_final: 0.8322 (mt-10)
REVERT: C   41 GLN cc_start: 0.8886 (mm110) cc_final: 0.8168 (mm-40)
REVERT: D  184 ASP cc_start: 0.8911 (m-30) cc_final: 0.8708 (m-30)
  outliers start: 13
  outliers final: 5
  residues processed: 94
  average time/residue: 0.6842
  time to fit residues: 69.3046
Evaluate side-chains
  93 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue  132 MET
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain C residue  305 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 136 optimal weight:    0.5980
   chunk 104 optimal weight:    0.7980
   chunk 140 optimal weight:    2.9990
   chunk 121 optimal weight:    0.0770
   chunk 10 optimal weight:    0.3980
   chunk 7 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 129 optimal weight:    0.5980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
C  12 ASN
C  49 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.077988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.064630 restraints weight = 23165.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 2.28
r_work: 0.2780 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2622 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12116  Z= 0.109
  Angle     :  0.554   6.894  16452  Z= 0.264
  Chirality :  0.045   0.141   1808
  Planarity :  0.003   0.041   2092
  Dihedral  :  7.404  85.391   1672
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 10.91 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.23), residues: 1468
  helix:  0.64 (0.24), residues: 560
  sheet: -0.31 (0.32), residues: 268
  loop :  0.81 (0.27), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 183 
 TYR   0.009   0.001   TYR D  69 
 PHE   0.007   0.001   PHE C  31 
 TRP   0.009   0.001   TRP D 340 
 HIS   0.003   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (12112)
  covalent geometry    : angle       0.55438 (16452)
  hydrogen bonds       : bond        0.02705 (  457)
  hydrogen bonds       : angle       4.24933 ( 1206)
  Misc. bond           : bond        0.00015 (    4)

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

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

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8563 (p0)
REVERT: B  205 GLU cc_start: 0.8760 (mp0) cc_final: 0.8310 (mt-10)
REVERT: B  305 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8859 (mtp)
REVERT: C   41 GLN cc_start: 0.8887 (mm110) cc_final: 0.8156 (mm-40)
REVERT: D  184 ASP cc_start: 0.8898 (m-30) cc_final: 0.8694 (m-30)
  outliers start: 11
  outliers final: 4
  residues processed: 99
  average time/residue: 0.6023
  time to fit residues: 64.6481
Evaluate side-chains
  97 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain B residue  305 MET
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain C residue  305 MET
Chi-restraints excluded: chain D residue   34 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9990
   chunk 129 optimal weight:    1.9990
   chunk 117 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 47 optimal weight:    0.4980
   chunk 132 optimal weight:    2.9990
   chunk 130 optimal weight:    0.0370
   chunk 120 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 99 optimal weight:    0.6980
   overall best weight:    0.5860

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.078295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.064616 restraints weight = 23496.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 2.32
r_work: 0.2775 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2616 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12116  Z= 0.116
  Angle     :  0.553   7.119  16452  Z= 0.262
  Chirality :  0.045   0.163   1808
  Planarity :  0.003   0.040   2092
  Dihedral  :  7.268  86.332   1672
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 11.46 %
    Favored  : 87.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.23), residues: 1468
  helix:  0.69 (0.24), residues: 560
  sheet: -0.24 (0.32), residues: 268
  loop :  0.85 (0.27), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 183 
 TYR   0.009   0.001   TYR A  69 
 PHE   0.007   0.001   PHE C  31 
 TRP   0.009   0.001   TRP D 340 
 HIS   0.003   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (12112)
  covalent geometry    : angle       0.55327 (16452)
  hydrogen bonds       : bond        0.02681 (  457)
  hydrogen bonds       : angle       4.19708 ( 1206)
  Misc. bond           : bond        0.00013 (    4)

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

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

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2936 Ramachandran restraints generated.
    1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8562 (p0)
REVERT: B  205 GLU cc_start: 0.8775 (mp0) cc_final: 0.8328 (mp0)
REVERT: B  305 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8858 (mtp)
REVERT: C   41 GLN cc_start: 0.8888 (mm110) cc_final: 0.8157 (mm-40)
REVERT: D  184 ASP cc_start: 0.8914 (m-30) cc_final: 0.8712 (m-30)
  outliers start: 7
  outliers final: 5
  residues processed: 96
  average time/residue: 0.6280
  time to fit residues: 65.3492
Evaluate side-chains
  97 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  257 CYS
Chi-restraints excluded: chain B residue  305 MET
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain C residue  305 MET
Chi-restraints excluded: chain D residue   34 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 111 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 136 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0980
   chunk 5 optimal weight:    3.9990
   chunk 146 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 104 optimal weight:    0.7980
   overall best weight:    0.7182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.078131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.064429 restraints weight = 23408.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 2.32
r_work: 0.2773 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2613 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8738
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12116  Z= 0.129
  Angle     :  0.557   6.781  16452  Z= 0.265
  Chirality :  0.045   0.138   1808
  Planarity :  0.003   0.040   2092
  Dihedral  :  7.264  86.810   1672
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 11.39 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.23), residues: 1468
  helix:  0.68 (0.23), residues: 560
  sheet: -0.25 (0.32), residues: 268
  loop :  0.86 (0.27), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 183 
 TYR   0.009   0.001   TYR A  69 
 PHE   0.007   0.001   PHE C  31 
 TRP   0.009   0.001   TRP D 340 
 HIS   0.003   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (12112)
  covalent geometry    : angle       0.55723 (16452)
  hydrogen bonds       : bond        0.02710 (  457)
  hydrogen bonds       : angle       4.19824 ( 1206)
  Misc. bond           : bond        0.00012 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3134.07 seconds
wall clock time: 54 minutes 21.05 seconds (3261.05 seconds total)