Starting phenix.real_space_refine
on Thu May  1 05:44:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pvf_17964/05_2025/8pvf_17964.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pvf_17964/05_2025/8pvf_17964.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pvf_17964/05_2025/8pvf_17964.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pvf_17964/05_2025/8pvf_17964.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pvf_17964/05_2025/8pvf_17964.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pvf_17964/05_2025/8pvf_17964.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      72      5.16       5
     C    6372      2.51       5
     N    1704      2.21       5
     O    1984      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10140
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2491
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 15, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAD': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 5.07, per 1000 atoms: 0.50
  Number of scatterers: 10140
  At special positions: 0
  Unit cell: (95.0895, 84.9915, 96.7725, 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      72     16.00
     P       8     15.00
     O    1984      8.00
     N    1704      7.00
     C    6372      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: 2.45
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2440

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 12 sheets defined
      36.5% alpha, 30.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 38
      removed outlier: 3.519A  pdb=" N   GLU A  38 " --> pdb=" O   ARG A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 63
    Processing helix  chain 'A' and resid 95 through 99
    Processing helix  chain 'A' and resid 100 through 105
    Processing helix  chain 'A' and resid 118 through 123
    Processing helix  chain 'A' and resid 124 through 127
    Processing helix  chain 'A' and resid 151 through 155
    Processing helix  chain 'A' and resid 167 through 184
      Proline residue:  A 175  - end of helix
    Processing helix  chain 'A' and resid 230 through 239
      removed outlier: 3.787A  pdb=" N   GLY A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LYS A 237 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 243
    Processing helix  chain 'A' and resid 272 through 285
    Processing helix  chain 'A' and resid 300 through 305
    Processing helix  chain 'A' and resid 316 through 318
      No H-bonds generated for 'chain 'A' and resid 316 through 318'
    Processing helix  chain 'A' and resid 335 through 352
    Processing helix  chain 'B' and resid 26 through 38
      removed outlier: 3.519A  pdb=" N   GLU B  38 " --> pdb=" O   ARG B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 63
    Processing helix  chain 'B' and resid 95 through 99
    Processing helix  chain 'B' and resid 100 through 105
    Processing helix  chain 'B' and resid 118 through 123
    Processing helix  chain 'B' and resid 124 through 127
    Processing helix  chain 'B' and resid 151 through 155
    Processing helix  chain 'B' and resid 167 through 184
      Proline residue:  B 175  - end of helix
    Processing helix  chain 'B' and resid 230 through 239
      removed outlier: 3.787A  pdb=" N   GLY B 236 " --> pdb=" O   ALA B 232 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LYS B 237 " --> pdb=" O   LYS B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 243
    Processing helix  chain 'B' and resid 272 through 285
    Processing helix  chain 'B' and resid 300 through 305
    Processing helix  chain 'B' and resid 316 through 318
      No H-bonds generated for 'chain 'B' and resid 316 through 318'
    Processing helix  chain 'B' and resid 335 through 352
    Processing helix  chain 'C' and resid 26 through 38
      removed outlier: 3.519A  pdb=" N   GLU C  38 " --> pdb=" O   ARG C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 63
    Processing helix  chain 'C' and resid 95 through 99
    Processing helix  chain 'C' and resid 100 through 105
    Processing helix  chain 'C' and resid 118 through 123
    Processing helix  chain 'C' and resid 124 through 127
    Processing helix  chain 'C' and resid 151 through 155
    Processing helix  chain 'C' and resid 167 through 184
      Proline residue:  C 175  - end of helix
    Processing helix  chain 'C' and resid 230 through 239
      removed outlier: 3.787A  pdb=" N   GLY C 236 " --> pdb=" O   ALA C 232 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LYS C 237 " --> pdb=" O   LYS C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 240 through 243
    Processing helix  chain 'C' and resid 272 through 285
    Processing helix  chain 'C' and resid 300 through 305
    Processing helix  chain 'C' and resid 316 through 318
      No H-bonds generated for 'chain 'C' and resid 316 through 318'
    Processing helix  chain 'C' and resid 335 through 352
    Processing helix  chain 'D' and resid 26 through 38
      removed outlier: 3.519A  pdb=" N   GLU D  38 " --> pdb=" O   ARG D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 63
    Processing helix  chain 'D' and resid 95 through 99
    Processing helix  chain 'D' and resid 100 through 105
    Processing helix  chain 'D' and resid 118 through 123
    Processing helix  chain 'D' and resid 124 through 127
    Processing helix  chain 'D' and resid 151 through 155
    Processing helix  chain 'D' and resid 167 through 184
      Proline residue:  D 175  - end of helix
    Processing helix  chain 'D' and resid 230 through 239
      removed outlier: 3.787A  pdb=" N   GLY D 236 " --> pdb=" O   ALA D 232 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LYS D 237 " --> pdb=" O   LYS D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 240 through 243
    Processing helix  chain 'D' and resid 272 through 285
    Processing helix  chain 'D' and resid 300 through 305
    Processing helix  chain 'D' and resid 316 through 318
      No H-bonds generated for 'chain 'D' and resid 316 through 318'
    Processing helix  chain 'D' and resid 335 through 352
    Processing sheet with id=1, first strand: chain 'A' and resid 74 through 76
      removed outlier: 10.094A  pdb=" N   VAL A  87 " --> pdb=" O   THR A  43 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   VAL A  45 " --> pdb=" O   VAL A  87 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   LEU A  20 " --> pdb=" O   VAL A  45 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ILE A  47 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ILE A  22 " --> pdb=" O   ILE A  47 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   THR A  19 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   CYS A 110 " --> pdb=" O   THR A  19 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   GLY A  21 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   VAL A 109 " --> pdb=" O   ILE A 134 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'A' and resid 225 through 228
      removed outlier: 9.310A  pdb=" N   THR A 247 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   GLY A 189 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
      removed outlier: 8.597A  pdb=" N   MET A 249 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   MET A 191 " --> pdb=" O   MET A 249 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   ILE A 251 " --> pdb=" O   MET A 191 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   THR A 193 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LYS A 266 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLY A 189 " --> pdb=" O   THR A 264 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   THR A 264 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   MET A 191 " --> pdb=" O   ASP A 262 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ASP A 262 " --> pdb=" O   MET A 191 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR A 193 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   VAL A 260 " --> pdb=" O   THR A 193 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   ILE A 329 " --> pdb=" O   ASP A 314 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'A' and resid 225 through 228
      removed outlier: 9.310A  pdb=" N   THR A 247 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   GLY A 189 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
      removed outlier: 8.597A  pdb=" N   MET A 249 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   MET A 191 " --> pdb=" O   MET A 249 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   ILE A 251 " --> pdb=" O   MET A 191 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   THR A 193 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LYS A 266 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLY A 189 " --> pdb=" O   THR A 264 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   THR A 264 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   MET A 191 " --> pdb=" O   ASP A 262 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ASP A 262 " --> pdb=" O   MET A 191 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR A 193 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   VAL A 260 " --> pdb=" O   THR A 193 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   PHE A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
    Processing sheet with id=4, first strand: chain 'B' and resid 74 through 76
      removed outlier: 10.094A  pdb=" N   VAL B  87 " --> pdb=" O   THR B  43 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   VAL B  45 " --> pdb=" O   VAL B  87 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   LEU B  20 " --> pdb=" O   VAL B  45 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ILE B  47 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ILE B  22 " --> pdb=" O   ILE B  47 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   THR B  19 " --> pdb=" O   ILE B 108 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   CYS B 110 " --> pdb=" O   THR B  19 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   GLY B  21 " --> pdb=" O   CYS B 110 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   VAL B 109 " --> pdb=" O   ILE B 134 " (cutoff:3.500A)
    Processing sheet with id=5, first strand: chain 'B' and resid 225 through 228
      removed outlier: 9.310A  pdb=" N   THR B 247 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   GLY B 189 " --> pdb=" O   THR B 247 " (cutoff:3.500A)
      removed outlier: 8.597A  pdb=" N   MET B 249 " --> pdb=" O   GLY B 189 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   MET B 191 " --> pdb=" O   MET B 249 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   ILE B 251 " --> pdb=" O   MET B 191 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   THR B 193 " --> pdb=" O   ILE B 251 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LYS B 266 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLY B 189 " --> pdb=" O   THR B 264 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   THR B 264 " --> pdb=" O   GLY B 189 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   MET B 191 " --> pdb=" O   ASP B 262 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ASP B 262 " --> pdb=" O   MET B 191 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR B 193 " --> pdb=" O   VAL B 260 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   VAL B 260 " --> pdb=" O   THR B 193 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   ILE B 329 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing sheet with id=6, first strand: chain 'B' and resid 225 through 228
      removed outlier: 9.310A  pdb=" N   THR B 247 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   GLY B 189 " --> pdb=" O   THR B 247 " (cutoff:3.500A)
      removed outlier: 8.597A  pdb=" N   MET B 249 " --> pdb=" O   GLY B 189 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   MET B 191 " --> pdb=" O   MET B 249 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   ILE B 251 " --> pdb=" O   MET B 191 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   THR B 193 " --> pdb=" O   ILE B 251 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LYS B 266 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLY B 189 " --> pdb=" O   THR B 264 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   THR B 264 " --> pdb=" O   GLY B 189 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   MET B 191 " --> pdb=" O   ASP B 262 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ASP B 262 " --> pdb=" O   MET B 191 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR B 193 " --> pdb=" O   VAL B 260 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   VAL B 260 " --> pdb=" O   THR B 193 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   PHE B 325 " --> pdb=" O   LEU B 321 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'C' and resid 74 through 76
      removed outlier: 10.094A  pdb=" N   VAL C  87 " --> pdb=" O   THR C  43 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   VAL C  45 " --> pdb=" O   VAL C  87 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   LEU C  20 " --> pdb=" O   VAL C  45 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ILE C  47 " --> pdb=" O   LEU C  20 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ILE C  22 " --> pdb=" O   ILE C  47 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   THR C  19 " --> pdb=" O   ILE C 108 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   CYS C 110 " --> pdb=" O   THR C  19 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   GLY C  21 " --> pdb=" O   CYS C 110 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   VAL C 109 " --> pdb=" O   ILE C 134 " (cutoff:3.500A)
    Processing sheet with id=8, first strand: chain 'C' and resid 225 through 228
      removed outlier: 9.310A  pdb=" N   THR C 247 " --> pdb=" O   VAL C 187 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   GLY C 189 " --> pdb=" O   THR C 247 " (cutoff:3.500A)
      removed outlier: 8.597A  pdb=" N   MET C 249 " --> pdb=" O   GLY C 189 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   MET C 191 " --> pdb=" O   MET C 249 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   ILE C 251 " --> pdb=" O   MET C 191 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   THR C 193 " --> pdb=" O   ILE C 251 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LYS C 266 " --> pdb=" O   VAL C 187 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLY C 189 " --> pdb=" O   THR C 264 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   THR C 264 " --> pdb=" O   GLY C 189 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   MET C 191 " --> pdb=" O   ASP C 262 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ASP C 262 " --> pdb=" O   MET C 191 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR C 193 " --> pdb=" O   VAL C 260 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   VAL C 260 " --> pdb=" O   THR C 193 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   ILE C 329 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
    Processing sheet with id=9, first strand: chain 'C' and resid 225 through 228
      removed outlier: 9.310A  pdb=" N   THR C 247 " --> pdb=" O   VAL C 187 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   GLY C 189 " --> pdb=" O   THR C 247 " (cutoff:3.500A)
      removed outlier: 8.597A  pdb=" N   MET C 249 " --> pdb=" O   GLY C 189 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   MET C 191 " --> pdb=" O   MET C 249 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   ILE C 251 " --> pdb=" O   MET C 191 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   THR C 193 " --> pdb=" O   ILE C 251 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LYS C 266 " --> pdb=" O   VAL C 187 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLY C 189 " --> pdb=" O   THR C 264 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   THR C 264 " --> pdb=" O   GLY C 189 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   MET C 191 " --> pdb=" O   ASP C 262 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ASP C 262 " --> pdb=" O   MET C 191 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR C 193 " --> pdb=" O   VAL C 260 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   VAL C 260 " --> pdb=" O   THR C 193 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   PHE C 325 " --> pdb=" O   LEU C 321 " (cutoff:3.500A)
    Processing sheet with id=10, first strand: chain 'D' and resid 74 through 76
      removed outlier: 10.094A  pdb=" N   VAL D  87 " --> pdb=" O   THR D  43 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   VAL D  45 " --> pdb=" O   VAL D  87 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   LEU D  20 " --> pdb=" O   VAL D  45 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ILE D  47 " --> pdb=" O   LEU D  20 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ILE D  22 " --> pdb=" O   ILE D  47 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   THR D  19 " --> pdb=" O   ILE D 108 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   CYS D 110 " --> pdb=" O   THR D  19 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   GLY D  21 " --> pdb=" O   CYS D 110 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   VAL D 109 " --> pdb=" O   ILE D 134 " (cutoff:3.500A)
    Processing sheet with id=11, first strand: chain 'D' and resid 225 through 228
      removed outlier: 9.310A  pdb=" N   THR D 247 " --> pdb=" O   VAL D 187 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   GLY D 189 " --> pdb=" O   THR D 247 " (cutoff:3.500A)
      removed outlier: 8.597A  pdb=" N   MET D 249 " --> pdb=" O   GLY D 189 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   MET D 191 " --> pdb=" O   MET D 249 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   ILE D 251 " --> pdb=" O   MET D 191 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   THR D 193 " --> pdb=" O   ILE D 251 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LYS D 266 " --> pdb=" O   VAL D 187 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLY D 189 " --> pdb=" O   THR D 264 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   THR D 264 " --> pdb=" O   GLY D 189 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   MET D 191 " --> pdb=" O   ASP D 262 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ASP D 262 " --> pdb=" O   MET D 191 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR D 193 " --> pdb=" O   VAL D 260 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   VAL D 260 " --> pdb=" O   THR D 193 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   ILE D 329 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=12, first strand: chain 'D' and resid 225 through 228
      removed outlier: 9.310A  pdb=" N   THR D 247 " --> pdb=" O   VAL D 187 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   GLY D 189 " --> pdb=" O   THR D 247 " (cutoff:3.500A)
      removed outlier: 8.597A  pdb=" N   MET D 249 " --> pdb=" O   GLY D 189 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   MET D 191 " --> pdb=" O   MET D 249 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   ILE D 251 " --> pdb=" O   MET D 191 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   THR D 193 " --> pdb=" O   ILE D 251 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LYS D 266 " --> pdb=" O   VAL D 187 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLY D 189 " --> pdb=" O   THR D 264 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   THR D 264 " --> pdb=" O   GLY D 189 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   MET D 191 " --> pdb=" O   ASP D 262 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ASP D 262 " --> pdb=" O   MET D 191 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR D 193 " --> pdb=" O   VAL D 260 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   VAL D 260 " --> pdb=" O   THR D 193 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   PHE D 325 " --> pdb=" O   LEU D 321 " (cutoff:3.500A)

    452 hydrogen bonds defined for protein.
    1176 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: 3.56

  Time building geometry restraints manager: 2.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2212
        1.34 -     1.46: 2900
        1.46 -     1.58: 5096
        1.58 -     1.70: 16
        1.70 -     1.82: 108
  Bond restraints: 10332
  Sorted by residual:
  bond pdb=" C1D NAD B 401 "
       pdb=" O4D NAD B 401 "
    ideal  model  delta    sigma   weight residual
    1.376  1.433 -0.057 2.00e-02 2.50e+03 8.26e+00
  bond pdb=" C1D NAD A 401 "
       pdb=" O4D NAD A 401 "
    ideal  model  delta    sigma   weight residual
    1.376  1.433 -0.057 2.00e-02 2.50e+03 8.26e+00
  bond pdb=" C1D NAD D 401 "
       pdb=" O4D NAD D 401 "
    ideal  model  delta    sigma   weight residual
    1.376  1.433 -0.057 2.00e-02 2.50e+03 8.26e+00
  bond pdb=" C1D NAD C 401 "
       pdb=" O4D NAD C 401 "
    ideal  model  delta    sigma   weight residual
    1.376  1.433 -0.057 2.00e-02 2.50e+03 8.26e+00
  bond pdb=" C   ALA D 137 "
       pdb=" N   PRO D 138 "
    ideal  model  delta    sigma   weight residual
    1.329  1.362 -0.033 1.18e-02 7.18e+03 7.74e+00
  ... (remaining 10327 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 10508
        1.96 -     3.92: 3048
        3.92 -     5.88: 428
        5.88 -     7.84: 68
        7.84 -     9.80: 12
  Bond angle restraints: 14064
  Sorted by residual:
  angle pdb=" CA  ASP C  95 "
        pdb=" CB  ASP C  95 "
        pdb=" CG  ASP C  95 "
      ideal   model   delta    sigma   weight residual
     112.60  119.09   -6.49 1.00e+00 1.00e+00 4.21e+01
  angle pdb=" CA  ASP D  95 "
        pdb=" CB  ASP D  95 "
        pdb=" CG  ASP D  95 "
      ideal   model   delta    sigma   weight residual
     112.60  119.09   -6.49 1.00e+00 1.00e+00 4.21e+01
  angle pdb=" CA  ASP B  95 "
        pdb=" CB  ASP B  95 "
        pdb=" CG  ASP B  95 "
      ideal   model   delta    sigma   weight residual
     112.60  119.07   -6.47 1.00e+00 1.00e+00 4.18e+01
  angle pdb=" CA  ASP A  95 "
        pdb=" CB  ASP A  95 "
        pdb=" CG  ASP A  95 "
      ideal   model   delta    sigma   weight residual
     112.60  119.07   -6.47 1.00e+00 1.00e+00 4.18e+01
  angle pdb=" C   ASP A 262 "
        pdb=" CA  ASP A 262 "
        pdb=" CB  ASP A 262 "
      ideal   model   delta    sigma   weight residual
     111.17  120.97   -9.80 1.54e+00 4.22e-01 4.05e+01
  ... (remaining 14059 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.41: 5468
       15.41 -    30.81: 676
       30.81 -    46.21: 92
       46.21 -    61.61: 44
       61.61 -    77.01: 24
  Dihedral angle restraints: 6304
    sinusoidal: 2476
      harmonic: 3828
  Sorted by residual:
  dihedral pdb=" CA  MET B 191 "
           pdb=" C   MET B 191 "
           pdb=" N   THR B 192 "
           pdb=" CA  THR B 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.00   25.00     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  MET C 191 "
           pdb=" C   MET C 191 "
           pdb=" N   THR C 192 "
           pdb=" CA  THR C 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.00   25.00     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  MET A 191 "
           pdb=" C   MET A 191 "
           pdb=" N   THR A 192 "
           pdb=" CA  THR A 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.00   25.00     0      5.00e+00 4.00e-02 2.50e+01
  ... (remaining 6301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 826
       0.062 -    0.124: 510
       0.124 -    0.186: 260
       0.186 -    0.248: 36
       0.248 -    0.310: 8
  Chirality restraints: 1640
  Sorted by residual:
  chirality pdb=" CB  ILE C 108 "
            pdb=" CA  ILE C 108 "
            pdb=" CG1 ILE C 108 "
            pdb=" CG2 ILE C 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.41e+00
  chirality pdb=" CB  ILE A 108 "
            pdb=" CA  ILE A 108 "
            pdb=" CG1 ILE A 108 "
            pdb=" CG2 ILE A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.41e+00
  chirality pdb=" CB  ILE D 108 "
            pdb=" CA  ILE D 108 "
            pdb=" CG1 ILE D 108 "
            pdb=" CG2 ILE D 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.41e+00
  ... (remaining 1637 not shown)

  Planarity restraints: 1792
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 252 "    0.172 9.50e-02 1.11e+02   8.18e-02 1.31e+01
        pdb=" NE  ARG C 252 "   -0.028 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 252 "    0.051 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 252 "   -0.019 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 252 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 252 "    0.172 9.50e-02 1.11e+02   8.18e-02 1.31e+01
        pdb=" NE  ARG D 252 "   -0.028 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 252 "    0.051 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 252 "   -0.019 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 252 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 252 "   -0.172 9.50e-02 1.11e+02   8.18e-02 1.31e+01
        pdb=" NE  ARG B 252 "    0.028 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 252 "   -0.051 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 252 "    0.019 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 252 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1789 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 3824
        2.91 -     3.41: 9600
        3.41 -     3.91: 18864
        3.91 -     4.40: 22038
        4.40 -     4.90: 35102
  Nonbonded interactions: 89428
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 137 "
            pdb=" OG  SER A 164 "
     model   vdw
     2.413 3.040
  nonbonded pdb=" O   ALA B 137 "
            pdb=" OG  SER B 164 "
     model   vdw
     2.413 3.040
  nonbonded pdb=" O   ALA C 137 "
            pdb=" OG  SER C 164 "
     model   vdw
     2.413 3.040
  nonbonded pdb=" O   ALA D 137 "
            pdb=" OG  SER D 164 "
     model   vdw
     2.413 3.040
  nonbonded pdb=" O   SER B 136 "
            pdb=" OG  SER B 136 "
     model   vdw
     2.493 3.040
  ... (remaining 89423 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     25.430
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
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      :  0.010   0.057  10332  Z= 0.651
  Angle     :  1.803   9.801  14064  Z= 1.192
  Chirality :  0.091   0.310   1640
  Planarity :  0.011   0.091   1792
  Dihedral  : 14.887  77.012   3864
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 0.60
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  4.18 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  7.43 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.33 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.21), residues: 1340
  helix: -0.96 (0.22), residues: 352
  sheet: -1.41 (0.28), residues: 272
  loop : -0.23 (0.23), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.008   TRP B 101 
 HIS   0.008   0.004   HIS A 125 
 PHE   0.026   0.007   PHE D 304 
 TYR   0.040   0.008   TYR B 146 
 ARG   0.053   0.008   ARG C 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17967 (  400)
  hydrogen bonds       : angle       7.29457 ( 1176)
  covalent geometry    : bond        0.01023 (10332)
  covalent geometry    : angle       1.80274 (14064)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 304
  time to evaluate  : 1.057 
Fit side-chains
REVERT: A   37 MET cc_start: 0.7451 (mmt) cc_final: 0.7128 (mpm)
REVERT: A   43 THR cc_start: 0.7608 (t) cc_final: 0.7330 (m)
REVERT: A   55 GLU cc_start: 0.6945 (mp0) cc_final: 0.6592 (mp0)
REVERT: A   71 ASN cc_start: 0.7216 (t0) cc_final: 0.6593 (m-40)
REVERT: A   75 GLU cc_start: 0.7628 (pt0) cc_final: 0.7360 (pt0)
REVERT: A   89 LYS cc_start: 0.7003 (mtpt) cc_final: 0.6682 (mtpt)
REVERT: A  120 GLU cc_start: 0.7692 (tt0) cc_final: 0.7109 (mp0)
REVERT: A  131 LYS cc_start: 0.7686 (mmtp) cc_final: 0.7183 (mttm)
REVERT: A  159 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6564 (ttmm)
REVERT: A  160 PHE cc_start: 0.7491 (m-80) cc_final: 0.7260 (m-80)
REVERT: A  183 LYS cc_start: 0.7221 (tptt) cc_final: 0.6942 (tptm)
REVERT: A  247 THR cc_start: 0.8509 (t) cc_final: 0.8162 (p)
REVERT: A  252 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7030 (mpp80)
REVERT: A  282 GLU cc_start: 0.6790 (tt0) cc_final: 0.6441 (mt-10)
REVERT: A  289 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7449 (ttmm)
REVERT: A  308 LYS cc_start: 0.7991 (mttp) cc_final: 0.7762 (mttp)
REVERT: A  327 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7766 (tppp)
REVERT: B   37 MET cc_start: 0.7451 (mmt) cc_final: 0.7128 (mpm)
REVERT: B   43 THR cc_start: 0.7606 (t) cc_final: 0.7330 (m)
REVERT: B   55 GLU cc_start: 0.6947 (mp0) cc_final: 0.6594 (mp0)
REVERT: B   71 ASN cc_start: 0.7218 (t0) cc_final: 0.6593 (m-40)
REVERT: B   75 GLU cc_start: 0.7630 (pt0) cc_final: 0.7361 (pt0)
REVERT: B   89 LYS cc_start: 0.7004 (mtpt) cc_final: 0.6683 (mtpt)
REVERT: B  120 GLU cc_start: 0.7693 (tt0) cc_final: 0.7109 (mp0)
REVERT: B  131 LYS cc_start: 0.7684 (mmtp) cc_final: 0.7180 (mttm)
REVERT: B  159 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6565 (ttmm)
REVERT: B  160 PHE cc_start: 0.7491 (m-80) cc_final: 0.7261 (m-80)
REVERT: B  183 LYS cc_start: 0.7219 (tptt) cc_final: 0.6940 (tptm)
REVERT: B  247 THR cc_start: 0.8509 (t) cc_final: 0.8161 (p)
REVERT: B  252 ARG cc_start: 0.7538 (mtt180) cc_final: 0.7030 (mpp80)
REVERT: B  282 GLU cc_start: 0.6790 (tt0) cc_final: 0.6441 (mt-10)
REVERT: B  289 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7451 (ttmm)
REVERT: B  308 LYS cc_start: 0.7991 (mttp) cc_final: 0.7760 (mttp)
REVERT: B  327 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7767 (tppp)
REVERT: C   37 MET cc_start: 0.7452 (mmt) cc_final: 0.7128 (mpm)
REVERT: C   43 THR cc_start: 0.7609 (t) cc_final: 0.7332 (m)
REVERT: C   55 GLU cc_start: 0.6947 (mp0) cc_final: 0.6594 (mp0)
REVERT: C   71 ASN cc_start: 0.7217 (t0) cc_final: 0.6592 (m-40)
REVERT: C   75 GLU cc_start: 0.7630 (pt0) cc_final: 0.7360 (pt0)
REVERT: C   89 LYS cc_start: 0.7005 (mtpt) cc_final: 0.6683 (mtpt)
REVERT: C  120 GLU cc_start: 0.7693 (tt0) cc_final: 0.7109 (mp0)
REVERT: C  131 LYS cc_start: 0.7685 (mmtp) cc_final: 0.7182 (mttm)
REVERT: C  159 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6563 (ttmm)
REVERT: C  160 PHE cc_start: 0.7492 (m-80) cc_final: 0.7260 (m-80)
REVERT: C  183 LYS cc_start: 0.7221 (tptt) cc_final: 0.6941 (tptm)
REVERT: C  247 THR cc_start: 0.8508 (t) cc_final: 0.8162 (p)
REVERT: C  252 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7029 (mpp80)
REVERT: C  282 GLU cc_start: 0.6792 (tt0) cc_final: 0.6442 (mt-10)
REVERT: C  289 LYS cc_start: 0.7954 (ttpt) cc_final: 0.7450 (ttmm)
REVERT: C  308 LYS cc_start: 0.7993 (mttp) cc_final: 0.7762 (mttp)
REVERT: C  327 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7769 (tppp)
REVERT: D   37 MET cc_start: 0.7451 (mmt) cc_final: 0.7127 (mpm)
REVERT: D   43 THR cc_start: 0.7607 (t) cc_final: 0.7330 (m)
REVERT: D   55 GLU cc_start: 0.6947 (mp0) cc_final: 0.6593 (mp0)
REVERT: D   71 ASN cc_start: 0.7218 (t0) cc_final: 0.6594 (m-40)
REVERT: D   75 GLU cc_start: 0.7629 (pt0) cc_final: 0.7359 (pt0)
REVERT: D   89 LYS cc_start: 0.7003 (mtpt) cc_final: 0.6681 (mtpt)
REVERT: D  120 GLU cc_start: 0.7694 (tt0) cc_final: 0.7109 (mp0)
REVERT: D  131 LYS cc_start: 0.7685 (mmtp) cc_final: 0.7182 (mttm)
REVERT: D  159 LYS cc_start: 0.6957 (mmtt) cc_final: 0.6563 (ttmm)
REVERT: D  160 PHE cc_start: 0.7492 (m-80) cc_final: 0.7261 (m-80)
REVERT: D  183 LYS cc_start: 0.7223 (tptt) cc_final: 0.6944 (tptm)
REVERT: D  247 THR cc_start: 0.8509 (t) cc_final: 0.8163 (p)
REVERT: D  252 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7030 (mpp80)
REVERT: D  282 GLU cc_start: 0.6790 (tt0) cc_final: 0.6439 (mt-10)
REVERT: D  289 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7449 (ttmm)
REVERT: D  308 LYS cc_start: 0.7992 (mttp) cc_final: 0.7762 (mttp)
REVERT: D  327 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7766 (tppp)
  outliers start: 12
  outliers final: 8
  residues processed: 308
  average time/residue: 1.3675
  time to fit residues: 447.6808
Evaluate side-chains
  232 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 224
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 ASP
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain B residue   95 ASP
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain C residue   95 ASP
Chi-restraints excluded: chain C residue  261 VAL
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue  261 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 119 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  92 GLN
A 107 GLN
A 195 HIS
A 340 ASN
** B  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 GLN
B 107 GLN
B 195 HIS
B 340 ASN
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  92 GLN
C 107 GLN
C 195 HIS
C 340 ASN
** D  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  92 GLN
D 107 GLN
D 195 HIS
D 340 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.107829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.094464 restraints weight = 12207.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 1.34
r_work: 0.2891 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10332  Z= 0.135
  Angle     :  0.553   6.036  14064  Z= 0.292
  Chirality :  0.047   0.157   1640
  Planarity :  0.004   0.036   1792
  Dihedral  :  9.085  79.380   1656
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.99 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.15 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.24), residues: 1340
  helix:  0.61 (0.26), residues: 396
  sheet: -1.25 (0.29), residues: 292
  loop :  0.53 (0.26), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 101 
 HIS   0.005   0.001   HIS B  67 
 PHE   0.013   0.002   PHE D 304 
 TYR   0.011   0.001   TYR B 146 
 ARG   0.002   0.001   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03515 (  400)
  hydrogen bonds       : angle       4.86718 ( 1176)
  covalent geometry    : bond        0.00308 (10332)
  covalent geometry    : angle       0.55302 (14064)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 224
  time to evaluate  : 1.072 
Fit side-chains
REVERT: A   71 ASN cc_start: 0.7668 (t0) cc_final: 0.7184 (m-40)
REVERT: A  119 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6787 (tm-30)
REVERT: A  120 GLU cc_start: 0.7912 (tt0) cc_final: 0.7491 (mp0)
REVERT: A  131 LYS cc_start: 0.8233 (mmtp) cc_final: 0.7748 (mttm)
REVERT: A  289 LYS cc_start: 0.8267 (ttpt) cc_final: 0.7805 (ttmm)
REVERT: B   71 ASN cc_start: 0.7650 (t0) cc_final: 0.7169 (m-40)
REVERT: B  119 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6786 (tm-30)
REVERT: B  120 GLU cc_start: 0.7906 (tt0) cc_final: 0.7488 (mp0)
REVERT: B  131 LYS cc_start: 0.8234 (mmtp) cc_final: 0.7747 (mttm)
REVERT: B  289 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7809 (ttmm)
REVERT: C   71 ASN cc_start: 0.7653 (t0) cc_final: 0.7170 (m-40)
REVERT: C  119 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6781 (tm-30)
REVERT: C  120 GLU cc_start: 0.7910 (tt0) cc_final: 0.7487 (mp0)
REVERT: C  131 LYS cc_start: 0.8231 (mmtp) cc_final: 0.7745 (mttm)
REVERT: C  289 LYS cc_start: 0.8252 (ttpt) cc_final: 0.7802 (ttmm)
REVERT: D   71 ASN cc_start: 0.7668 (t0) cc_final: 0.7183 (m-40)
REVERT: D  119 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6774 (tm-30)
REVERT: D  120 GLU cc_start: 0.7908 (tt0) cc_final: 0.7482 (mp0)
REVERT: D  131 LYS cc_start: 0.8231 (mmtp) cc_final: 0.7741 (mttm)
REVERT: D  289 LYS cc_start: 0.8261 (ttpt) cc_final: 0.7809 (ttmm)
  outliers start: 20
  outliers final: 8
  residues processed: 240
  average time/residue: 1.2682
  time to fit residues: 327.0308
Evaluate side-chains
  188 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 180
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  342 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 105 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 124 optimal weight:    0.0970
   chunk 80 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0770
   chunk 118 optimal weight:    0.3980
   chunk 55 optimal weight:    0.0770
   overall best weight:    0.2894

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 107 GLN
A 195 HIS
A 201 GLN
** B  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 GLN
B 195 HIS
B 201 GLN
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 GLN
C 195 HIS
C 201 GLN
** D  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 107 GLN
D 195 HIS
D 201 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.111196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.098140 restraints weight = 12413.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 1.36
r_work: 0.2944 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10332  Z= 0.087
  Angle     :  0.482   5.163  14064  Z= 0.254
  Chirality :  0.045   0.151   1640
  Planarity :  0.003   0.034   1792
  Dihedral  :  8.436  78.807   1644
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.99 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.47 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.24), residues: 1340
  helix:  1.11 (0.27), residues: 396
  sheet: -0.97 (0.29), residues: 292
  loop :  0.78 (0.27), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 331 
 HIS   0.004   0.002   HIS B 125 
 PHE   0.010   0.001   PHE D 304 
 TYR   0.009   0.001   TYR B 338 
 ARG   0.002   0.000   ARG D 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02862 (  400)
  hydrogen bonds       : angle       4.25172 ( 1176)
  covalent geometry    : bond        0.00195 (10332)
  covalent geometry    : angle       0.48192 (14064)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 184
  time to evaluate  : 1.160 
Fit side-chains
REVERT: A   71 ASN cc_start: 0.7619 (t0) cc_final: 0.7222 (m-40)
REVERT: A  120 GLU cc_start: 0.7896 (tt0) cc_final: 0.7673 (mp0)
REVERT: A  131 LYS cc_start: 0.8227 (mmtp) cc_final: 0.7759 (mttm)
REVERT: A  229 THR cc_start: 0.8020 (t) cc_final: 0.7738 (m)
REVERT: A  289 LYS cc_start: 0.8177 (ttpt) cc_final: 0.7849 (ttmm)
REVERT: A  319 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8171 (tp)
REVERT: A  324 SER cc_start: 0.7935 (t) cc_final: 0.7558 (p)
REVERT: B   71 ASN cc_start: 0.7608 (t0) cc_final: 0.7215 (m-40)
REVERT: B  120 GLU cc_start: 0.7911 (tt0) cc_final: 0.7676 (mp0)
REVERT: B  131 LYS cc_start: 0.8226 (mmtp) cc_final: 0.7758 (mttm)
REVERT: B  229 THR cc_start: 0.8009 (t) cc_final: 0.7726 (m)
REVERT: B  289 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7848 (ttmm)
REVERT: B  319 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8170 (tp)
REVERT: B  324 SER cc_start: 0.7937 (t) cc_final: 0.7565 (p)
REVERT: C   71 ASN cc_start: 0.7604 (t0) cc_final: 0.7210 (m-40)
REVERT: C  120 GLU cc_start: 0.7931 (tt0) cc_final: 0.7664 (mp0)
REVERT: C  131 LYS cc_start: 0.8231 (mmtp) cc_final: 0.7762 (mttm)
REVERT: C  229 THR cc_start: 0.8012 (t) cc_final: 0.7729 (m)
REVERT: C  289 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7833 (ttmm)
REVERT: C  319 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8171 (tp)
REVERT: C  324 SER cc_start: 0.7939 (t) cc_final: 0.7570 (p)
REVERT: D   71 ASN cc_start: 0.7627 (t0) cc_final: 0.7227 (m-40)
REVERT: D  120 GLU cc_start: 0.7913 (tt0) cc_final: 0.7656 (mp0)
REVERT: D  131 LYS cc_start: 0.8229 (mmtp) cc_final: 0.7758 (mttm)
REVERT: D  229 THR cc_start: 0.8009 (t) cc_final: 0.7727 (m)
REVERT: D  289 LYS cc_start: 0.8149 (ttpt) cc_final: 0.7832 (ttmm)
REVERT: D  319 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8173 (tp)
REVERT: D  324 SER cc_start: 0.7929 (t) cc_final: 0.7549 (p)
  outliers start: 28
  outliers final: 8
  residues processed: 196
  average time/residue: 1.1636
  time to fit residues: 245.8151
Evaluate side-chains
  192 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 180
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue  193 THR
Chi-restraints excluded: chain B residue  319 ILE
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  319 ILE
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  319 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0970
   chunk 26 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 112 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
A  48 ASN
A 107 GLN
A 195 HIS
** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  48 ASN
B 107 GLN
B 195 HIS
** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  48 ASN
C 107 GLN
C 195 HIS
** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  48 ASN
D 107 GLN
D 195 HIS
** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.108709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.095256 restraints weight = 12337.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 1.38
r_work: 0.2900 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10332  Z= 0.166
  Angle     :  0.530   6.316  14064  Z= 0.277
  Chirality :  0.047   0.143   1640
  Planarity :  0.004   0.034   1792
  Dihedral  :  8.708  82.637   1644
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.69 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 17.10 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.24), residues: 1340
  helix:  0.91 (0.26), residues: 396
  sheet: -0.89 (0.31), residues: 280
  loop :  0.61 (0.26), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 101 
 HIS   0.004   0.002   HIS B 125 
 PHE   0.011   0.002   PHE D 304 
 TYR   0.013   0.002   TYR D 146 
 ARG   0.003   0.001   ARG D  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03267 (  400)
  hydrogen bonds       : angle       4.53738 ( 1176)
  covalent geometry    : bond        0.00395 (10332)
  covalent geometry    : angle       0.52962 (14064)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 193
  time to evaluate  : 1.074 
Fit side-chains
REVERT: A   71 ASN cc_start: 0.7725 (t0) cc_final: 0.7337 (m-40)
REVERT: A   89 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7479 (mmtp)
REVERT: A  120 GLU cc_start: 0.7897 (tt0) cc_final: 0.7648 (mp0)
REVERT: A  131 LYS cc_start: 0.8172 (mmtp) cc_final: 0.7722 (mttm)
REVERT: A  274 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7411 (mp0)
REVERT: A  289 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7895 (ttmm)
REVERT: A  315 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8577 (tttt)
REVERT: B   71 ASN cc_start: 0.7727 (t0) cc_final: 0.7338 (m-40)
REVERT: B   89 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7468 (mmtp)
REVERT: B  120 GLU cc_start: 0.7899 (tt0) cc_final: 0.7648 (mp0)
REVERT: B  131 LYS cc_start: 0.8172 (mmtp) cc_final: 0.7722 (mttm)
REVERT: B  274 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7421 (mp0)
REVERT: B  289 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7897 (ttmm)
REVERT: B  315 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8564 (tttt)
REVERT: C   71 ASN cc_start: 0.7737 (t0) cc_final: 0.7350 (m-40)
REVERT: C   89 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7469 (mmtp)
REVERT: C  120 GLU cc_start: 0.7921 (tt0) cc_final: 0.7645 (mp0)
REVERT: C  131 LYS cc_start: 0.8169 (mmtp) cc_final: 0.7722 (mttm)
REVERT: C  274 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7430 (mp0)
REVERT: C  289 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7897 (ttmm)
REVERT: C  315 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8565 (tttt)
REVERT: D   71 ASN cc_start: 0.7736 (t0) cc_final: 0.7343 (m-40)
REVERT: D   89 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7477 (mmtp)
REVERT: D  120 GLU cc_start: 0.7893 (tt0) cc_final: 0.7636 (mp0)
REVERT: D  131 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7727 (mttm)
REVERT: D  274 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7417 (mp0)
REVERT: D  289 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7892 (ttmm)
REVERT: D  315 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8569 (tttt)
  outliers start: 56
  outliers final: 24
  residues processed: 225
  average time/residue: 1.3182
  time to fit residues: 317.5886
Evaluate side-chains
  215 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 183
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   89 LYS
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  315 LYS
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain B residue  193 THR
Chi-restraints excluded: chain B residue  315 LYS
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain C residue   37 MET
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   89 LYS
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  315 LYS
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain D residue   37 MET
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   89 LYS
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  191 MET
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  315 LYS
Chi-restraints excluded: chain D residue  342 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 112 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 39 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  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 195 HIS
** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 GLN
B 195 HIS
** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 195 HIS
** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 107 GLN
D 195 HIS
** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.108545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.095044 restraints weight = 12496.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 1.41
r_work: 0.2894 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10332  Z= 0.157
  Angle     :  0.514   6.363  14064  Z= 0.269
  Chirality :  0.047   0.145   1640
  Planarity :  0.004   0.036   1792
  Dihedral  :  8.731  84.655   1644
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.28 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 18.49 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.24), residues: 1340
  helix:  0.94 (0.27), residues: 396
  sheet: -0.79 (0.31), residues: 272
  loop :  0.61 (0.26), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C 101 
 HIS   0.004   0.002   HIS B 125 
 PHE   0.012   0.002   PHE D 304 
 TYR   0.011   0.002   TYR D 146 
 ARG   0.006   0.001   ARG A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03216 (  400)
  hydrogen bonds       : angle       4.48097 ( 1176)
  covalent geometry    : bond        0.00375 (10332)
  covalent geometry    : angle       0.51368 (14064)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 173
  time to evaluate  : 1.091 
Fit side-chains
REVERT: A   39 ARG cc_start: 0.7785 (mtt90) cc_final: 0.7161 (mtt-85)
REVERT: A   71 ASN cc_start: 0.7768 (t0) cc_final: 0.7300 (m-40)
REVERT: A   89 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7359 (mmtp)
REVERT: A  120 GLU cc_start: 0.7984 (tt0) cc_final: 0.7579 (mp0)
REVERT: A  131 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7839 (mttm)
REVERT: A  229 THR cc_start: 0.8387 (m) cc_final: 0.8126 (m)
REVERT: A  249 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.6946 (ppp)
REVERT: A  289 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7873 (ttmm)
REVERT: A  308 LYS cc_start: 0.8767 (mttp) cc_final: 0.8550 (mttp)
REVERT: B   39 ARG cc_start: 0.7801 (mtt90) cc_final: 0.7176 (mtt-85)
REVERT: B   71 ASN cc_start: 0.7760 (t0) cc_final: 0.7291 (m-40)
REVERT: B   89 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7361 (mmtp)
REVERT: B  120 GLU cc_start: 0.7995 (tt0) cc_final: 0.7585 (mp0)
REVERT: B  131 LYS cc_start: 0.8169 (mmtp) cc_final: 0.7838 (mttm)
REVERT: B  229 THR cc_start: 0.8389 (m) cc_final: 0.8129 (m)
REVERT: B  249 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.6965 (ppp)
REVERT: B  289 LYS cc_start: 0.8277 (ttpt) cc_final: 0.7876 (ttmm)
REVERT: B  308 LYS cc_start: 0.8773 (mttp) cc_final: 0.8556 (mttp)
REVERT: C   39 ARG cc_start: 0.7798 (mtt90) cc_final: 0.7175 (mtt-85)
REVERT: C   71 ASN cc_start: 0.7762 (t0) cc_final: 0.7292 (m-40)
REVERT: C   89 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7361 (mmtp)
REVERT: C  120 GLU cc_start: 0.8002 (tt0) cc_final: 0.7585 (mp0)
REVERT: C  131 LYS cc_start: 0.8169 (mmtp) cc_final: 0.7838 (mttm)
REVERT: C  229 THR cc_start: 0.8390 (m) cc_final: 0.8129 (m)
REVERT: C  249 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.6950 (ppp)
REVERT: C  289 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7862 (ttmm)
REVERT: C  308 LYS cc_start: 0.8775 (mttp) cc_final: 0.8562 (mttp)
REVERT: D   39 ARG cc_start: 0.7778 (mtt90) cc_final: 0.7154 (mtt-85)
REVERT: D   71 ASN cc_start: 0.7765 (t0) cc_final: 0.7287 (m-40)
REVERT: D   89 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7360 (mmtp)
REVERT: D  120 GLU cc_start: 0.8004 (tt0) cc_final: 0.7575 (mp0)
REVERT: D  131 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7841 (mttm)
REVERT: D  229 THR cc_start: 0.8385 (m) cc_final: 0.8123 (m)
REVERT: D  249 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.6948 (ppp)
REVERT: D  289 LYS cc_start: 0.8267 (ttpt) cc_final: 0.7866 (ttmm)
  outliers start: 40
  outliers final: 24
  residues processed: 193
  average time/residue: 1.4577
  time to fit residues: 300.2323
Evaluate side-chains
  208 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 176
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   89 LYS
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain B residue  193 THR
Chi-restraints excluded: chain B residue  249 MET
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain C residue   37 MET
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   89 LYS
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  249 MET
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain D residue   37 MET
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   89 LYS
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  191 MET
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  249 MET
Chi-restraints excluded: chain D residue  342 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 121 optimal weight:    0.6980
   chunk 82 optimal weight:    0.6980
   chunk 116 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 107 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   chunk 122 optimal weight:    0.6980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 107 GLN
A 201 GLN
** B  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 GLN
B 201 GLN
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 GLN
C 201 GLN
** D  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 107 GLN
D 201 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.110242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.097002 restraints weight = 12353.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 1.39
r_work: 0.2951 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10332  Z= 0.115
  Angle     :  0.492   6.986  14064  Z= 0.256
  Chirality :  0.045   0.147   1640
  Planarity :  0.003   0.035   1792
  Dihedral  :  8.504  84.653   1644
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.69 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 19.70 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.24), residues: 1340
  helix:  1.14 (0.27), residues: 396
  sheet: -1.05 (0.30), residues: 292
  loop :  0.67 (0.27), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP D 101 
 HIS   0.004   0.002   HIS A 125 
 PHE   0.011   0.001   PHE A 304 
 TYR   0.007   0.001   TYR C 338 
 ARG   0.004   0.001   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02929 (  400)
  hydrogen bonds       : angle       4.25786 ( 1176)
  covalent geometry    : bond        0.00276 (10332)
  covalent geometry    : angle       0.49173 (14064)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 183
  time to evaluate  : 1.306 
Fit side-chains
REVERT: A   39 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7231 (mpt-90)
REVERT: A   71 ASN cc_start: 0.7778 (t0) cc_final: 0.7367 (m-40)
REVERT: A  120 GLU cc_start: 0.7931 (tt0) cc_final: 0.7641 (mp0)
REVERT: A  229 THR cc_start: 0.8377 (m) cc_final: 0.8121 (m)
REVERT: A  289 LYS cc_start: 0.8253 (ttpt) cc_final: 0.7903 (ttmm)
REVERT: A  315 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8322 (tttt)
REVERT: B   39 ARG cc_start: 0.7827 (mtt90) cc_final: 0.7250 (mpt-90)
REVERT: B   71 ASN cc_start: 0.7755 (t0) cc_final: 0.7341 (m-40)
REVERT: B  120 GLU cc_start: 0.7941 (tt0) cc_final: 0.7644 (mp0)
REVERT: B  229 THR cc_start: 0.8376 (m) cc_final: 0.8121 (m)
REVERT: B  289 LYS cc_start: 0.8255 (ttpt) cc_final: 0.7904 (ttmm)
REVERT: B  315 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8344 (tttt)
REVERT: C   39 ARG cc_start: 0.7820 (mtt90) cc_final: 0.7238 (mpt-90)
REVERT: C   71 ASN cc_start: 0.7762 (t0) cc_final: 0.7351 (m-40)
REVERT: C  120 GLU cc_start: 0.7966 (tt0) cc_final: 0.7646 (mp0)
REVERT: C  229 THR cc_start: 0.8373 (m) cc_final: 0.8116 (m)
REVERT: C  289 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7893 (ttmm)
REVERT: C  315 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8304 (tttt)
REVERT: D   39 ARG cc_start: 0.7802 (mtt90) cc_final: 0.7224 (mpt-90)
REVERT: D   71 ASN cc_start: 0.7798 (t0) cc_final: 0.7374 (m-40)
REVERT: D  120 GLU cc_start: 0.7974 (tt0) cc_final: 0.7637 (mp0)
REVERT: D  229 THR cc_start: 0.8360 (m) cc_final: 0.8100 (m)
REVERT: D  289 LYS cc_start: 0.8244 (ttpt) cc_final: 0.7896 (ttmm)
REVERT: D  315 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8316 (tttt)
  outliers start: 33
  outliers final: 24
  residues processed: 196
  average time/residue: 1.2116
  time to fit residues: 255.3313
Evaluate side-chains
  194 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  315 LYS
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain B residue  193 THR
Chi-restraints excluded: chain B residue  315 LYS
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain C residue   37 MET
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  315 LYS
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain D residue   37 MET
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  191 MET
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  315 LYS
Chi-restraints excluded: chain D residue  342 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 118 optimal weight:    0.0970
   chunk 4 optimal weight:    4.9990
   chunk 68 optimal weight:    0.0000
   chunk 12 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.7986

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

Flipped N/Q/H residues before XYZ refinement:
A  48 ASN
A 107 GLN
A 201 GLN
** B  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 GLN
B 201 GLN
C  48 ASN
C 107 GLN
C 201 GLN
** D  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 107 GLN
D 201 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.111576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.095426 restraints weight = 12061.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 1.88
r_work: 0.2899 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10332  Z= 0.114
  Angle     :  0.487   6.680  14064  Z= 0.253
  Chirality :  0.045   0.145   1640
  Planarity :  0.003   0.035   1792
  Dihedral  :  8.407  85.122   1644
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.69 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.80 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.24), residues: 1340
  helix:  1.23 (0.27), residues: 396
  sheet: -1.04 (0.30), residues: 292
  loop :  0.68 (0.27), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 101 
 HIS   0.003   0.002   HIS A 125 
 PHE   0.010   0.001   PHE B 304 
 TYR   0.008   0.001   TYR A 146 
 ARG   0.004   0.001   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02892 (  400)
  hydrogen bonds       : angle       4.24944 ( 1176)
  covalent geometry    : bond        0.00275 (10332)
  covalent geometry    : angle       0.48706 (14064)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 174
  time to evaluate  : 1.040 
Fit side-chains
REVERT: A   39 ARG cc_start: 0.7765 (mtt90) cc_final: 0.7132 (mpt-90)
REVERT: A   71 ASN cc_start: 0.7909 (t0) cc_final: 0.7458 (m-40)
REVERT: A   89 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7405 (mmtp)
REVERT: A  120 GLU cc_start: 0.8002 (tt0) cc_final: 0.7508 (mp0)
REVERT: A  229 THR cc_start: 0.8292 (m) cc_final: 0.8052 (m)
REVERT: A  289 LYS cc_start: 0.8332 (ttpt) cc_final: 0.7904 (ttmm)
REVERT: A  315 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8257 (tttt)
REVERT: B   39 ARG cc_start: 0.7783 (mtt90) cc_final: 0.7130 (mpt-90)
REVERT: B   71 ASN cc_start: 0.7900 (t0) cc_final: 0.7449 (m-40)
REVERT: B   89 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7403 (mmtp)
REVERT: B  120 GLU cc_start: 0.7992 (tt0) cc_final: 0.7499 (mp0)
REVERT: B  229 THR cc_start: 0.8301 (m) cc_final: 0.8065 (m)
REVERT: B  289 LYS cc_start: 0.8338 (ttpt) cc_final: 0.7903 (ttmm)
REVERT: B  315 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8240 (tttt)
REVERT: C   39 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7142 (mpt-90)
REVERT: C   71 ASN cc_start: 0.7897 (t0) cc_final: 0.7449 (m-40)
REVERT: C   89 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7405 (mmtp)
REVERT: C  120 GLU cc_start: 0.8014 (tt0) cc_final: 0.7506 (mp0)
REVERT: C  229 THR cc_start: 0.8284 (m) cc_final: 0.8044 (m)
REVERT: C  289 LYS cc_start: 0.8349 (ttpt) cc_final: 0.7919 (ttmm)
REVERT: D   39 ARG cc_start: 0.7771 (mtt90) cc_final: 0.7135 (mpt-90)
REVERT: D   71 ASN cc_start: 0.7933 (t0) cc_final: 0.7479 (m-40)
REVERT: D   89 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7399 (mmtp)
REVERT: D  120 GLU cc_start: 0.8012 (tt0) cc_final: 0.7513 (mp0)
REVERT: D  229 THR cc_start: 0.8288 (m) cc_final: 0.8048 (m)
REVERT: D  289 LYS cc_start: 0.8340 (ttpt) cc_final: 0.7919 (ttmm)
REVERT: D  315 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8257 (tttt)
  outliers start: 40
  outliers final: 24
  residues processed: 194
  average time/residue: 1.1941
  time to fit residues: 249.7070
Evaluate side-chains
  201 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 170
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   89 LYS
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  315 LYS
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain B residue  193 THR
Chi-restraints excluded: chain B residue  315 LYS
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain C residue   37 MET
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   89 LYS
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain D residue   37 MET
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   89 LYS
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  191 MET
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  315 LYS
Chi-restraints excluded: chain D residue  342 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 102 optimal weight:    4.9990
   chunk 112 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 126 optimal weight:    7.9990
   chunk 44 optimal weight:    0.5980
   chunk 106 optimal weight:    0.7980
   chunk 114 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 130 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   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  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 107 GLN
A 201 GLN
B  48 ASN
B 107 GLN
B 201 GLN
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 GLN
C 201 GLN
D  48 ASN
D 107 GLN
D 201 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.111230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.096059 restraints weight = 12139.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 1.75
r_work: 0.2915 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.3209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10332  Z= 0.127
  Angle     :  0.505   6.922  14064  Z= 0.263
  Chirality :  0.045   0.144   1640
  Planarity :  0.003   0.035   1792
  Dihedral  :  8.440  86.271   1644
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.69 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 19.89 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.24), residues: 1340
  helix:  1.18 (0.27), residues: 396
  sheet: -1.07 (0.30), residues: 292
  loop :  0.66 (0.27), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 101 
 HIS   0.003   0.002   HIS A  67 
 PHE   0.010   0.002   PHE C 304 
 TYR   0.008   0.001   TYR C 146 
 ARG   0.003   0.001   ARG C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02975 (  400)
  hydrogen bonds       : angle       4.31213 ( 1176)
  covalent geometry    : bond        0.00308 (10332)
  covalent geometry    : angle       0.50471 (14064)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 172
  time to evaluate  : 1.991 
Fit side-chains
REVERT: A   39 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7258 (mpt-90)
REVERT: A   71 ASN cc_start: 0.7922 (t0) cc_final: 0.7501 (m-40)
REVERT: A   89 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7405 (mmtp)
REVERT: A  119 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7329 (tp30)
REVERT: A  120 GLU cc_start: 0.8023 (tt0) cc_final: 0.7631 (mp0)
REVERT: A  229 THR cc_start: 0.8335 (m) cc_final: 0.8090 (m)
REVERT: A  289 LYS cc_start: 0.8337 (ttpt) cc_final: 0.7980 (ttmm)
REVERT: A  315 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8317 (tttt)
REVERT: B   39 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7254 (mpt-90)
REVERT: B   71 ASN cc_start: 0.7912 (t0) cc_final: 0.7490 (m-40)
REVERT: B   89 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7425 (mmtp)
REVERT: B  119 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7312 (tp30)
REVERT: B  120 GLU cc_start: 0.7997 (tt0) cc_final: 0.7628 (mp0)
REVERT: B  229 THR cc_start: 0.8334 (m) cc_final: 0.8095 (m)
REVERT: B  289 LYS cc_start: 0.8346 (ttpt) cc_final: 0.7982 (ttmm)
REVERT: C   39 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7258 (mpt-90)
REVERT: C   71 ASN cc_start: 0.7902 (t0) cc_final: 0.7484 (m-40)
REVERT: C   89 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7446 (mmtp)
REVERT: C  119 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7321 (tp30)
REVERT: C  120 GLU cc_start: 0.8029 (tt0) cc_final: 0.7626 (mp0)
REVERT: C  229 THR cc_start: 0.8331 (m) cc_final: 0.8088 (m)
REVERT: C  289 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7987 (ttmm)
REVERT: D   39 ARG cc_start: 0.7849 (mtt90) cc_final: 0.7250 (mpt-90)
REVERT: D   71 ASN cc_start: 0.7944 (t0) cc_final: 0.7518 (m-40)
REVERT: D   89 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7432 (mmtp)
REVERT: D  119 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7309 (tp30)
REVERT: D  120 GLU cc_start: 0.8012 (tt0) cc_final: 0.7630 (mp0)
REVERT: D  229 THR cc_start: 0.8329 (m) cc_final: 0.8084 (m)
REVERT: D  289 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7982 (ttmm)
REVERT: D  315 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8321 (tttt)
  outliers start: 41
  outliers final: 24
  residues processed: 193
  average time/residue: 1.2537
  time to fit residues: 262.6240
Evaluate side-chains
  198 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 168
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   89 LYS
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  315 LYS
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain B residue  193 THR
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain C residue   37 MET
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   89 LYS
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain D residue   37 MET
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   89 LYS
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  191 MET
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  315 LYS
Chi-restraints excluded: chain D residue  342 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 84 optimal weight:    7.9990
   chunk 104 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 86 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 107 GLN
A 201 GLN
** B  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 GLN
B 201 GLN
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 GLN
C 201 GLN
** D  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 107 GLN
D 201 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.109258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.093469 restraints weight = 12139.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 1.78
r_work: 0.2876 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  10332  Z= 0.216
  Angle     :  0.575   7.850  14064  Z= 0.299
  Chirality :  0.048   0.145   1640
  Planarity :  0.004   0.037   1792
  Dihedral  :  8.876  87.839   1644
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.21 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 21.00 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.24), residues: 1340
  helix:  0.53 (0.26), residues: 420
  sheet: -1.19 (0.31), residues: 280
  loop :  0.30 (0.26), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 331 
 HIS   0.003   0.001   HIS D  67 
 PHE   0.013   0.002   PHE C 304 
 TYR   0.014   0.002   TYR D 146 
 ARG   0.004   0.001   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03457 (  400)
  hydrogen bonds       : angle       4.76141 ( 1176)
  covalent geometry    : bond        0.00520 (10332)
  covalent geometry    : angle       0.57504 (14064)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 166
  time to evaluate  : 1.461 
Fit side-chains
REVERT: A   71 ASN cc_start: 0.7969 (t0) cc_final: 0.7518 (m-40)
REVERT: A   89 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7416 (mmtp)
REVERT: A  120 GLU cc_start: 0.7934 (tt0) cc_final: 0.7524 (mp0)
REVERT: A  229 THR cc_start: 0.8450 (m) cc_final: 0.8183 (m)
REVERT: A  289 LYS cc_start: 0.8387 (ttpt) cc_final: 0.7992 (ttmm)
REVERT: A  315 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8408 (tptt)
REVERT: B   71 ASN cc_start: 0.7962 (t0) cc_final: 0.7512 (m-40)
REVERT: B   89 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7424 (mmtp)
REVERT: B  120 GLU cc_start: 0.7934 (tt0) cc_final: 0.7583 (mp0)
REVERT: B  229 THR cc_start: 0.8453 (m) cc_final: 0.8191 (m)
REVERT: B  289 LYS cc_start: 0.8381 (ttpt) cc_final: 0.7984 (ttmm)
REVERT: C   71 ASN cc_start: 0.7968 (t0) cc_final: 0.7514 (m-40)
REVERT: C   89 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7433 (mmtp)
REVERT: C  120 GLU cc_start: 0.7909 (tt0) cc_final: 0.7525 (mp0)
REVERT: C  229 THR cc_start: 0.8443 (m) cc_final: 0.8179 (m)
REVERT: C  289 LYS cc_start: 0.8387 (ttpt) cc_final: 0.8001 (ttmm)
REVERT: D   71 ASN cc_start: 0.7974 (t0) cc_final: 0.7519 (m-40)
REVERT: D   89 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7420 (mmtp)
REVERT: D  120 GLU cc_start: 0.7892 (tt0) cc_final: 0.7571 (mp0)
REVERT: D  229 THR cc_start: 0.8436 (m) cc_final: 0.8166 (m)
REVERT: D  289 LYS cc_start: 0.8381 (ttpt) cc_final: 0.7997 (ttmm)
REVERT: D  315 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8403 (tptt)
  outliers start: 34
  outliers final: 24
  residues processed: 184
  average time/residue: 1.2914
  time to fit residues: 254.8402
Evaluate side-chains
  199 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 169
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   89 LYS
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  315 LYS
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain B residue  193 THR
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain C residue   37 MET
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   89 LYS
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain D residue   37 MET
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   89 LYS
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  191 MET
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  315 LYS
Chi-restraints excluded: chain D residue  342 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 88 optimal weight:    0.0770
   chunk 46 optimal weight:    0.2980
   chunk 72 optimal weight:    0.9980
   chunk 110 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 87 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 107 GLN
A 201 GLN
** B  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 GLN
B 201 GLN
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 GLN
C 201 GLN
** D  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 107 GLN
D 201 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.112397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.096969 restraints weight = 12012.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 1.77
r_work: 0.2936 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2794 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10332  Z= 0.102
  Angle     :  0.508   6.771  14064  Z= 0.265
  Chirality :  0.045   0.146   1640
  Planarity :  0.004   0.035   1792
  Dihedral  :  8.492  87.780   1644
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.39 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.00 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.24), residues: 1340
  helix:  0.90 (0.26), residues: 424
  sheet: -1.11 (0.30), residues: 292
  loop :  0.36 (0.27), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 101 
 HIS   0.005   0.002   HIS B 125 
 PHE   0.010   0.001   PHE A 304 
 TYR   0.008   0.001   TYR B 338 
 ARG   0.002   0.000   ARG D 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02832 (  400)
  hydrogen bonds       : angle       4.29330 ( 1176)
  covalent geometry    : bond        0.00249 (10332)
  covalent geometry    : angle       0.50834 (14064)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 173
  time to evaluate  : 1.127 
Fit side-chains
REVERT: A   71 ASN cc_start: 0.7979 (t0) cc_final: 0.7558 (m-40)
REVERT: A   89 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7518 (mmtp)
REVERT: A  119 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7354 (tp30)
REVERT: A  120 GLU cc_start: 0.7957 (tt0) cc_final: 0.7620 (mp0)
REVERT: A  229 THR cc_start: 0.8292 (m) cc_final: 0.8035 (m)
REVERT: A  289 LYS cc_start: 0.8284 (ttpt) cc_final: 0.7935 (ttmm)
REVERT: B   71 ASN cc_start: 0.7975 (t0) cc_final: 0.7548 (m-40)
REVERT: B   89 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7529 (mmtp)
REVERT: B  119 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7389 (tp30)
REVERT: B  120 GLU cc_start: 0.7923 (tt0) cc_final: 0.7612 (mp0)
REVERT: B  229 THR cc_start: 0.8290 (m) cc_final: 0.8036 (m)
REVERT: B  289 LYS cc_start: 0.8287 (ttpt) cc_final: 0.7944 (ttmm)
REVERT: C   71 ASN cc_start: 0.7968 (t0) cc_final: 0.7543 (m-40)
REVERT: C   89 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7532 (mmtp)
REVERT: C  119 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7354 (tp30)
REVERT: C  120 GLU cc_start: 0.7901 (tt0) cc_final: 0.7611 (mp0)
REVERT: C  229 THR cc_start: 0.8298 (m) cc_final: 0.8046 (m)
REVERT: C  289 LYS cc_start: 0.8291 (ttpt) cc_final: 0.7951 (ttmm)
REVERT: D   71 ASN cc_start: 0.7993 (t0) cc_final: 0.7565 (m-40)
REVERT: D   89 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7529 (mmtp)
REVERT: D  119 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7336 (tp30)
REVERT: D  120 GLU cc_start: 0.7878 (tt0) cc_final: 0.7599 (mp0)
REVERT: D  229 THR cc_start: 0.8285 (m) cc_final: 0.8027 (m)
REVERT: D  289 LYS cc_start: 0.8286 (ttpt) cc_final: 0.7952 (ttmm)
  outliers start: 30
  outliers final: 20
  residues processed: 186
  average time/residue: 1.2971
  time to fit residues: 260.1467
Evaluate side-chains
  198 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 174
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   89 LYS
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  191 MET
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain B residue  193 THR
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain C residue   37 MET
Chi-restraints excluded: chain C residue   89 LYS
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain D residue   37 MET
Chi-restraints excluded: chain D residue   89 LYS
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  191 MET
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  342 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 117 optimal weight:    0.7980
   chunk 11 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 126 optimal weight:    0.0030
   chunk 76 optimal weight:    0.9990
   chunk 115 optimal weight:    0.4980
   chunk 86 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.4590

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 107 GLN
** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 GLN
** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 GLN
** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 107 GLN
** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.113866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.098053 restraints weight = 11989.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 1.84
r_work: 0.2945 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10332  Z= 0.096
  Angle     :  0.487   5.957  14064  Z= 0.254
  Chirality :  0.045   0.146   1640
  Planarity :  0.003   0.034   1792
  Dihedral  :  8.253  87.401   1644
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.39 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.28 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.24), residues: 1340
  helix:  1.06 (0.27), residues: 424
  sheet: -1.04 (0.30), residues: 292
  loop :  0.43 (0.27), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 101 
 HIS   0.003   0.001   HIS B 125 
 PHE   0.010   0.001   PHE C 325 
 TYR   0.007   0.001   TYR C 338 
 ARG   0.002   0.000   ARG B 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02728 (  400)
  hydrogen bonds       : angle       4.14048 ( 1176)
  covalent geometry    : bond        0.00234 (10332)
  covalent geometry    : angle       0.48657 (14064)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7290.69 seconds
wall clock time: 128 minutes 20.52 seconds (7700.52 seconds total)