Starting phenix.real_space_refine
on Thu Sep 18 13:43:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tj2_25915/09_2025/7tj2_25915.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tj2_25915/09_2025/7tj2_25915.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tj2_25915/09_2025/7tj2_25915.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tj2_25915/09_2025/7tj2_25915.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tj2_25915/09_2025/7tj2_25915.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tj2_25915/09_2025/7tj2_25915.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.107
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      62      5.49       5
     S      57      5.16       5
     C   10718      2.51       5
     N    2788      2.21       5
     O    3458      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17083
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2733
          Classifications: {'peptide': 348}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 333}
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 2731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 2731
          Classifications: {'peptide': 347}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 332}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 2734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 2734
          Classifications: {'peptide': 347}
          Link IDs: {'PTRANS': 14, 'TRANS': 332}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 2108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2108
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 257}
          Chain breaks: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 2731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 2731
          Classifications: {'peptide': 347}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 332}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 2731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 2731
          Classifications: {'peptide': 347}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 332}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 664
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 664
          Classifications: {'RNA': 31}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 18, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 1, 'rna3p': 29}
    Chain: "H"
      Number of atoms: 651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 651
          Classifications: {'RNA': 31}
          Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 18}
          Link IDs: {'rna3p': 30}
  Time building chain proxies: 4.75, per 1000 atoms: 0.28
  Number of scatterers: 17083
  At special positions: 0
  Unit cell: (119.087, 121.835, 134.659, 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      57     16.00
     P      62     15.00
     O    3458      8.00
     N    2788      7.00
     C   10718      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.62
  Conformation dependent library (CDL) restraints added in 701.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3746

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 42 sheets defined
      25.2% alpha, 23.6% beta
      30 base pairs and 34 stacking pairs defined.
    Time for finding SS restraints: 1.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 14
    Processing helix  chain 'A' and resid 51 through 61
    Processing helix  chain 'A' and resid 69 through 77
    Processing helix  chain 'A' and resid 130 through 138
    Processing helix  chain 'A' and resid 208 through 217
    Processing helix  chain 'A' and resid 218 through 226
    Processing helix  chain 'A' and resid 232 through 237
    Processing helix  chain 'A' and resid 251 through 262
    Processing helix  chain 'A' and resid 299 through 308
    Processing helix  chain 'B' and resid 2 through 14
    Processing helix  chain 'B' and resid 51 through 61
    Processing helix  chain 'B' and resid 69 through 77
    Processing helix  chain 'B' and resid 130 through 138
    Processing helix  chain 'B' and resid 208 through 217
    Processing helix  chain 'B' and resid 218 through 227
    Processing helix  chain 'B' and resid 232 through 237
    Processing helix  chain 'B' and resid 251 through 262
    Processing helix  chain 'B' and resid 299 through 309
    Processing helix  chain 'C' and resid 2 through 14
    Processing helix  chain 'C' and resid 51 through 61
    Processing helix  chain 'C' and resid 69 through 77
    Processing helix  chain 'C' and resid 130 through 138
    Processing helix  chain 'C' and resid 208 through 217
    Processing helix  chain 'C' and resid 218 through 227
    Processing helix  chain 'C' and resid 232 through 237
      removed outlier: 3.750A  pdb=" N   VAL C 237 " --> pdb=" O   PHE C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 251 through 262
    Processing helix  chain 'C' and resid 299 through 308
    Processing helix  chain 'D' and resid 2 through 14
    Processing helix  chain 'D' and resid 51 through 61
    Processing helix  chain 'D' and resid 69 through 77
    Processing helix  chain 'D' and resid 130 through 138
    Processing helix  chain 'D' and resid 251 through 262
    Processing helix  chain 'E' and resid 2 through 14
    Processing helix  chain 'E' and resid 51 through 61
    Processing helix  chain 'E' and resid 69 through 77
    Processing helix  chain 'E' and resid 130 through 138
    Processing helix  chain 'E' and resid 208 through 217
    Processing helix  chain 'E' and resid 218 through 227
    Processing helix  chain 'E' and resid 232 through 237
      removed outlier: 3.752A  pdb=" N   VAL E 237 " --> pdb=" O   PHE E 233 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 251 through 262
    Processing helix  chain 'E' and resid 299 through 309
    Processing helix  chain 'F' and resid 2 through 14
    Processing helix  chain 'F' and resid 51 through 61
    Processing helix  chain 'F' and resid 69 through 77
    Processing helix  chain 'F' and resid 130 through 138
    Processing helix  chain 'F' and resid 208 through 217
    Processing helix  chain 'F' and resid 218 through 227
    Processing helix  chain 'F' and resid 232 through 237
      removed outlier: 3.776A  pdb=" N   VAL F 237 " --> pdb=" O   PHE F 233 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 251 through 262
    Processing helix  chain 'F' and resid 299 through 308
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28
      removed outlier: 6.658A  pdb=" N   VAL A  32 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81
      removed outlier: 7.238A  pdb=" N   ILE A  80 " --> pdb=" O   PHE A 123 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER A 155 " --> pdb=" O   TYR A 179 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81
      removed outlier: 7.238A  pdb=" N   ILE A  80 " --> pdb=" O   PHE A 123 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LYS A 181 " --> pdb=" O   GLN A 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88
    Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 163
    Processing sheet with id=AA6, first strand: chain 'A' and resid 264 through 267
      removed outlier: 5.080A  pdb=" N   ILE A 281 " --> pdb=" O   CYS A 291 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   CYS A 291 " --> pdb=" O   ILE A 281 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ASP A 283 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   SER A 289 " --> pdb=" O   ASP A 283 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 316 through 323
      removed outlier: 4.825A  pdb=" N   SER A 329 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   TYR A 343 " --> pdb=" O   MET A 331 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   LYS A 335 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   VAL A 339 " --> pdb=" O   LYS A 335 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 28
      removed outlier: 6.658A  pdb=" N   VAL B  32 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 80 through 81
      removed outlier: 7.237A  pdb=" N   ILE B  80 " --> pdb=" O   PHE B 123 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER B 155 " --> pdb=" O   TYR B 179 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81
      removed outlier: 7.237A  pdb=" N   ILE B  80 " --> pdb=" O   PHE B 123 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LYS B 181 " --> pdb=" O   GLN B 188 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 87 through 88
    Processing sheet with id=AB3, first strand: chain 'B' and resid 161 through 163
    Processing sheet with id=AB4, first strand: chain 'B' and resid 264 through 267
      removed outlier: 5.080A  pdb=" N   ILE B 281 " --> pdb=" O   CYS B 291 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   CYS B 291 " --> pdb=" O   ILE B 281 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ASP B 283 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
      removed outlier: 5.629A  pdb=" N   SER B 289 " --> pdb=" O   ASP B 283 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 316 through 323
    Processing sheet with id=AB6, first strand: chain 'C' and resid 25 through 28
      removed outlier: 6.658A  pdb=" N   VAL C  32 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 80 through 81
      removed outlier: 7.238A  pdb=" N   ILE C  80 " --> pdb=" O   PHE C 123 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER C 155 " --> pdb=" O   TYR C 179 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 80 through 81
      removed outlier: 7.238A  pdb=" N   ILE C  80 " --> pdb=" O   PHE C 123 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   LYS C 181 " --> pdb=" O   GLN C 188 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 87 through 88
    Processing sheet with id=AC1, first strand: chain 'C' and resid 161 through 163
    Processing sheet with id=AC2, first strand: chain 'C' and resid 264 through 267
      removed outlier: 5.080A  pdb=" N   ILE C 281 " --> pdb=" O   CYS C 291 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   CYS C 291 " --> pdb=" O   ILE C 281 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ASP C 283 " --> pdb=" O   SER C 289 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   SER C 289 " --> pdb=" O   ASP C 283 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 316 through 323
      removed outlier: 5.239A  pdb=" N   LYS C 335 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   VAL C 339 " --> pdb=" O   LYS C 335 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 25 through 28
      removed outlier: 6.659A  pdb=" N   VAL D  32 " --> pdb=" O   LEU D  43 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 80 through 81
      removed outlier: 7.238A  pdb=" N   ILE D  80 " --> pdb=" O   PHE D 123 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER D 155 " --> pdb=" O   TYR D 179 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 80 through 81
      removed outlier: 7.238A  pdb=" N   ILE D  80 " --> pdb=" O   PHE D 123 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LYS D 181 " --> pdb=" O   GLN D 188 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 87 through 88
    Processing sheet with id=AC8, first strand: chain 'D' and resid 161 through 163
    Processing sheet with id=AC9, first strand: chain 'D' and resid 264 through 267
      removed outlier: 5.080A  pdb=" N   ILE D 281 " --> pdb=" O   CYS D 291 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   CYS D 291 " --> pdb=" O   ILE D 281 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ASP D 283 " --> pdb=" O   SER D 289 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   SER D 289 " --> pdb=" O   ASP D 283 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'D' and resid 320 through 323
    Processing sheet with id=AD2, first strand: chain 'E' and resid 25 through 28
      removed outlier: 6.659A  pdb=" N   VAL E  32 " --> pdb=" O   LEU E  43 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'E' and resid 80 through 81
      removed outlier: 7.238A  pdb=" N   ILE E  80 " --> pdb=" O   PHE E 123 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER E 155 " --> pdb=" O   TYR E 179 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'E' and resid 80 through 81
      removed outlier: 7.238A  pdb=" N   ILE E  80 " --> pdb=" O   PHE E 123 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LYS E 181 " --> pdb=" O   GLN E 188 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'E' and resid 87 through 88
    Processing sheet with id=AD6, first strand: chain 'E' and resid 161 through 163
    Processing sheet with id=AD7, first strand: chain 'E' and resid 264 through 267
      removed outlier: 5.080A  pdb=" N   ILE E 281 " --> pdb=" O   CYS E 291 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   CYS E 291 " --> pdb=" O   ILE E 281 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ASP E 283 " --> pdb=" O   SER E 289 " (cutoff:3.500A)
      removed outlier: 5.629A  pdb=" N   SER E 289 " --> pdb=" O   ASP E 283 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'E' and resid 316 through 323
    Processing sheet with id=AD9, first strand: chain 'F' and resid 25 through 28
      removed outlier: 6.658A  pdb=" N   VAL F  32 " --> pdb=" O   LEU F  43 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'F' and resid 80 through 81
      removed outlier: 7.238A  pdb=" N   ILE F  80 " --> pdb=" O   PHE F 123 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER F 155 " --> pdb=" O   TYR F 179 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'F' and resid 80 through 81
      removed outlier: 7.238A  pdb=" N   ILE F  80 " --> pdb=" O   PHE F 123 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LYS F 181 " --> pdb=" O   GLN F 188 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'F' and resid 87 through 88
    Processing sheet with id=AE4, first strand: chain 'F' and resid 161 through 163
    Processing sheet with id=AE5, first strand: chain 'F' and resid 264 through 267
      removed outlier: 5.080A  pdb=" N   ILE F 281 " --> pdb=" O   CYS F 291 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   CYS F 291 " --> pdb=" O   ILE F 281 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ASP F 283 " --> pdb=" O   SER F 289 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   SER F 289 " --> pdb=" O   ASP F 283 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'F' and resid 316 through 323

    636 hydrogen bonds defined for protein.
    1683 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      73 hydrogen bonds
      146 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      34 stacking parallelities
  Total time for adding SS restraints: 2.97

  Time building geometry restraints manager: 2.17 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: 5248
        1.34 -     1.45: 2661
        1.45 -     1.57: 9439
        1.57 -     1.69: 122
        1.69 -     1.81: 85
  Bond restraints: 17555
  Sorted by residual:
  bond pdb=" C   ALA E 118 "
       pdb=" N   PRO E 119 "
    ideal  model  delta    sigma   weight residual
    1.339  1.375 -0.036 3.40e-02 8.65e+02 1.12e+00
  bond pdb=" C   ALA B 118 "
       pdb=" N   PRO B 119 "
    ideal  model  delta    sigma   weight residual
    1.339  1.375 -0.036 3.40e-02 8.65e+02 1.10e+00
  bond pdb=" C   ALA D 118 "
       pdb=" N   PRO D 119 "
    ideal  model  delta    sigma   weight residual
    1.339  1.375 -0.035 3.40e-02 8.65e+02 1.08e+00
  bond pdb=" C   ALA A 118 "
       pdb=" N   PRO A 119 "
    ideal  model  delta    sigma   weight residual
    1.339  1.374 -0.035 3.40e-02 8.65e+02 1.07e+00
  bond pdb=" C   ALA C 118 "
       pdb=" N   PRO C 119 "
    ideal  model  delta    sigma   weight residual
    1.339  1.374 -0.035 3.40e-02 8.65e+02 1.07e+00
  ... (remaining 17550 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.12: 23723
        1.12 -     2.24: 271
        2.24 -     3.35: 104
        3.35 -     4.47: 9
        4.47 -     5.59: 1
  Bond angle restraints: 24108
  Sorted by residual:
  angle pdb=" C   THR F  49 "
        pdb=" N   LEU F  50 "
        pdb=" CA  LEU F  50 "
      ideal   model   delta    sigma   weight residual
     121.48  124.92   -3.44 2.04e+00 2.40e-01 2.84e+00
  angle pdb=" C   GLN F 310 "
        pdb=" N   ASP F 311 "
        pdb=" CA  ASP F 311 "
      ideal   model   delta    sigma   weight residual
     121.54  124.60   -3.06 1.91e+00 2.74e-01 2.56e+00
  angle pdb=" C   GLN C 310 "
        pdb=" N   ASP C 311 "
        pdb=" CA  ASP C 311 "
      ideal   model   delta    sigma   weight residual
     121.54  124.39   -2.85 1.91e+00 2.74e-01 2.22e+00
  angle pdb=" C2'   G G   8 "
        pdb=" C1'   G G   8 "
        pdb=" N9    G G   8 "
      ideal   model   delta    sigma   weight residual
     112.00  114.13   -2.13 1.50e+00 4.44e-01 2.02e+00
  angle pdb=" C   GLN E 310 "
        pdb=" N   ASP E 311 "
        pdb=" CA  ASP E 311 "
      ideal   model   delta    sigma   weight residual
     121.54  124.20   -2.66 1.91e+00 2.74e-01 1.94e+00
  ... (remaining 24103 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.04: 10137
       18.04 -    36.09: 276
       36.09 -    54.13: 69
       54.13 -    72.18: 71
       72.18 -    90.22: 16
  Dihedral angle restraints: 10569
    sinusoidal: 4762
      harmonic: 5807
  Sorted by residual:
  dihedral pdb=" CA  CYS F 334 "
           pdb=" C   CYS F 334 "
           pdb=" N   LYS F 335 "
           pdb=" CA  LYS F 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.35   15.65     0      5.00e+00 4.00e-02 9.79e+00
  dihedral pdb=" O5'   U H  31 "
           pdb=" C5'   U H  31 "
           pdb=" C4'   U H  31 "
           pdb=" C3'   U H  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.00  113.85  -58.85     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" N   GLN B 310 "
           pdb=" CA  GLN B 310 "
           pdb=" CB  GLN B 310 "
           pdb=" CG  GLN B 310 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -121.71  -58.29     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 10566 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1703
       0.026 -    0.052: 629
       0.052 -    0.078: 254
       0.078 -    0.103: 124
       0.103 -    0.129: 114
  Chirality restraints: 2824
  Sorted by residual:
  chirality pdb=" CA  ILE C  80 "
            pdb=" N   ILE C  80 "
            pdb=" C   ILE C  80 "
            pdb=" CB  ILE C  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.17e-01
  chirality pdb=" CA  ILE F  80 "
            pdb=" N   ILE F  80 "
            pdb=" C   ILE F  80 "
            pdb=" CB  ILE F  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  ILE E  80 "
            pdb=" N   ILE E  80 "
            pdb=" C   ILE E  80 "
            pdb=" CB  ILE E  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  ... (remaining 2821 not shown)

  Planarity restraints: 2873
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 334 "   -0.006 2.00e-02 2.50e+03   1.17e-02 1.37e+00
        pdb=" C   CYS B 334 "    0.020 2.00e-02 2.50e+03
        pdb=" O   CYS B 334 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LYS B 335 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D  50 "    0.018 5.00e-02 4.00e+02   2.73e-02 1.20e+00
        pdb=" N   PRO D  51 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO D  51 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO D  51 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  50 "   -0.018 5.00e-02 4.00e+02   2.72e-02 1.19e+00
        pdb=" N   PRO B  51 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO B  51 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B  51 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 2870 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1067
        2.74 -     3.28: 15965
        3.28 -     3.82: 28253
        3.82 -     4.36: 34467
        4.36 -     4.90: 58658
  Nonbonded interactions: 138410
  Sorted by model distance:
  nonbonded pdb=" O   GLY B  77 "
            pdb=" OG1 THR B 121 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   GLY C  77 "
            pdb=" OG1 THR C 121 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   GLY E  77 "
            pdb=" OG1 THR E 121 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   GLY A  77 "
            pdb=" OG1 THR A 121 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   GLY F  77 "
            pdb=" OG1 THR F 121 "
     model   vdw
     2.196 3.040
  ... (remaining 138405 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid -1 through 345)
  selection = chain 'B'
  selection = (chain 'C' and (resid -1 through 0 or (resid 1 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 2 through 345))
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.560
  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:             0.020
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.240
  Find NCS groups from input model:        0.290
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
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      :  0.002   0.036  17555  Z= 0.075
  Angle     :  0.370   5.591  24108  Z= 0.191
  Chirality :  0.041   0.129   2824
  Planarity :  0.003   0.027   2873
  Dihedral  : 11.301  90.221   6823
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  2.37 %
    Favored  : 95.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.20), residues: 1990
  helix:  1.26 (0.24), residues: 492
  sheet:  0.55 (0.33), residues: 316
  loop : -0.48 (0.18), residues: 1182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 199 
 TYR   0.006   0.001   TYR A 226 
 PHE   0.006   0.001   PHE A 342 
 TRP   0.004   0.001   TRP C  87 
 HIS   0.001   0.000   HIS F 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00171 (17555)
  covalent geometry    : angle       0.37004 (24108)
  hydrogen bonds       : bond        0.19934 (  655)
  hydrogen bonds       : angle       8.24035 ( 1829)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  418 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 389
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.8597 (mttt) cc_final: 0.8350 (mmtm)
REVERT: A  267 GLU cc_start: 0.7933 (tt0) cc_final: 0.7638 (tm-30)
REVERT: B   47 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8212 (mmtp)
REVERT: B  105 MET cc_start: 0.8115 (mmm) cc_final: 0.7368 (mpp)
REVERT: B  107 ASP cc_start: 0.7999 (m-30) cc_final: 0.7724 (m-30)
REVERT: B  343 TYR cc_start: 0.8254 (p90) cc_final: 0.7959 (p90)
REVERT: C   40 ASP cc_start: 0.8115 (m-30) cc_final: 0.7515 (m-30)
REVERT: C  150 LYS cc_start: 0.8070 (mttt) cc_final: 0.7651 (mmtm)
REVERT: C  153 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7777 (mm-40)
REVERT: C  166 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8182 (m)
REVERT: D   19 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6789 (mm-40)
REVERT: D  105 MET cc_start: 0.7242 (mmm) cc_final: 0.6931 (mpp)
REVERT: D  107 ASP cc_start: 0.7880 (m-30) cc_final: 0.6838 (p0)
REVERT: E  245 GLN cc_start: 0.5823 (mt0) cc_final: 0.5061 (pp30)
REVERT: E  252 LEU cc_start: 0.7821 (tp) cc_final: 0.7544 (tp)
REVERT: F  107 ASP cc_start: 0.8291 (m-30) cc_final: 0.8025 (m-30)
REVERT: F  168 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7892 (pp)
REVERT: F  305 GLU cc_start: 0.7592 (tt0) cc_final: 0.7360 (mt-10)
REVERT: F  308 LYS cc_start: 0.7097 (mttt) cc_final: 0.6499 (ptmm)
  outliers start: 29
  outliers final: 10
  residues processed: 409
  average time/residue: 0.1325
  time to fit residues: 80.8361
Evaluate side-chains
  232 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 220
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue  338 HIS
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   49 THR
Chi-restraints excluded: chain E residue  301 ASP
Chi-restraints excluded: chain F residue  168 LEU
Chi-restraints excluded: chain F residue  301 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 194 optimal weight:    6.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 200 optimal weight:   30.0000
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    6.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  29 ASN
A 310 GLN
B  29 ASN
B  30 ASN
B  83 ASN
B 140 ASN
B 176 GLN
D  30 ASN
D  83 ASN
E  29 ASN
E  30 ASN
F  29 ASN
F  30 ASN
F  75 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.203465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.130582 restraints weight = 19170.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.17
r_work: 0.3242 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  17555  Z= 0.212
  Angle     :  0.552   9.871  24108  Z= 0.292
  Chirality :  0.046   0.365   2824
  Planarity :  0.004   0.065   2873
  Dihedral  : 12.737  91.910   3070
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  :  8.65 %
    Favored  : 88.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.19), residues: 1990
  helix:  0.78 (0.24), residues: 509
  sheet:  0.52 (0.30), residues: 348
  loop : -0.49 (0.18), residues: 1133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 258 
 TYR   0.014   0.001   TYR F 226 
 PHE   0.017   0.002   PHE E 269 
 TRP   0.012   0.002   TRP C  87 
 HIS   0.004   0.001   HIS E  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 (17555)
  covalent geometry    : angle       0.55186 (24108)
  hydrogen bonds       : bond        0.04344 (  655)
  hydrogen bonds       : angle       5.67726 ( 1829)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 219
  time to evaluate  : 0.634 
Fit side-chains
REVERT: A   47 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8340 (mmtm)
REVERT: A  110 LYS cc_start: 0.9114 (mttt) cc_final: 0.8537 (mmtm)
REVERT: A  265 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7634 (mt-10)
REVERT: B  105 MET cc_start: 0.8529 (mmm) cc_final: 0.7392 (mpp)
REVERT: B  209 GLN cc_start: 0.7839 (tp40) cc_final: 0.7412 (pp30)
REVERT: B  213 ASP cc_start: 0.8011 (m-30) cc_final: 0.7574 (m-30)
REVERT: B  331 MET cc_start: 0.6933 (mmm) cc_final: 0.6386 (mmm)
REVERT: B  343 TYR cc_start: 0.8214 (p90) cc_final: 0.7705 (p90)
REVERT: C   75 ASN cc_start: 0.8815 (m-40) cc_final: 0.8602 (m-40)
REVERT: C  150 LYS cc_start: 0.8359 (mttt) cc_final: 0.7865 (mmtm)
REVERT: C  166 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7895 (m)
REVERT: D  105 MET cc_start: 0.7442 (mmm) cc_final: 0.6926 (mpt)
REVERT: D  194 TYR cc_start: 0.7229 (m-80) cc_final: 0.6798 (m-80)
REVERT: E  245 GLN cc_start: 0.5760 (mt0) cc_final: 0.4930 (pp30)
REVERT: F  194 TYR cc_start: 0.8377 (m-80) cc_final: 0.8122 (m-80)
REVERT: F  195 PHE cc_start: 0.8061 (m-80) cc_final: 0.7859 (m-10)
REVERT: F  273 ASP cc_start: 0.7843 (t70) cc_final: 0.7607 (t70)
REVERT: F  300 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7455 (mp)
REVERT: F  305 GLU cc_start: 0.7844 (tt0) cc_final: 0.7393 (mt-10)
REVERT: F  308 LYS cc_start: 0.7143 (mttt) cc_final: 0.6703 (ptmm)
  outliers start: 55
  outliers final: 33
  residues processed: 259
  average time/residue: 0.1291
  time to fit residues: 50.8731
Evaluate side-chains
  219 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 184
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  220 ASP
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  193 THR
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain B residue  338 HIS
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain D residue   31 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   49 THR
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  276 VAL
Chi-restraints excluded: chain E residue  282 THR
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  113 THR
Chi-restraints excluded: chain F residue  281 ILE
Chi-restraints excluded: chain F residue  282 THR
Chi-restraints excluded: chain F residue  300 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 178 optimal weight:   30.0000
   chunk 138 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 154 optimal weight:    9.9990
   chunk 19 optimal weight:    0.4980
   chunk 26 optimal weight:    2.9990
   chunk 73 optimal weight:    0.2980
   chunk 87 optimal weight:    0.7980
   chunk 142 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 137 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN
A 189 GLN
C 176 GLN
E 176 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.206395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.135399 restraints weight = 19220.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.08
r_work: 0.3326 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  17555  Z= 0.093
  Angle     :  0.446   8.608  24108  Z= 0.238
  Chirality :  0.043   0.245   2824
  Planarity :  0.003   0.039   2873
  Dihedral  : 12.525  96.987   3062
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 11.19 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.19), residues: 1990
  helix:  1.01 (0.24), residues: 509
  sheet:  0.65 (0.29), residues: 348
  loop : -0.53 (0.18), residues: 1133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 139 
 TYR   0.015   0.001   TYR E 180 
 PHE   0.017   0.001   PHE D 195 
 TRP   0.008   0.001   TRP F 333 
 HIS   0.002   0.000   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 (17555)
  covalent geometry    : angle       0.44555 (24108)
  hydrogen bonds       : bond        0.03263 (  655)
  hydrogen bonds       : angle       5.00085 ( 1829)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 211
  time to evaluate  : 0.649 
Fit side-chains
REVERT: A   47 LYS cc_start: 0.8643 (mmtt) cc_final: 0.8341 (mmtp)
REVERT: A  110 LYS cc_start: 0.9117 (mttt) cc_final: 0.8575 (mmtm)
REVERT: A  139 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7600 (mtp180)
REVERT: B   47 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8592 (mmtp)
REVERT: B  105 MET cc_start: 0.8480 (mmm) cc_final: 0.7400 (mpp)
REVERT: B  209 GLN cc_start: 0.7858 (tp40) cc_final: 0.7413 (pp30)
REVERT: B  213 ASP cc_start: 0.8021 (m-30) cc_final: 0.7615 (m-30)
REVERT: B  331 MET cc_start: 0.6897 (mmm) cc_final: 0.6524 (mmm)
REVERT: B  343 TYR cc_start: 0.8220 (p90) cc_final: 0.7827 (p90)
REVERT: C  150 LYS cc_start: 0.8365 (mttt) cc_final: 0.7957 (mmtm)
REVERT: C  166 VAL cc_start: 0.8205 (p) cc_final: 0.7870 (m)
REVERT: D  105 MET cc_start: 0.7336 (mmm) cc_final: 0.7035 (mpp)
REVERT: D  194 TYR cc_start: 0.7224 (m-80) cc_final: 0.6803 (m-80)
REVERT: E  199 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7989 (mtt180)
REVERT: E  245 GLN cc_start: 0.5791 (mt0) cc_final: 0.5017 (pp30)
REVERT: E  251 LEU cc_start: 0.5544 (OUTLIER) cc_final: 0.5272 (mt)
REVERT: F  164 ASN cc_start: 0.7684 (t0) cc_final: 0.7474 (t0)
REVERT: F  194 TYR cc_start: 0.8364 (m-80) cc_final: 0.8140 (m-80)
REVERT: F  299 LEU cc_start: 0.7332 (tt) cc_final: 0.7129 (tt)
REVERT: F  300 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7614 (mt)
REVERT: F  305 GLU cc_start: 0.8058 (tt0) cc_final: 0.7542 (mt-10)
REVERT: F  308 LYS cc_start: 0.7232 (mttt) cc_final: 0.6735 (ptmm)
  outliers start: 33
  outliers final: 18
  residues processed: 237
  average time/residue: 0.1417
  time to fit residues: 50.2390
Evaluate side-chains
  202 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 181
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  338 HIS
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  199 ARG
Chi-restraints excluded: chain E residue  251 LEU
Chi-restraints excluded: chain E residue  276 VAL
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain F residue  282 THR
Chi-restraints excluded: chain F residue  300 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 173 optimal weight:    0.4980
   chunk 74 optimal weight:    0.6980
   chunk 158 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 144 optimal weight:    9.9990
   chunk 117 optimal weight:    0.6980
   chunk 50 optimal weight:    5.9990
   chunk 102 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 64 optimal weight:    0.0970
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
C  19 GLN
C  75 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.208528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.155270 restraints weight = 19322.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 3.97
r_work: 0.3230 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  17555  Z= 0.083
  Angle     :  0.433   7.573  24108  Z= 0.231
  Chirality :  0.042   0.199   2824
  Planarity :  0.003   0.040   2873
  Dihedral  : 12.450  96.844   3059
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 11.48 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.19), residues: 1990
  helix:  1.30 (0.24), residues: 499
  sheet:  0.63 (0.29), residues: 348
  loop : -0.61 (0.18), residues: 1143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 139 
 TYR   0.013   0.001   TYR E 180 
 PHE   0.013   0.001   PHE D 280 
 TRP   0.010   0.001   TRP F 333 
 HIS   0.004   0.000   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 (17555)
  covalent geometry    : angle       0.43330 (24108)
  hydrogen bonds       : bond        0.02865 (  655)
  hydrogen bonds       : angle       4.66624 ( 1829)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 204
  time to evaluate  : 0.657 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8156 (tt0)
REVERT: A   47 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8357 (mmtm)
REVERT: A  110 LYS cc_start: 0.9121 (mttt) cc_final: 0.8619 (mmtm)
REVERT: A  139 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7576 (mtp180)
REVERT: B   47 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8565 (mmtp)
REVERT: B  105 MET cc_start: 0.8412 (mmm) cc_final: 0.7375 (mpp)
REVERT: B  173 VAL cc_start: 0.8399 (m) cc_final: 0.8185 (p)
REVERT: B  209 GLN cc_start: 0.7926 (tp40) cc_final: 0.6938 (tm-30)
REVERT: B  213 ASP cc_start: 0.7944 (m-30) cc_final: 0.7029 (m-30)
REVERT: B  331 MET cc_start: 0.6715 (mmm) cc_final: 0.6361 (mmm)
REVERT: B  343 TYR cc_start: 0.8117 (p90) cc_final: 0.7778 (p90)
REVERT: C  150 LYS cc_start: 0.8374 (mttt) cc_final: 0.7965 (mmtm)
REVERT: C  166 VAL cc_start: 0.8132 (p) cc_final: 0.7831 (m)
REVERT: D  105 MET cc_start: 0.7255 (mmm) cc_final: 0.7033 (mpp)
REVERT: D  194 TYR cc_start: 0.7136 (m-80) cc_final: 0.6699 (m-80)
REVERT: E  194 TYR cc_start: 0.7447 (m-80) cc_final: 0.7145 (m-80)
REVERT: E  245 GLN cc_start: 0.5913 (mt0) cc_final: 0.4991 (pp30)
REVERT: F  194 TYR cc_start: 0.8252 (m-80) cc_final: 0.7913 (m-80)
REVERT: F  255 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6833 (mm)
REVERT: F  300 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7447 (mt)
REVERT: F  305 GLU cc_start: 0.8097 (tt0) cc_final: 0.7849 (tm-30)
REVERT: F  308 LYS cc_start: 0.7153 (mttt) cc_final: 0.6716 (ptmm)
  outliers start: 49
  outliers final: 24
  residues processed: 241
  average time/residue: 0.1427
  time to fit residues: 51.9444
Evaluate side-chains
  213 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 186
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 GLU
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  338 HIS
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  274 SER
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  276 VAL
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain F residue  237 VAL
Chi-restraints excluded: chain F residue  255 LEU
Chi-restraints excluded: chain F residue  282 THR
Chi-restraints excluded: chain F residue  300 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 146 optimal weight:    6.9990
   chunk 176 optimal weight:    5.9990
   chunk 135 optimal weight:    0.9980
   chunk 140 optimal weight:    0.0770
   chunk 45 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 46 optimal weight:    0.3980
   chunk 171 optimal weight:    3.9990
   chunk 92 optimal weight:    0.2980
   chunk 97 optimal weight:    6.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.7540

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.207448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.155762 restraints weight = 19087.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 4.11
r_work: 0.3230 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  17555  Z= 0.090
  Angle     :  0.436   7.631  24108  Z= 0.230
  Chirality :  0.042   0.175   2824
  Planarity :  0.003   0.042   2873
  Dihedral  : 12.453  97.322   3059
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.32 %
    Favored  : 85.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.19), residues: 1990
  helix:  1.32 (0.24), residues: 499
  sheet:  0.63 (0.28), residues: 348
  loop : -0.62 (0.18), residues: 1143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 139 
 TYR   0.014   0.001   TYR E 180 
 PHE   0.015   0.001   PHE D 280 
 TRP   0.008   0.001   TRP F 333 
 HIS   0.002   0.000   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 (17555)
  covalent geometry    : angle       0.43582 (24108)
  hydrogen bonds       : bond        0.02847 (  655)
  hydrogen bonds       : angle       4.57820 ( 1829)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 196
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.9162 (mttt) cc_final: 0.8643 (mmtm)
REVERT: A  139 ARG cc_start: 0.7908 (ttp80) cc_final: 0.7546 (mtp180)
REVERT: A  265 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7904 (tp30)
REVERT: B   47 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8566 (mmtp)
REVERT: B  105 MET cc_start: 0.8352 (mmm) cc_final: 0.7367 (mpp)
REVERT: B  173 VAL cc_start: 0.8450 (m) cc_final: 0.8238 (p)
REVERT: B  209 GLN cc_start: 0.7918 (tp40) cc_final: 0.6943 (tm-30)
REVERT: B  213 ASP cc_start: 0.7968 (m-30) cc_final: 0.7023 (m-30)
REVERT: B  331 MET cc_start: 0.6773 (mmm) cc_final: 0.6359 (mmm)
REVERT: B  343 TYR cc_start: 0.8065 (p90) cc_final: 0.7761 (p90)
REVERT: C   40 ASP cc_start: 0.8185 (m-30) cc_final: 0.7974 (m-30)
REVERT: C  150 LYS cc_start: 0.8418 (mttt) cc_final: 0.7956 (mmtm)
REVERT: C  166 VAL cc_start: 0.8127 (p) cc_final: 0.7827 (m)
REVERT: D  105 MET cc_start: 0.7219 (mmm) cc_final: 0.7014 (mpp)
REVERT: D  131 GLN cc_start: 0.6807 (mm-40) cc_final: 0.6480 (mm-40)
REVERT: D  194 TYR cc_start: 0.7094 (m-80) cc_final: 0.6623 (m-80)
REVERT: D  197 GLN cc_start: 0.7493 (mm110) cc_final: 0.6082 (tt0)
REVERT: E  194 TYR cc_start: 0.7444 (m-80) cc_final: 0.7132 (m-80)
REVERT: E  245 GLN cc_start: 0.5927 (mt0) cc_final: 0.5004 (pp30)
REVERT: F  194 TYR cc_start: 0.8201 (m-80) cc_final: 0.7956 (m-80)
REVERT: F  300 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7334 (mt)
REVERT: F  308 LYS cc_start: 0.7094 (mttt) cc_final: 0.6694 (ptmm)
  outliers start: 37
  outliers final: 25
  residues processed: 226
  average time/residue: 0.1478
  time to fit residues: 50.2847
Evaluate side-chains
  208 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 181
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  338 HIS
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  274 SER
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  276 VAL
Chi-restraints excluded: chain E residue  282 THR
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain F residue  282 THR
Chi-restraints excluded: chain F residue  300 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 188 optimal weight:    9.9990
   chunk 61 optimal weight:    0.6980
   chunk 56 optimal weight:    7.9990
   chunk 108 optimal weight:    1.9990
   chunk 177 optimal weight:    7.9990
   chunk 199 optimal weight:   30.0000
   chunk 150 optimal weight:    7.9990
   chunk 141 optimal weight:    4.9990
   chunk 129 optimal weight:    0.7980
   chunk 104 optimal weight:    0.4980
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
C  19 GLN
D 164 ASN
F 140 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.200816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.146217 restraints weight = 19058.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 4.38
r_work: 0.3075 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  17555  Z= 0.155
  Angle     :  0.478   7.053  24108  Z= 0.251
  Chirality :  0.044   0.169   2824
  Planarity :  0.003   0.042   2873
  Dihedral  : 12.516  96.692   3059
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 12.21 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.19), residues: 1990
  helix:  1.22 (0.24), residues: 499
  sheet:  0.56 (0.28), residues: 348
  loop : -0.65 (0.18), residues: 1143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 127 
 TYR   0.013   0.001   TYR E 180 
 PHE   0.015   0.001   PHE D 280 
 TRP   0.010   0.001   TRP F 333 
 HIS   0.003   0.001   HIS E  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (17555)
  covalent geometry    : angle       0.47799 (24108)
  hydrogen bonds       : bond        0.03246 (  655)
  hydrogen bonds       : angle       4.74001 ( 1829)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 189
  time to evaluate  : 0.553 
Fit side-chains
REVERT: A  110 LYS cc_start: 0.9083 (mttt) cc_final: 0.8515 (mmtm)
REVERT: A  139 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7510 (mtp180)
REVERT: A  265 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7915 (tp30)
REVERT: B  105 MET cc_start: 0.8455 (mmm) cc_final: 0.7286 (mpp)
REVERT: B  173 VAL cc_start: 0.8409 (m) cc_final: 0.8166 (p)
REVERT: B  209 GLN cc_start: 0.7968 (tp40) cc_final: 0.7012 (tm-30)
REVERT: B  213 ASP cc_start: 0.7922 (m-30) cc_final: 0.7002 (m-30)
REVERT: B  331 MET cc_start: 0.6778 (mmm) cc_final: 0.6451 (mmm)
REVERT: B  343 TYR cc_start: 0.8066 (p90) cc_final: 0.7780 (p90)
REVERT: C  150 LYS cc_start: 0.8395 (mttt) cc_final: 0.7878 (mmtm)
REVERT: C  166 VAL cc_start: 0.8106 (p) cc_final: 0.7768 (m)
REVERT: D  105 MET cc_start: 0.7305 (mmm) cc_final: 0.6829 (mpp)
REVERT: D  131 GLN cc_start: 0.6807 (mm-40) cc_final: 0.6393 (mm-40)
REVERT: D  194 TYR cc_start: 0.7091 (m-80) cc_final: 0.6598 (m-80)
REVERT: E  194 TYR cc_start: 0.7315 (m-80) cc_final: 0.6993 (m-80)
REVERT: E  245 GLN cc_start: 0.5708 (mt0) cc_final: 0.4822 (pp30)
REVERT: F  219 MET cc_start: 0.6861 (mtt) cc_final: 0.6519 (mmt)
REVERT: F  255 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6823 (mm)
REVERT: F  300 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7375 (mt)
REVERT: F  308 LYS cc_start: 0.7175 (mttt) cc_final: 0.6587 (ptmm)
  outliers start: 53
  outliers final: 41
  residues processed: 230
  average time/residue: 0.1384
  time to fit residues: 48.2351
Evaluate side-chains
  216 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 173
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   79 ASP
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  338 HIS
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  219 MET
Chi-restraints excluded: chain C residue  274 SER
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain D residue   17 ASP
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   97 ILE
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  276 VAL
Chi-restraints excluded: chain E residue  282 THR
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  113 THR
Chi-restraints excluded: chain F residue  237 VAL
Chi-restraints excluded: chain F residue  255 LEU
Chi-restraints excluded: chain F residue  281 ILE
Chi-restraints excluded: chain F residue  282 THR
Chi-restraints excluded: chain F residue  300 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 201 optimal weight:   20.0000
   chunk 17 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0670
   chunk 184 optimal weight:    8.9990
   chunk 103 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 137 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9990
   chunk 146 optimal weight:    8.9990
   overall best weight:    0.9922

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

Flipped N/Q/H residues before XYZ refinement:
C  19 GLN
C 164 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.202146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.147672 restraints weight = 19111.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 4.42
r_work: 0.3102 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  17555  Z= 0.101
  Angle     :  0.451   9.049  24108  Z= 0.236
  Chirality :  0.043   0.160   2824
  Planarity :  0.003   0.044   2873
  Dihedral  : 12.485  97.826   3059
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.40 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.19), residues: 1990
  helix:  1.26 (0.24), residues: 499
  sheet:  0.58 (0.28), residues: 348
  loop : -0.67 (0.18), residues: 1143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 139 
 TYR   0.016   0.001   TYR E 180 
 PHE   0.016   0.001   PHE F 259 
 TRP   0.009   0.001   TRP C  87 
 HIS   0.002   0.000   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (17555)
  covalent geometry    : angle       0.45058 (24108)
  hydrogen bonds       : bond        0.02894 (  655)
  hydrogen bonds       : angle       4.58025 ( 1829)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 181
  time to evaluate  : 0.655 
Fit side-chains
REVERT: A  110 LYS cc_start: 0.9095 (mttt) cc_final: 0.8509 (mmtm)
REVERT: A  139 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7538 (mtp180)
REVERT: B   47 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8503 (mmtp)
REVERT: B  105 MET cc_start: 0.8428 (mmm) cc_final: 0.7226 (mpp)
REVERT: B  173 VAL cc_start: 0.8350 (m) cc_final: 0.8124 (p)
REVERT: B  209 GLN cc_start: 0.7964 (tp40) cc_final: 0.6994 (tm-30)
REVERT: B  213 ASP cc_start: 0.7860 (m-30) cc_final: 0.6933 (m-30)
REVERT: B  331 MET cc_start: 0.6735 (mmm) cc_final: 0.6445 (mmm)
REVERT: B  343 TYR cc_start: 0.8053 (p90) cc_final: 0.7797 (p90)
REVERT: C  150 LYS cc_start: 0.8388 (mttt) cc_final: 0.7873 (mmtm)
REVERT: C  166 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7763 (m)
REVERT: D  105 MET cc_start: 0.7273 (mmm) cc_final: 0.6773 (mpp)
REVERT: D  131 GLN cc_start: 0.6787 (mm-40) cc_final: 0.6453 (mm-40)
REVERT: D  159 LYS cc_start: 0.6349 (tptt) cc_final: 0.5877 (tttp)
REVERT: D  194 TYR cc_start: 0.6981 (m-80) cc_final: 0.6490 (m-80)
REVERT: E  194 TYR cc_start: 0.7327 (m-80) cc_final: 0.7034 (m-80)
REVERT: E  245 GLN cc_start: 0.5817 (mt0) cc_final: 0.4964 (pp30)
REVERT: F  219 MET cc_start: 0.6888 (mtt) cc_final: 0.6466 (mmm)
REVERT: F  255 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6812 (mm)
REVERT: F  300 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7310 (mt)
REVERT: F  308 LYS cc_start: 0.7177 (mttt) cc_final: 0.6581 (ptmm)
  outliers start: 38
  outliers final: 33
  residues processed: 210
  average time/residue: 0.1450
  time to fit residues: 45.7709
Evaluate side-chains
  213 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 177
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  338 HIS
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  274 SER
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   97 ILE
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  282 THR
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain F residue  237 VAL
Chi-restraints excluded: chain F residue  255 LEU
Chi-restraints excluded: chain F residue  282 THR
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain F residue  300 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 117 optimal weight:   40.0000
   chunk 11 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 186 optimal weight:    9.9990
   chunk 39 optimal weight:    0.2980
   chunk 136 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 179 optimal weight:    8.9990
   chunk 49 optimal weight:    9.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
F  75 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.207388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.154786 restraints weight = 19222.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 4.37
r_work: 0.3245 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  17555  Z= 0.082
  Angle     :  0.431   6.526  24108  Z= 0.226
  Chirality :  0.042   0.155   2824
  Planarity :  0.003   0.045   2873
  Dihedral  : 12.456  98.106   3059
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 13.40 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.19), residues: 1990
  helix:  1.28 (0.24), residues: 504
  sheet:  0.69 (0.28), residues: 347
  loop : -0.64 (0.18), residues: 1139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 139 
 TYR   0.016   0.001   TYR E 180 
 PHE   0.011   0.001   PHE D 280 
 TRP   0.009   0.001   TRP F 333 
 HIS   0.002   0.000   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 (17555)
  covalent geometry    : angle       0.43147 (24108)
  hydrogen bonds       : bond        0.02696 (  655)
  hydrogen bonds       : angle       4.44901 ( 1829)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 192
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.9101 (mttt) cc_final: 0.8587 (mmtm)
REVERT: A  139 ARG cc_start: 0.7839 (ttp80) cc_final: 0.7454 (mtp180)
REVERT: B   47 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8501 (mmtp)
REVERT: B  105 MET cc_start: 0.8337 (mmm) cc_final: 0.7348 (mpp)
REVERT: B  209 GLN cc_start: 0.7992 (tp40) cc_final: 0.7052 (tm-30)
REVERT: B  213 ASP cc_start: 0.7943 (m-30) cc_final: 0.7071 (m-30)
REVERT: B  331 MET cc_start: 0.6819 (mmm) cc_final: 0.6537 (mmm)
REVERT: B  343 TYR cc_start: 0.8063 (p90) cc_final: 0.7859 (p90)
REVERT: C  139 ARG cc_start: 0.7095 (mtp85) cc_final: 0.6742 (mtp-110)
REVERT: C  150 LYS cc_start: 0.8399 (mttt) cc_final: 0.7845 (mmtm)
REVERT: C  166 VAL cc_start: 0.8134 (p) cc_final: 0.7747 (m)
REVERT: D  105 MET cc_start: 0.7214 (mmm) cc_final: 0.6932 (mpp)
REVERT: D  131 GLN cc_start: 0.6830 (mm-40) cc_final: 0.6480 (mm-40)
REVERT: D  159 LYS cc_start: 0.6314 (tptt) cc_final: 0.6003 (tttp)
REVERT: D  194 TYR cc_start: 0.7043 (m-80) cc_final: 0.6559 (m-80)
REVERT: D  197 GLN cc_start: 0.7489 (mm110) cc_final: 0.6126 (tt0)
REVERT: E  194 TYR cc_start: 0.7305 (m-80) cc_final: 0.7049 (m-80)
REVERT: E  245 GLN cc_start: 0.5849 (mt0) cc_final: 0.5020 (pp30)
REVERT: F  219 MET cc_start: 0.6931 (mtt) cc_final: 0.6532 (pmm)
REVERT: F  255 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6750 (mm)
REVERT: F  272 MET cc_start: 0.7847 (ttp) cc_final: 0.7519 (ttt)
REVERT: F  300 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7265 (mt)
REVERT: F  308 LYS cc_start: 0.7181 (mttt) cc_final: 0.6627 (ptmm)
  outliers start: 44
  outliers final: 35
  residues processed: 225
  average time/residue: 0.1338
  time to fit residues: 45.8548
Evaluate side-chains
  218 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 181
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   79 ASP
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  338 HIS
Chi-restraints excluded: chain C residue   40 ASP
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  274 SER
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   97 ILE
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  116 ILE
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  282 THR
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  113 THR
Chi-restraints excluded: chain F residue  255 LEU
Chi-restraints excluded: chain F residue  282 THR
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain F residue  300 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 146 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 147 optimal weight:    0.9990
   chunk 155 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 17 optimal weight:    0.4980
   chunk 34 optimal weight:    8.9990
   chunk 187 optimal weight:   20.0000
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
B 310 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.208115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.153506 restraints weight = 19370.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3763 rms_B_bonded: 4.18
r_work: 0.3205 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  17555  Z= 0.096
  Angle     :  0.448   9.306  24108  Z= 0.234
  Chirality :  0.042   0.156   2824
  Planarity :  0.003   0.044   2873
  Dihedral  : 12.471  97.939   3059
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 13.91 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.19), residues: 1990
  helix:  1.32 (0.24), residues: 504
  sheet:  0.69 (0.28), residues: 347
  loop : -0.62 (0.18), residues: 1139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 225 
 TYR   0.016   0.001   TYR E 180 
 PHE   0.013   0.001   PHE D 280 
 TRP   0.009   0.001   TRP F 333 
 HIS   0.002   0.000   HIS E  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (17555)
  covalent geometry    : angle       0.44775 (24108)
  hydrogen bonds       : bond        0.02761 (  655)
  hydrogen bonds       : angle       4.45684 ( 1829)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 182
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.9130 (mttt) cc_final: 0.8635 (mmtm)
REVERT: A  139 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7535 (mtp180)
REVERT: B  105 MET cc_start: 0.8400 (mmm) cc_final: 0.7388 (mpp)
REVERT: B  209 GLN cc_start: 0.8026 (tp40) cc_final: 0.7099 (tm-30)
REVERT: B  213 ASP cc_start: 0.7969 (m-30) cc_final: 0.7080 (m-30)
REVERT: B  331 MET cc_start: 0.6768 (mmm) cc_final: 0.6552 (mmm)
REVERT: B  343 TYR cc_start: 0.7999 (p90) cc_final: 0.7785 (p90)
REVERT: C  139 ARG cc_start: 0.7136 (mtp85) cc_final: 0.6798 (mtp-110)
REVERT: C  150 LYS cc_start: 0.8332 (mttt) cc_final: 0.7837 (mmtm)
REVERT: C  166 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7793 (m)
REVERT: D  105 MET cc_start: 0.7362 (mmm) cc_final: 0.7005 (mpp)
REVERT: D  131 GLN cc_start: 0.6867 (mm-40) cc_final: 0.6559 (mm-40)
REVERT: D  159 LYS cc_start: 0.6280 (tptt) cc_final: 0.6077 (tttp)
REVERT: D  194 TYR cc_start: 0.7024 (m-80) cc_final: 0.6556 (m-80)
REVERT: D  197 GLN cc_start: 0.7591 (mm110) cc_final: 0.6200 (tt0)
REVERT: D  281 ILE cc_start: 0.6968 (tp) cc_final: 0.6480 (mt)
REVERT: D  285 GLN cc_start: 0.5964 (tt0) cc_final: 0.5375 (mp10)
REVERT: E  194 TYR cc_start: 0.7483 (m-80) cc_final: 0.7236 (m-80)
REVERT: E  245 GLN cc_start: 0.5789 (mt0) cc_final: 0.4975 (pp30)
REVERT: E  265 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6219 (tt0)
REVERT: F  219 MET cc_start: 0.6789 (mtt) cc_final: 0.6487 (pmm)
REVERT: F  255 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6849 (mm)
REVERT: F  272 MET cc_start: 0.7879 (ttp) cc_final: 0.7538 (ttt)
REVERT: F  300 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7244 (mt)
REVERT: F  305 GLU cc_start: 0.8177 (tt0) cc_final: 0.7967 (tt0)
REVERT: F  308 LYS cc_start: 0.7238 (mttt) cc_final: 0.6524 (ptmm)
  outliers start: 41
  outliers final: 37
  residues processed: 210
  average time/residue: 0.1286
  time to fit residues: 40.9412
Evaluate side-chains
  219 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 179
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   79 ASP
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  310 GLN
Chi-restraints excluded: chain B residue  338 HIS
Chi-restraints excluded: chain C residue   40 ASP
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  274 SER
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   97 ILE
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  116 ILE
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  282 THR
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  113 THR
Chi-restraints excluded: chain F residue  255 LEU
Chi-restraints excluded: chain F residue  282 THR
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain F residue  300 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 168 optimal weight:    0.7980
   chunk 128 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   chunk 92 optimal weight:    0.5980
   chunk 110 optimal weight:    2.9990
   chunk 186 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 163 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 310 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.207498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.154977 restraints weight = 19075.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 4.10
r_work: 0.3220 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  17555  Z= 0.091
  Angle     :  0.444   8.443  24108  Z= 0.232
  Chirality :  0.042   0.155   2824
  Planarity :  0.003   0.044   2873
  Dihedral  : 12.468  98.164   3059
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.91 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.19), residues: 1990
  helix:  1.29 (0.24), residues: 504
  sheet:  0.71 (0.28), residues: 347
  loop : -0.62 (0.18), residues: 1139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 139 
 TYR   0.016   0.001   TYR E 180 
 PHE   0.022   0.001   PHE B 342 
 TRP   0.010   0.001   TRP B 333 
 HIS   0.002   0.000   HIS E  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 (17555)
  covalent geometry    : angle       0.44408 (24108)
  hydrogen bonds       : bond        0.02707 (  655)
  hydrogen bonds       : angle       4.42348 ( 1829)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 186
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 ASP cc_start: 0.8366 (m-30) cc_final: 0.8057 (m-30)
REVERT: A  110 LYS cc_start: 0.9119 (mttt) cc_final: 0.8658 (mmtm)
REVERT: A  139 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7532 (mtp180)
REVERT: B   47 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8540 (mmtp)
REVERT: B  105 MET cc_start: 0.8362 (mmm) cc_final: 0.7385 (mpp)
REVERT: B  209 GLN cc_start: 0.8047 (tp40) cc_final: 0.7151 (tm-30)
REVERT: B  213 ASP cc_start: 0.7956 (m-30) cc_final: 0.7082 (m-30)
REVERT: B  343 TYR cc_start: 0.8043 (p90) cc_final: 0.7840 (p90)
REVERT: C  150 LYS cc_start: 0.8315 (mttt) cc_final: 0.7836 (mmtm)
REVERT: C  166 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7775 (m)
REVERT: C  331 MET cc_start: 0.7193 (mmm) cc_final: 0.6977 (tpp)
REVERT: D  105 MET cc_start: 0.7323 (mmm) cc_final: 0.7005 (mpp)
REVERT: D  131 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6590 (mm-40)
REVERT: D  194 TYR cc_start: 0.7026 (m-80) cc_final: 0.6548 (m-80)
REVERT: D  197 GLN cc_start: 0.7581 (mm110) cc_final: 0.6183 (tt0)
REVERT: D  281 ILE cc_start: 0.6960 (tp) cc_final: 0.6553 (mt)
REVERT: D  285 GLN cc_start: 0.5923 (tt0) cc_final: 0.5328 (mp10)
REVERT: E  107 ASP cc_start: 0.8066 (m-30) cc_final: 0.7809 (m-30)
REVERT: E  194 TYR cc_start: 0.7507 (m-80) cc_final: 0.7283 (m-80)
REVERT: E  245 GLN cc_start: 0.5785 (mt0) cc_final: 0.4980 (pp30)
REVERT: E  265 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6231 (tt0)
REVERT: F   22 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7283 (mt-10)
REVERT: F  219 MET cc_start: 0.6895 (mtt) cc_final: 0.6545 (pmm)
REVERT: F  255 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6850 (mm)
REVERT: F  272 MET cc_start: 0.7861 (ttp) cc_final: 0.7528 (ttt)
REVERT: F  300 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7300 (mt)
REVERT: F  308 LYS cc_start: 0.7189 (mttt) cc_final: 0.6526 (ptmm)
  outliers start: 43
  outliers final: 38
  residues processed: 216
  average time/residue: 0.1300
  time to fit residues: 42.9806
Evaluate side-chains
  221 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 179
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   79 ASP
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  310 GLN
Chi-restraints excluded: chain B residue  338 HIS
Chi-restraints excluded: chain C residue   40 ASP
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  274 SER
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   97 ILE
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  116 ILE
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  282 THR
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain F residue   22 GLU
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  113 THR
Chi-restraints excluded: chain F residue  255 LEU
Chi-restraints excluded: chain F residue  282 THR
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain F residue  300 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 184 optimal weight:    0.4980
   chunk 3 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 131 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0070
   chunk 116 optimal weight:    9.9990
   chunk 120 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 195 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   overall best weight:    0.8800

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

Flipped N/Q/H residues before XYZ refinement:
B 310 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.208439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.157183 restraints weight = 19321.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 4.58
r_work: 0.3238 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.3467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  17555  Z= 0.097
  Angle     :  0.449   8.266  24108  Z= 0.235
  Chirality :  0.042   0.156   2824
  Planarity :  0.003   0.044   2873
  Dihedral  : 12.468  98.159   3059
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 13.96 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.19), residues: 1990
  helix:  1.22 (0.24), residues: 509
  sheet:  0.71 (0.28), residues: 347
  loop : -0.59 (0.18), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 139 
 TYR   0.016   0.001   TYR E 180 
 PHE   0.023   0.001   PHE F 259 
 TRP   0.018   0.001   TRP B 333 
 HIS   0.002   0.000   HIS E  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (17555)
  covalent geometry    : angle       0.44933 (24108)
  hydrogen bonds       : bond        0.02741 (  655)
  hydrogen bonds       : angle       4.42747 ( 1829)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4788.43 seconds
wall clock time: 82 minutes 33.18 seconds (4953.18 seconds total)