Starting phenix.real_space_refine
on Wed Feb  4 20:25:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tul_41624/02_2026/8tul_41624.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tul_41624/02_2026/8tul_41624.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tul_41624/02_2026/8tul_41624.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tul_41624/02_2026/8tul_41624.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tul_41624/02_2026/8tul_41624.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tul_41624/02_2026/8tul_41624.map"
  }
  resolution = 2.8
  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=   0.005 sd=   0.268
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Mg     14      5.21       5
     S      65      5.16       5
     C    8195      2.51       5
     N    2150      2.21       5
     O    2646      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13070
  Number of models: 1
  Model: ""
    Number of chains: 15
    Chain: "A"
      Number of atoms: 2555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2555
          Classifications: {'peptide': 317}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 7, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 2555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2555
          Classifications: {'peptide': 317}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 7, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "C"
      Number of atoms: 2555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2555
          Classifications: {'peptide': 317}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 7, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "D"
      Number of atoms: 2555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2555
          Classifications: {'peptide': 317}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 7, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "E"
      Number of atoms: 2555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2555
          Classifications: {'peptide': 317}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 7, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' MG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 57
          Classifications: {'water': 57}
          Link IDs: {None: 56}
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 56
          Classifications: {'water': 56}
          Link IDs: {None: 55}
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 56
          Classifications: {'water': 56}
          Link IDs: {None: 55}
    Chain: "D"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 56
          Classifications: {'water': 56}
          Link IDs: {None: 55}
    Chain: "E"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 56
          Classifications: {'water': 56}
          Link IDs: {None: 55}
  Time building chain proxies: 3.66, per 1000 atoms: 0.28
  Number of scatterers: 13070
  At special positions: 0
  Unit cell: (106.24, 107.07, 140.27, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      65     16.00
     Mg     14     11.99
     O    2646      8.00
     N    2150      7.00
     C    8195      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: 1.05
  Conformation dependent library (CDL) restraints added in 615.2 milliseconds
  

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3020

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 5 sheets defined
      68.1% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 103 through 112
      removed outlier: 3.675A  pdb=" N   GLN A 109 " --> pdb=" O   THR A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 165
    Processing helix  chain 'A' and resid 166 through 173
      removed outlier: 3.754A  pdb=" N   GLY A 173 " --> pdb=" O   SER A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 219
      Proline residue:  A 209  - end of helix
      removed outlier: 3.607A  pdb=" N   ALA A 217 " --> pdb=" O   GLU A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 261
      removed outlier: 3.533A  pdb=" N   LEU A 231 " --> pdb=" O   ASP A 227 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   HIS A 232 " --> pdb=" O   ARG A 228 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ILE A 233 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE A 258 " --> pdb=" O   SER A 254 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLU A 261 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 268
      removed outlier: 3.633A  pdb=" N   LEU A 268 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 275
      removed outlier: 3.610A  pdb=" N   TRP A 273 " --> pdb=" O   CYS A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 4.026A  pdb=" N   SER A 282 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 359
      removed outlier: 3.535A  pdb=" N   TYR A 299 " --> pdb=" O   LEU A 295 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASN A 333 " --> pdb=" O   ASP A 329 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   MET A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLY A 356 " --> pdb=" O   PHE A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 399
      removed outlier: 3.509A  pdb=" N   LEU A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 112
      removed outlier: 3.676A  pdb=" N   GLN B 109 " --> pdb=" O   THR B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 165
    Processing helix  chain 'B' and resid 166 through 173
      removed outlier: 3.754A  pdb=" N   GLY B 173 " --> pdb=" O   SER B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 219
      Proline residue:  B 209  - end of helix
      removed outlier: 3.607A  pdb=" N   ALA B 217 " --> pdb=" O   GLU B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 261
      removed outlier: 3.533A  pdb=" N   LEU B 231 " --> pdb=" O   ASP B 227 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   HIS B 232 " --> pdb=" O   ARG B 228 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ILE B 233 " --> pdb=" O   SER B 229 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ILE B 258 " --> pdb=" O   SER B 254 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLU B 261 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 268
      removed outlier: 3.632A  pdb=" N   LEU B 268 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 275
      removed outlier: 3.610A  pdb=" N   TRP B 273 " --> pdb=" O   CYS B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 282
      removed outlier: 4.026A  pdb=" N   SER B 282 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 359
      removed outlier: 3.535A  pdb=" N   TYR B 299 " --> pdb=" O   LEU B 295 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASN B 333 " --> pdb=" O   ASP B 329 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   MET B 355 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLY B 356 " --> pdb=" O   PHE B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 399
      removed outlier: 3.509A  pdb=" N   LEU B 396 " --> pdb=" O   LEU B 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 112
      removed outlier: 3.675A  pdb=" N   GLN C 109 " --> pdb=" O   THR C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 165
    Processing helix  chain 'C' and resid 166 through 173
      removed outlier: 3.754A  pdb=" N   GLY C 173 " --> pdb=" O   SER C 169 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 219
      Proline residue:  C 209  - end of helix
      removed outlier: 3.607A  pdb=" N   ALA C 217 " --> pdb=" O   GLU C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 261
      removed outlier: 3.533A  pdb=" N   LEU C 231 " --> pdb=" O   ASP C 227 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   HIS C 232 " --> pdb=" O   ARG C 228 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ILE C 233 " --> pdb=" O   SER C 229 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ILE C 258 " --> pdb=" O   SER C 254 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLU C 261 " --> pdb=" O   GLU C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 268
      removed outlier: 3.632A  pdb=" N   LEU C 268 " --> pdb=" O   LEU C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 275
      removed outlier: 3.610A  pdb=" N   TRP C 273 " --> pdb=" O   CYS C 269 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 282
      removed outlier: 4.027A  pdb=" N   SER C 282 " --> pdb=" O   VAL C 278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 359
      removed outlier: 3.535A  pdb=" N   TYR C 299 " --> pdb=" O   LEU C 295 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASN C 333 " --> pdb=" O   ASP C 329 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   MET C 355 " --> pdb=" O   LEU C 351 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   GLY C 356 " --> pdb=" O   PHE C 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 373 through 399
      removed outlier: 3.509A  pdb=" N   LEU C 396 " --> pdb=" O   LEU C 392 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 112
      removed outlier: 3.675A  pdb=" N   GLN D 109 " --> pdb=" O   THR D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 160 through 165
    Processing helix  chain 'D' and resid 166 through 173
      removed outlier: 3.755A  pdb=" N   GLY D 173 " --> pdb=" O   SER D 169 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 183 through 219
      Proline residue:  D 209  - end of helix
      removed outlier: 3.607A  pdb=" N   ALA D 217 " --> pdb=" O   GLU D 213 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 261
      removed outlier: 3.533A  pdb=" N   LEU D 231 " --> pdb=" O   ASP D 227 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   HIS D 232 " --> pdb=" O   ARG D 228 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE D 233 " --> pdb=" O   SER D 229 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE D 258 " --> pdb=" O   SER D 254 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLU D 261 " --> pdb=" O   GLU D 257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 261 through 268
      removed outlier: 3.632A  pdb=" N   LEU D 268 " --> pdb=" O   LEU D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 275
      removed outlier: 3.610A  pdb=" N   TRP D 273 " --> pdb=" O   CYS D 269 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 277 through 282
      removed outlier: 4.026A  pdb=" N   SER D 282 " --> pdb=" O   VAL D 278 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 288 through 359
      removed outlier: 3.536A  pdb=" N   TYR D 299 " --> pdb=" O   LEU D 295 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ASN D 333 " --> pdb=" O   ASP D 329 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   MET D 355 " --> pdb=" O   LEU D 351 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   GLY D 356 " --> pdb=" O   PHE D 352 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 373 through 399
      removed outlier: 3.509A  pdb=" N   LEU D 396 " --> pdb=" O   LEU D 392 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 103 through 112
      removed outlier: 3.676A  pdb=" N   GLN E 109 " --> pdb=" O   THR E 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 165
    Processing helix  chain 'E' and resid 166 through 173
      removed outlier: 3.754A  pdb=" N   GLY E 173 " --> pdb=" O   SER E 169 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 183 through 219
      Proline residue:  E 209  - end of helix
      removed outlier: 3.608A  pdb=" N   ALA E 217 " --> pdb=" O   GLU E 213 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 227 through 261
      removed outlier: 3.533A  pdb=" N   LEU E 231 " --> pdb=" O   ASP E 227 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   HIS E 232 " --> pdb=" O   ARG E 228 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ILE E 233 " --> pdb=" O   SER E 229 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE E 258 " --> pdb=" O   SER E 254 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLU E 261 " --> pdb=" O   GLU E 257 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 261 through 268
      removed outlier: 3.632A  pdb=" N   LEU E 268 " --> pdb=" O   LEU E 264 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 275
      removed outlier: 3.610A  pdb=" N   TRP E 273 " --> pdb=" O   CYS E 269 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 277 through 282
      removed outlier: 4.026A  pdb=" N   SER E 282 " --> pdb=" O   VAL E 278 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 288 through 359
      removed outlier: 3.535A  pdb=" N   TYR E 299 " --> pdb=" O   LEU E 295 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ASN E 333 " --> pdb=" O   ASP E 329 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   MET E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   GLY E 356 " --> pdb=" O   PHE E 352 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 373 through 399
      removed outlier: 3.509A  pdb=" N   LEU E 396 " --> pdb=" O   LEU E 392 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 102
      removed outlier: 4.014A  pdb=" N   LYS A 141 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 102
      removed outlier: 4.013A  pdb=" N   LYS B 141 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 102
      removed outlier: 4.014A  pdb=" N   LYS C 141 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 102
      removed outlier: 4.014A  pdb=" N   LYS D 141 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 102
      removed outlier: 4.014A  pdb=" N   LYS E 141 " --> pdb=" O   LEU E 152 " (cutoff:3.500A)

    900 hydrogen bonds defined for protein.
    2640 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: 2.50

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3259
        1.33 -     1.45: 2212
        1.45 -     1.57: 7409
        1.57 -     1.69: 0
        1.69 -     1.81: 120
  Bond restraints: 13000
  Sorted by residual:
  bond pdb=" C   MET D 336 "
       pdb=" O   MET D 336 "
    ideal  model  delta    sigma   weight residual
    1.236  1.214  0.022 1.29e-02 6.01e+03 3.03e+00
  bond pdb=" C   MET E 336 "
       pdb=" O   MET E 336 "
    ideal  model  delta    sigma   weight residual
    1.236  1.215  0.022 1.29e-02 6.01e+03 2.80e+00
  bond pdb=" C   MET C 336 "
       pdb=" O   MET C 336 "
    ideal  model  delta    sigma   weight residual
    1.236  1.215  0.021 1.29e-02 6.01e+03 2.75e+00
  bond pdb=" C   MET B 336 "
       pdb=" O   MET B 336 "
    ideal  model  delta    sigma   weight residual
    1.236  1.215  0.021 1.29e-02 6.01e+03 2.75e+00
  bond pdb=" C   MET A 336 "
       pdb=" O   MET A 336 "
    ideal  model  delta    sigma   weight residual
    1.236  1.215  0.021 1.29e-02 6.01e+03 2.72e+00
  ... (remaining 12995 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 17151
        1.34 -     2.68: 344
        2.68 -     4.02: 32
        4.02 -     5.36: 18
        5.36 -     6.70: 10
  Bond angle restraints: 17555
  Sorted by residual:
  angle pdb=" N   GLY C 353 "
        pdb=" CA  GLY C 353 "
        pdb=" C   GLY C 353 "
      ideal   model   delta    sigma   weight residual
     115.32  111.27    4.05 1.31e+00 5.83e-01 9.56e+00
  angle pdb=" N   GLY B 353 "
        pdb=" CA  GLY B 353 "
        pdb=" C   GLY B 353 "
      ideal   model   delta    sigma   weight residual
     115.32  111.27    4.05 1.31e+00 5.83e-01 9.56e+00
  angle pdb=" N   GLY A 353 "
        pdb=" CA  GLY A 353 "
        pdb=" C   GLY A 353 "
      ideal   model   delta    sigma   weight residual
     115.32  111.29    4.03 1.31e+00 5.83e-01 9.45e+00
  angle pdb=" N   GLY E 353 "
        pdb=" CA  GLY E 353 "
        pdb=" C   GLY E 353 "
      ideal   model   delta    sigma   weight residual
     115.32  111.33    3.99 1.31e+00 5.83e-01 9.30e+00
  angle pdb=" N   GLY D 353 "
        pdb=" CA  GLY D 353 "
        pdb=" C   GLY D 353 "
      ideal   model   delta    sigma   weight residual
     115.32  111.33    3.99 1.31e+00 5.83e-01 9.27e+00
  ... (remaining 17550 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 6794
       17.97 -    35.95: 823
       35.95 -    53.92: 218
       53.92 -    71.89: 50
       71.89 -    89.87: 15
  Dihedral angle restraints: 7900
    sinusoidal: 3270
      harmonic: 4630
  Sorted by residual:
  dihedral pdb=" CB  GLU E 110 "
           pdb=" CG  GLU E 110 "
           pdb=" CD  GLU E 110 "
           pdb=" OE1 GLU E 110 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.87  -89.87     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU A 110 "
           pdb=" CG  GLU A 110 "
           pdb=" CD  GLU A 110 "
           pdb=" OE1 GLU A 110 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.85  -89.85     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU C 110 "
           pdb=" CG  GLU C 110 "
           pdb=" CD  GLU C 110 "
           pdb=" OE1 GLU C 110 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.84  -89.84     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 7897 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1234
       0.026 -    0.051: 495
       0.051 -    0.077: 204
       0.077 -    0.102: 51
       0.102 -    0.128: 36
  Chirality restraints: 2020
  Sorted by residual:
  chirality pdb=" CA  ILE B 126 "
            pdb=" N   ILE B 126 "
            pdb=" C   ILE B 126 "
            pdb=" CB  ILE B 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality pdb=" CA  ILE E 126 "
            pdb=" N   ILE E 126 "
            pdb=" C   ILE E 126 "
            pdb=" CB  ILE E 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  ILE D 126 "
            pdb=" N   ILE D 126 "
            pdb=" C   ILE D 126 "
            pdb=" CB  ILE D 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.05e-01
  ... (remaining 2017 not shown)

  Planarity restraints: 2230
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 145 "   -0.064 5.00e-02 4.00e+02   9.61e-02 1.48e+01
        pdb=" N   PRO C 146 "    0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO C 146 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO C 146 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR E 145 "    0.064 5.00e-02 4.00e+02   9.60e-02 1.47e+01
        pdb=" N   PRO E 146 "   -0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO E 146 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO E 146 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 145 "    0.064 5.00e-02 4.00e+02   9.58e-02 1.47e+01
        pdb=" N   PRO A 146 "   -0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO A 146 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 146 "    0.052 5.00e-02 4.00e+02
  ... (remaining 2227 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 241
        2.68 -     3.23: 11958
        3.23 -     3.79: 20225
        3.79 -     4.34: 29920
        4.34 -     4.90: 48448
  Nonbonded interactions: 110792
  Sorted by model distance:
  nonbonded pdb="MG    MG E 500 "
            pdb=" O   HOH D 646 "
     model   vdw
     2.121 2.170
  nonbonded pdb="MG    MG A 502 "
            pdb=" O   HOH E 645 "
     model   vdw
     2.121 2.170
  nonbonded pdb="MG    MG D 500 "
            pdb=" O   HOH C 646 "
     model   vdw
     2.122 2.170
  nonbonded pdb="MG    MG C 501 "
            pdb=" O   HOH B 646 "
     model   vdw
     2.122 2.170
  nonbonded pdb="MG    MG B 500 "
            pdb=" O   HOH A 646 "
     model   vdw
     2.122 2.170
  ... (remaining 110787 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 84 through 502)
  selection = chain 'B'
  selection = (chain 'C' and resid 84 through 502)
  selection = chain 'D'
  selection = chain 'E'
}

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:             3.230
  Set stop_for_unknowns flag:              0.010
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.320
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.040
  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:7.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
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   0.039  13000  Z= 0.141
  Angle     :  0.482   6.696  17555  Z= 0.262
  Chirality :  0.035   0.128   2020
  Planarity :  0.005   0.096   2230
  Dihedral  : 16.924  89.866   4880
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 23.56 %
    Favored  : 74.31 %
  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 (0.21), residues: 1575
  helix:  0.68 (0.15), residues: 1000
  sheet:  1.99 (0.42), residues: 145
  loop : -0.91 (0.33), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 228 
 TYR   0.008   0.001   TYR D 299 
 PHE   0.006   0.001   PHE B 352 
 TRP   0.004   0.001   TRP D 196 
 HIS   0.003   0.001   HIS E 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (13000)
  covalent geometry    : angle       0.48215 (17555)
  hydrogen bonds       : bond        0.18889 (  900)
  hydrogen bonds       : angle       6.33769 ( 2640)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 169
  time to evaluate  : 0.469 
Fit side-chains
REVERT: C  203 LYS cc_start: 0.8819 (mttt) cc_final: 0.8614 (mttt)
REVERT: C  270 VAL cc_start: 0.7502 (t) cc_final: 0.6930 (m)
REVERT: E  170 GLN cc_start: 0.8549 (mt0) cc_final: 0.8324 (mt0)
REVERT: E  368 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.5699 (mp0)
REVERT: E  390 ARG cc_start: 0.7275 (mmt180) cc_final: 0.7022 (mmt180)
  outliers start: 30
  outliers final: 19
  residues processed: 199
  average time/residue: 0.6493
  time to fit residues: 140.3053
Evaluate side-chains
  181 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 161
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  229 SER
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  229 SER
Chi-restraints excluded: chain C residue  368 GLU
Chi-restraints excluded: chain D residue   92 ASP
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  219 VAL
Chi-restraints excluded: chain D residue  229 SER
Chi-restraints excluded: chain D residue  368 GLU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  229 SER
Chi-restraints excluded: chain E residue  368 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.3980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    0.9980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 122 HIS
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 122 HIS
** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 122 HIS
** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 170 GLN
D 122 HIS
** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 194 GLN
E 122 HIS
** E 131 ASN ** 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 = 0.4081 r_free = 0.4081 target = 0.192433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.131605 restraints weight = 11892.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.59
r_work: 0.3045 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13000  Z= 0.157
  Angle     :  0.508   8.776  17555  Z= 0.267
  Chirality :  0.038   0.129   2020
  Planarity :  0.005   0.065   2230
  Dihedral  :  5.131  33.917   1740
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 21.21 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.16 (0.22), residues: 1575
  helix:  2.07 (0.16), residues: 1035
  sheet:  2.11 (0.41), residues: 145
  loop : -0.59 (0.34), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 332 
 TYR   0.012   0.002   TYR C 299 
 PHE   0.019   0.002   PHE E 186 
 TRP   0.007   0.001   TRP D 196 
 HIS   0.005   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (13000)
  covalent geometry    : angle       0.50790 (17555)
  hydrogen bonds       : bond        0.05975 (  900)
  hydrogen bonds       : angle       3.85666 ( 2640)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 180
  time to evaluate  : 0.552 
Fit side-chains
REVERT: A  270 VAL cc_start: 0.7252 (OUTLIER) cc_final: 0.6567 (m)
REVERT: A  337 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8331 (ttp-110)
REVERT: B  270 VAL cc_start: 0.7342 (OUTLIER) cc_final: 0.6721 (m)
REVERT: B  337 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8165 (ttp-110)
REVERT: C  124 MET cc_start: 0.9182 (tpt) cc_final: 0.8907 (tpt)
REVERT: C  203 LYS cc_start: 0.8736 (mttt) cc_final: 0.8530 (mttt)
REVERT: C  270 VAL cc_start: 0.7288 (OUTLIER) cc_final: 0.6614 (m)
REVERT: C  329 ASP cc_start: 0.8503 (m-30) cc_final: 0.8288 (m-30)
REVERT: C  337 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8168 (ttp-110)
REVERT: E  124 MET cc_start: 0.9179 (tpt) cc_final: 0.8847 (tpt)
REVERT: E  270 VAL cc_start: 0.7196 (OUTLIER) cc_final: 0.6566 (m)
REVERT: E  337 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8175 (ttp-110)
  outliers start: 49
  outliers final: 13
  residues processed: 216
  average time/residue: 0.6529
  time to fit residues: 152.9515
Evaluate side-chains
  192 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  337 ARG
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  232 HIS
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  337 ARG
Chi-restraints excluded: chain D residue  219 VAL
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  232 HIS
Chi-restraints excluded: chain E residue  270 VAL
Chi-restraints excluded: chain E residue  337 ARG
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  342 LEU
Chi-restraints excluded: chain E residue  363 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 139 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 129 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 130 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 145 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
A 327 ASN
B 298 ASN
B 327 ASN
E 298 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.192245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.126113 restraints weight = 11952.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.74
r_work: 0.2985 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13000  Z= 0.176
  Angle     :  0.526   9.114  17555  Z= 0.272
  Chirality :  0.039   0.132   2020
  Planarity :  0.004   0.053   2230
  Dihedral  :  4.108  31.760   1710
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 21.71 %
    Favored  : 74.45 %
  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:  2.41 (0.22), residues: 1575
  helix:  2.29 (0.16), residues: 1035
  sheet:  1.92 (0.40), residues: 145
  loop : -0.43 (0.35), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 332 
 TYR   0.016   0.002   TYR D 299 
 PHE   0.018   0.002   PHE E 359 
 TRP   0.008   0.001   TRP E 196 
 HIS   0.005   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (13000)
  covalent geometry    : angle       0.52607 (17555)
  hydrogen bonds       : bond        0.05727 (  900)
  hydrogen bonds       : angle       3.64876 ( 2640)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 176
  time to evaluate  : 0.605 
Fit side-chains
REVERT: A  337 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8200 (ttp-110)
REVERT: B  337 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8000 (ttp-110)
REVERT: C  203 LYS cc_start: 0.8683 (mttt) cc_final: 0.8482 (mttt)
REVERT: C  265 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7465 (tt)
REVERT: C  270 VAL cc_start: 0.7137 (OUTLIER) cc_final: 0.6832 (t)
REVERT: C  314 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.8216 (ttm170)
REVERT: C  387 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7245 (mt)
REVERT: D  329 ASP cc_start: 0.8571 (m-30) cc_final: 0.8312 (m-30)
REVERT: E  124 MET cc_start: 0.9209 (tpt) cc_final: 0.8848 (tpt)
REVERT: E  337 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8030 (ttp-110)
  outliers start: 54
  outliers final: 28
  residues processed: 214
  average time/residue: 0.6035
  time to fit residues: 141.1686
Evaluate side-chains
  198 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 164
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  337 ARG
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  213 GLU
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  232 HIS
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  219 VAL
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  363 LEU
Chi-restraints excluded: chain D residue  400 LEU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  232 HIS
Chi-restraints excluded: chain E residue  337 ARG
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  342 LEU
Chi-restraints excluded: chain E residue  363 LEU
Chi-restraints excluded: chain E residue  390 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 148 optimal weight:    0.5980
   chunk 77 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 127 optimal weight:    0.0040
   chunk 102 optimal weight:   20.0000
   chunk 32 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 31 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9980
   chunk 62 optimal weight:   10.0000
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
B 298 ASN
E 194 GLN
E 298 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.195440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.131938 restraints weight = 11960.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.71
r_work: 0.3036 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13000  Z= 0.116
  Angle     :  0.457   8.382  17555  Z= 0.238
  Chirality :  0.037   0.132   2020
  Planarity :  0.004   0.053   2230
  Dihedral  :  3.819  26.982   1710
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 22.06 %
    Favored  : 74.02 %
  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:  2.70 (0.22), residues: 1575
  helix:  2.57 (0.16), residues: 1035
  sheet:  1.83 (0.40), residues: 145
  loop : -0.42 (0.35), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 136 
 TYR   0.010   0.001   TYR D 299 
 PHE   0.025   0.001   PHE E 186 
 TRP   0.008   0.001   TRP B 196 
 HIS   0.003   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (13000)
  covalent geometry    : angle       0.45691 (17555)
  hydrogen bonds       : bond        0.04746 (  900)
  hydrogen bonds       : angle       3.44728 ( 2640)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 175
  time to evaluate  : 0.623 
Fit side-chains
REVERT: A  270 VAL cc_start: 0.6949 (OUTLIER) cc_final: 0.6621 (t)
REVERT: A  337 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8129 (ttp-110)
REVERT: B  270 VAL cc_start: 0.7089 (t) cc_final: 0.6782 (t)
REVERT: B  314 ARG cc_start: 0.8384 (ttm-80) cc_final: 0.8164 (mmt-90)
REVERT: B  337 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7996 (ttp-110)
REVERT: C  124 MET cc_start: 0.9221 (tpt) cc_final: 0.8992 (tpt)
REVERT: C  203 LYS cc_start: 0.8673 (mttt) cc_final: 0.8450 (mttt)
REVERT: C  270 VAL cc_start: 0.7046 (OUTLIER) cc_final: 0.6551 (m)
REVERT: C  314 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8056 (mmt-90)
REVERT: C  387 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7242 (mt)
REVERT: D  314 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.8069 (mmt-90)
REVERT: D  337 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7977 (ttp-110)
REVERT: E  124 MET cc_start: 0.9208 (tpt) cc_final: 0.8702 (tpt)
REVERT: E  337 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7958 (ttp-110)
  outliers start: 55
  outliers final: 17
  residues processed: 220
  average time/residue: 0.6115
  time to fit residues: 146.5014
Evaluate side-chains
  193 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 169
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  337 ARG
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  232 HIS
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain D residue  219 VAL
Chi-restraints excluded: chain D residue  337 ARG
Chi-restraints excluded: chain D residue  400 LEU
Chi-restraints excluded: chain E residue  213 GLU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  232 HIS
Chi-restraints excluded: chain E residue  337 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 148 optimal weight:    0.6980
   chunk 81 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 40 optimal weight:    0.2980
   chunk 140 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 125 optimal weight:    9.9990
   chunk 98 optimal weight:    1.9990
   chunk 118 optimal weight:    0.6980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
B 298 ASN
** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 298 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.194013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.125868 restraints weight = 12048.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 1.81
r_work: 0.3014 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13000  Z= 0.141
  Angle     :  0.487   8.524  17555  Z= 0.252
  Chirality :  0.038   0.134   2020
  Planarity :  0.004   0.050   2230
  Dihedral  :  3.913  29.491   1710
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 21.99 %
    Favored  : 74.02 %
  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:  2.60 (0.21), residues: 1575
  helix:  2.51 (0.16), residues: 1040
  sheet:  1.82 (0.40), residues: 145
  loop : -0.57 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 332 
 TYR   0.014   0.002   TYR D 299 
 PHE   0.013   0.001   PHE B 359 
 TRP   0.007   0.001   TRP B 196 
 HIS   0.004   0.001   HIS D 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (13000)
  covalent geometry    : angle       0.48670 (17555)
  hydrogen bonds       : bond        0.05040 (  900)
  hydrogen bonds       : angle       3.46365 ( 2640)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 174
  time to evaluate  : 0.526 
Fit side-chains
REVERT: A  337 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8154 (ttp-110)
REVERT: A  338 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8494 (tt)
REVERT: B  270 VAL cc_start: 0.7085 (t) cc_final: 0.6721 (m)
REVERT: B  314 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.8155 (ttm170)
REVERT: B  337 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7981 (ttp-110)
REVERT: C  203 LYS cc_start: 0.8677 (mttt) cc_final: 0.8455 (mttt)
REVERT: C  268 LEU cc_start: 0.8301 (mt) cc_final: 0.8100 (mp)
REVERT: C  270 VAL cc_start: 0.7052 (OUTLIER) cc_final: 0.6526 (m)
REVERT: C  314 ARG cc_start: 0.8375 (ttm-80) cc_final: 0.8062 (mmt-90)
REVERT: C  387 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7216 (mt)
REVERT: D  210 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7808 (mt)
REVERT: D  270 VAL cc_start: 0.7210 (t) cc_final: 0.6793 (m)
REVERT: D  314 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.8099 (ttm170)
REVERT: D  337 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8079 (ttp-110)
REVERT: E  110 GLU cc_start: 0.7655 (tp30) cc_final: 0.7172 (tp30)
REVERT: E  124 MET cc_start: 0.9211 (tpt) cc_final: 0.8709 (tpt)
REVERT: E  270 VAL cc_start: 0.7094 (t) cc_final: 0.6773 (t)
REVERT: E  337 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7951 (ttp-110)
  outliers start: 56
  outliers final: 29
  residues processed: 216
  average time/residue: 0.6434
  time to fit residues: 151.1248
Evaluate side-chains
  207 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 170
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  355 MET
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  337 ARG
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  213 GLU
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  232 HIS
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  219 VAL
Chi-restraints excluded: chain D residue  337 ARG
Chi-restraints excluded: chain D residue  400 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  213 GLU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  232 HIS
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  337 ARG
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  363 LEU
Chi-restraints excluded: chain E residue  390 ARG
Chi-restraints excluded: chain E residue  400 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 133 optimal weight:   20.0000
   chunk 44 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 119 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 141 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
B 298 ASN
B 327 ASN
C 298 ASN
C 327 ASN
D 298 ASN
E 298 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.192683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.123131 restraints weight = 11942.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.84
r_work: 0.3014 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13000  Z= 0.176
  Angle     :  0.527   8.809  17555  Z= 0.271
  Chirality :  0.039   0.135   2020
  Planarity :  0.004   0.046   2230
  Dihedral  :  4.072  31.367   1710
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 21.71 %
    Favored  : 74.52 %
  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:  2.47 (0.21), residues: 1575
  helix:  2.57 (0.16), residues: 1005
  sheet:  1.79 (0.40), residues: 145
  loop : -0.81 (0.32), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 332 
 TYR   0.016   0.002   TYR D 299 
 PHE   0.024   0.002   PHE E 186 
 TRP   0.007   0.001   TRP C 196 
 HIS   0.006   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (13000)
  covalent geometry    : angle       0.52708 (17555)
  hydrogen bonds       : bond        0.05447 (  900)
  hydrogen bonds       : angle       3.51831 ( 2640)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 172
  time to evaluate  : 0.534 
Fit side-chains
REVERT: A  268 LEU cc_start: 0.8393 (mt) cc_final: 0.8141 (mp)
REVERT: A  337 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8243 (ttp-110)
REVERT: A  338 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8541 (tt)
REVERT: B  270 VAL cc_start: 0.7242 (t) cc_final: 0.6863 (m)
REVERT: B  314 ARG cc_start: 0.8622 (ttm-80) cc_final: 0.8408 (ttm170)
REVERT: B  337 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8149 (ttp-110)
REVERT: B  383 MET cc_start: 0.6722 (mmt) cc_final: 0.6291 (mmm)
REVERT: C  203 LYS cc_start: 0.8695 (mttt) cc_final: 0.8481 (mttt)
REVERT: C  270 VAL cc_start: 0.7129 (OUTLIER) cc_final: 0.6540 (m)
REVERT: C  387 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7153 (mt)
REVERT: D  210 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7816 (mt)
REVERT: D  270 VAL cc_start: 0.7287 (t) cc_final: 0.6808 (m)
REVERT: D  314 ARG cc_start: 0.8581 (ttm-80) cc_final: 0.8343 (ttm170)
REVERT: D  337 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8220 (ttp-110)
REVERT: E  124 MET cc_start: 0.9218 (tpt) cc_final: 0.8704 (tpt)
REVERT: E  270 VAL cc_start: 0.7106 (t) cc_final: 0.6627 (m)
REVERT: E  337 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8261 (ttp-110)
  outliers start: 53
  outliers final: 32
  residues processed: 210
  average time/residue: 0.6848
  time to fit residues: 155.5578
Evaluate side-chains
  212 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 172
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  355 MET
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  337 ARG
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  213 GLU
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  232 HIS
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  219 VAL
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain D residue  337 ARG
Chi-restraints excluded: chain D residue  400 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  213 GLU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  232 HIS
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  337 ARG
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  363 LEU
Chi-restraints excluded: chain E residue  390 ARG
Chi-restraints excluded: chain E residue  400 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 112 optimal weight:   30.0000
   chunk 2 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 136 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 145 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 123 optimal weight:    5.9990
   chunk 59 optimal weight:    9.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
B 298 ASN
C 236 GLN
C 298 ASN
D 236 GLN
D 298 ASN
E 194 GLN
E 236 GLN
E 298 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.193419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.132155 restraints weight = 11914.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.73
r_work: 0.3019 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13000  Z= 0.153
  Angle     :  0.511   8.657  17555  Z= 0.263
  Chirality :  0.038   0.136   2020
  Planarity :  0.004   0.045   2230
  Dihedral  :  3.997  29.539   1710
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 22.21 %
    Favored  : 73.88 %
  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:  2.54 (0.21), residues: 1575
  helix:  2.63 (0.16), residues: 1005
  sheet:  1.80 (0.41), residues: 145
  loop : -0.79 (0.32), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 332 
 TYR   0.014   0.002   TYR D 299 
 PHE   0.015   0.001   PHE B 359 
 TRP   0.008   0.001   TRP C 196 
 HIS   0.005   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (13000)
  covalent geometry    : angle       0.51130 (17555)
  hydrogen bonds       : bond        0.05179 (  900)
  hydrogen bonds       : angle       3.47988 ( 2640)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 171
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A  228 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6516 (mtt-85)
REVERT: A  268 LEU cc_start: 0.8447 (mt) cc_final: 0.8210 (mp)
REVERT: A  337 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8221 (ttp-110)
REVERT: A  338 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8564 (tt)
REVERT: B  270 VAL cc_start: 0.7296 (t) cc_final: 0.7024 (m)
REVERT: B  301 ARG cc_start: 0.8428 (mtt90) cc_final: 0.8155 (mtt90)
REVERT: B  314 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.8205 (ttm170)
REVERT: B  337 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8009 (ttp-110)
REVERT: C  203 LYS cc_start: 0.8701 (mttt) cc_final: 0.8486 (mttt)
REVERT: C  270 VAL cc_start: 0.7337 (OUTLIER) cc_final: 0.6816 (m)
REVERT: C  387 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7383 (mt)
REVERT: D  210 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7903 (mt)
REVERT: D  270 VAL cc_start: 0.7474 (t) cc_final: 0.7060 (m)
REVERT: D  314 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.8135 (ttm170)
REVERT: D  337 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8125 (ttp-110)
REVERT: E  110 GLU cc_start: 0.7645 (tp30) cc_final: 0.7169 (tp30)
REVERT: E  124 MET cc_start: 0.9263 (tpt) cc_final: 0.8771 (tpt)
REVERT: E  270 VAL cc_start: 0.7316 (t) cc_final: 0.6895 (m)
REVERT: E  337 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8115 (ttp-110)
  outliers start: 55
  outliers final: 30
  residues processed: 211
  average time/residue: 0.5985
  time to fit residues: 137.5520
Evaluate side-chains
  208 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 169
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  228 ARG
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  355 MET
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  337 ARG
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  213 GLU
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  232 HIS
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  219 VAL
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain D residue  337 ARG
Chi-restraints excluded: chain D residue  400 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  213 GLU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  232 HIS
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  337 ARG
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  363 LEU
Chi-restraints excluded: chain E residue  390 ARG
Chi-restraints excluded: chain E residue  400 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 131 optimal weight:    5.9990
   chunk 50 optimal weight:   20.0000
   chunk 84 optimal weight:    2.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
C 298 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.191827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.122187 restraints weight = 11826.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 1.88
r_work: 0.3005 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  13000  Z= 0.194
  Angle     :  0.560   9.022  17555  Z= 0.285
  Chirality :  0.040   0.135   2020
  Planarity :  0.004   0.044   2230
  Dihedral  :  4.155  32.076   1710
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 21.99 %
    Favored  : 74.31 %
  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:  2.36 (0.21), residues: 1575
  helix:  2.46 (0.16), residues: 1005
  sheet:  1.82 (0.41), residues: 145
  loop : -0.81 (0.32), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 332 
 TYR   0.018   0.002   TYR D 299 
 PHE   0.024   0.002   PHE E 186 
 TRP   0.007   0.001   TRP E 196 
 HIS   0.007   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (13000)
  covalent geometry    : angle       0.55984 (17555)
  hydrogen bonds       : bond        0.05641 (  900)
  hydrogen bonds       : angle       3.55109 ( 2640)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 168
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A  228 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6589 (mtt-85)
REVERT: A  268 LEU cc_start: 0.8366 (mt) cc_final: 0.8125 (mp)
REVERT: A  337 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8246 (ttp-110)
REVERT: B  270 VAL cc_start: 0.7281 (t) cc_final: 0.6901 (m)
REVERT: B  314 ARG cc_start: 0.8627 (ttm-80) cc_final: 0.8411 (ttm170)
REVERT: B  337 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8141 (ttp-110)
REVERT: B  383 MET cc_start: 0.6719 (mmt) cc_final: 0.6288 (mmm)
REVERT: C  203 LYS cc_start: 0.8691 (mttt) cc_final: 0.8478 (mttt)
REVERT: C  270 VAL cc_start: 0.7270 (OUTLIER) cc_final: 0.6676 (m)
REVERT: C  387 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7140 (mt)
REVERT: D  210 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7788 (mt)
REVERT: D  270 VAL cc_start: 0.7385 (t) cc_final: 0.6912 (m)
REVERT: D  314 ARG cc_start: 0.8589 (ttm-80) cc_final: 0.8361 (ttm170)
REVERT: D  337 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8243 (ttp-110)
REVERT: E  124 MET cc_start: 0.9220 (tpt) cc_final: 0.8706 (tpt)
REVERT: E  270 VAL cc_start: 0.7168 (t) cc_final: 0.6727 (m)
REVERT: E  337 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8130 (ttp-110)
  outliers start: 52
  outliers final: 33
  residues processed: 205
  average time/residue: 0.5919
  time to fit residues: 132.1256
Evaluate side-chains
  203 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 162
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  228 ARG
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  355 MET
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  337 ARG
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  213 GLU
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  232 HIS
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  219 VAL
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain D residue  337 ARG
Chi-restraints excluded: chain D residue  400 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  213 GLU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  232 HIS
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  337 ARG
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  363 LEU
Chi-restraints excluded: chain E residue  390 ARG
Chi-restraints excluded: chain E residue  400 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 149 optimal weight:    0.5980
   chunk 147 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 113 optimal weight:    6.9990
   chunk 17 optimal weight:    0.5980
   chunk 131 optimal weight:    4.9990
   chunk 144 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 141 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
B 236 GLN
C 298 ASN
D 298 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.192767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.131294 restraints weight = 11957.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.59
r_work: 0.2990 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13000  Z= 0.166
  Angle     :  0.528   8.808  17555  Z= 0.272
  Chirality :  0.039   0.134   2020
  Planarity :  0.004   0.045   2230
  Dihedral  :  4.065  30.125   1710
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 22.70 %
    Favored  : 74.02 %
  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:  2.42 (0.21), residues: 1575
  helix:  2.52 (0.16), residues: 1005
  sheet:  1.82 (0.41), residues: 145
  loop : -0.81 (0.32), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 332 
 TYR   0.015   0.002   TYR D 299 
 PHE   0.017   0.002   PHE B 359 
 TRP   0.008   0.001   TRP E 196 
 HIS   0.005   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (13000)
  covalent geometry    : angle       0.52829 (17555)
  hydrogen bonds       : bond        0.05313 (  900)
  hydrogen bonds       : angle       3.50546 ( 2640)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 164
  time to evaluate  : 0.479 
Fit side-chains
REVERT: A  268 LEU cc_start: 0.8443 (mt) cc_final: 0.8213 (mp)
REVERT: A  270 VAL cc_start: 0.7238 (t) cc_final: 0.6656 (m)
REVERT: B  270 VAL cc_start: 0.7361 (t) cc_final: 0.6928 (m)
REVERT: B  301 ARG cc_start: 0.8451 (mtt90) cc_final: 0.8174 (mtt90)
REVERT: B  314 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8240 (ttm170)
REVERT: B  337 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8033 (ttp-110)
REVERT: C  203 LYS cc_start: 0.8700 (mttt) cc_final: 0.8491 (mttt)
REVERT: C  270 VAL cc_start: 0.7407 (OUTLIER) cc_final: 0.6812 (m)
REVERT: C  387 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7418 (mt)
REVERT: D  210 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7894 (mt)
REVERT: D  270 VAL cc_start: 0.7556 (t) cc_final: 0.7117 (m)
REVERT: D  314 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.8184 (ttm170)
REVERT: D  337 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8155 (ttp-110)
REVERT: E  124 MET cc_start: 0.9272 (tpt) cc_final: 0.8767 (tpt)
REVERT: E  270 VAL cc_start: 0.7328 (t) cc_final: 0.6902 (m)
REVERT: E  337 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8164 (ttp-110)
  outliers start: 46
  outliers final: 32
  residues processed: 195
  average time/residue: 0.5868
  time to fit residues: 124.4264
Evaluate side-chains
  204 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 166
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  355 MET
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  337 ARG
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  213 GLU
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  232 HIS
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  219 VAL
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain D residue  337 ARG
Chi-restraints excluded: chain D residue  400 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  213 GLU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  232 HIS
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  337 ARG
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  363 LEU
Chi-restraints excluded: chain E residue  390 ARG
Chi-restraints excluded: chain E residue  400 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 79 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 81 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 152 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 148 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 91 optimal weight:    7.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
B 298 ASN
C 298 ASN
D 298 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.192927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.130855 restraints weight = 11915.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.62
r_work: 0.3023 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13000  Z= 0.166
  Angle     :  0.534   8.876  17555  Z= 0.274
  Chirality :  0.039   0.135   2020
  Planarity :  0.004   0.044   2230
  Dihedral  :  4.067  30.308   1710
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.06 %
    Favored  : 73.95 %
  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:  2.42 (0.21), residues: 1575
  helix:  2.51 (0.16), residues: 1005
  sheet:  1.83 (0.41), residues: 145
  loop : -0.82 (0.32), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 332 
 TYR   0.016   0.002   TYR D 299 
 PHE   0.025   0.002   PHE E 186 
 TRP   0.008   0.001   TRP E 196 
 HIS   0.005   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (13000)
  covalent geometry    : angle       0.53353 (17555)
  hydrogen bonds       : bond        0.05307 (  900)
  hydrogen bonds       : angle       3.49833 ( 2640)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 165
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A  268 LEU cc_start: 0.8458 (mt) cc_final: 0.8212 (mp)
REVERT: A  270 VAL cc_start: 0.7273 (t) cc_final: 0.6720 (m)
REVERT: B  270 VAL cc_start: 0.7427 (t) cc_final: 0.6991 (m)
REVERT: B  301 ARG cc_start: 0.8427 (mtt90) cc_final: 0.8153 (mtt90)
REVERT: B  314 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.8192 (ttm170)
REVERT: B  337 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8040 (ttp-110)
REVERT: B  383 MET cc_start: 0.6902 (mmt) cc_final: 0.6491 (mmm)
REVERT: C  203 LYS cc_start: 0.8700 (mttt) cc_final: 0.8490 (mttt)
REVERT: C  270 VAL cc_start: 0.7460 (OUTLIER) cc_final: 0.6871 (m)
REVERT: C  387 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7435 (mt)
REVERT: D  210 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7904 (mt)
REVERT: D  270 VAL cc_start: 0.7580 (t) cc_final: 0.7156 (m)
REVERT: D  314 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.8132 (ttm170)
REVERT: D  337 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8113 (ttp-110)
REVERT: E  124 MET cc_start: 0.9267 (tpt) cc_final: 0.8763 (tpt)
REVERT: E  270 VAL cc_start: 0.7361 (t) cc_final: 0.6941 (m)
REVERT: E  337 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8099 (ttp-110)
  outliers start: 42
  outliers final: 33
  residues processed: 195
  average time/residue: 0.6179
  time to fit residues: 131.6198
Evaluate side-chains
  201 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 162
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  355 MET
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  337 ARG
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  213 GLU
Chi-restraints excluded: chain C residue  219 VAL
Chi-restraints excluded: chain C residue  232 HIS
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  219 VAL
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain D residue  337 ARG
Chi-restraints excluded: chain D residue  400 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  213 GLU
Chi-restraints excluded: chain E residue  219 VAL
Chi-restraints excluded: chain E residue  232 HIS
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  337 ARG
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  363 LEU
Chi-restraints excluded: chain E residue  390 ARG
Chi-restraints excluded: chain E residue  400 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 136 optimal weight:    0.6980
   chunk 145 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 44 optimal weight:    0.3980
   chunk 85 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 298 ASN
C 298 ASN
D 298 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.194724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.138268 restraints weight = 11847.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.50
r_work: 0.3059 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13000  Z= 0.131
  Angle     :  0.495   8.485  17555  Z= 0.256
  Chirality :  0.038   0.134   2020
  Planarity :  0.004   0.044   2230
  Dihedral  :  3.902  27.798   1710
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 23.49 %
    Favored  : 73.81 %
  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:  2.60 (0.21), residues: 1575
  helix:  2.69 (0.16), residues: 1005
  sheet:  1.85 (0.41), residues: 145
  loop : -0.80 (0.32), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 332 
 TYR   0.012   0.002   TYR D 299 
 PHE   0.020   0.001   PHE A 186 
 TRP   0.009   0.001   TRP B 196 
 HIS   0.004   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (13000)
  covalent geometry    : angle       0.49545 (17555)
  hydrogen bonds       : bond        0.04819 (  900)
  hydrogen bonds       : angle       3.41598 ( 2640)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5202.48 seconds
wall clock time: 89 minutes 27.65 seconds (5367.65 seconds total)