Starting phenix.real_space_refine
on Wed Mar  4 16:54:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uv9_26809/03_2026/7uv9_26809.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uv9_26809/03_2026/7uv9_26809.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/7uv9_26809/03_2026/7uv9_26809.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uv9_26809/03_2026/7uv9_26809.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uv9_26809/03_2026/7uv9_26809.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uv9_26809/03_2026/7uv9_26809.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=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     P     292      5.49       5
     S      33      5.16       5
     C    8766      2.51       5
     N    2815      2.21       5
     O    3435      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15342
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 815
          Classifications: {'peptide': 103}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 821
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 783
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 821
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3014
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "J"
      Number of atoms: 2972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2972
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "K"
      Number of atoms: 3379
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 407, 3379
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 19, 'TRANS': 387}
          Chain breaks: 3
    Chain: "K"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {' FE': 1, 'OH0': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.56, per 1000 atoms: 0.23
  Number of scatterers: 15342
  At special positions: 0
  Unit cell: (91, 158.34, 152.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      1     26.01
     S      33     16.00
     P     292     15.00
     O    3435      8.00
     N    2815      7.00
     C    8766      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: 1.37
  Conformation dependent library (CDL) restraints added in 302.2 milliseconds
  

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2178

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 11 sheets defined
      62.4% alpha, 6.6% beta
      142 base pairs and 245 stacking pairs defined.
    Time for finding SS restraints: 2.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
      removed outlier: 3.553A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 76
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.649A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.594A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLY A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.044A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.755A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 36
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.501A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'D' and resid 37 through 47
      removed outlier: 3.569A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.736A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.817A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   SER D 124 " --> pdb=" O   LYS D 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.781A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.587A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 50 through 76
      removed outlier: 3.866A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.715A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 36
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.604A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
      removed outlier: 3.515A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.602A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL H  48 " --> pdb=" O   VAL H  44 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.644A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.501A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 123
      removed outlier: 3.766A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 39 through 46
    Processing helix  chain 'K' and resid 58 through 62
    Processing helix  chain 'K' and resid 63 through 71
    Processing helix  chain 'K' and resid 94 through 103
    Processing helix  chain 'K' and resid 123 through 132
    Processing helix  chain 'K' and resid 133 through 137
    Processing helix  chain 'K' and resid 153 through 157
    Processing helix  chain 'K' and resid 160 through 167
      removed outlier: 3.721A  pdb=" N   ASP K 164 " --> pdb=" O   PRO K 160 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE K 165 " --> pdb=" O   SER K 161 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE K 166 " --> pdb=" O   THR K 162 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 167 through 173
      removed outlier: 3.583A  pdb=" N   TRP K 173 " --> pdb=" O   VAL K 169 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 174 through 179
    Processing helix  chain 'K' and resid 187 through 191
    Processing helix  chain 'K' and resid 214 through 218
    Processing helix  chain 'K' and resid 237 through 251
      removed outlier: 3.539A  pdb=" N   GLY K 251 " --> pdb=" O   TRP K 247 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 257 through 262
      removed outlier: 3.789A  pdb=" N   ARG K 261 " --> pdb=" O   PHE K 257 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 304 through 318
    Processing helix  chain 'K' and resid 321 through 325
    Processing helix  chain 'K' and resid 328 through 346
    Processing helix  chain 'K' and resid 351 through 363
    Processing helix  chain 'K' and resid 454 through 470
    Processing helix  chain 'K' and resid 472 through 477
      removed outlier: 4.420A  pdb=" N   CYS K 477 " --> pdb=" O   LEU K 473 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 484 through 500
    Processing helix  chain 'K' and resid 503 through 508
      removed outlier: 3.835A  pdb=" N   LEU K 508 " --> pdb=" O   PRO K 504 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.157A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.547A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.460A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.992A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.910A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.574A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.072A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB1, first strand: chain 'K' and resid 55 through 56
      removed outlier: 6.388A  pdb=" N   THR K  55 " --> pdb=" O   ILE K  77 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   LEU K 293 " --> pdb=" O   HIS K 225 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   CYS K 200 " --> pdb=" O   SER K 145 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   SER K 145 " --> pdb=" O   CYS K 200 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   ILE K 144 " --> pdb=" O   ASP K 109 " (cutoff:3.500A)
      removed outlier: 8.743A  pdb=" N   ASP K 109 " --> pdb=" O   ILE K 144 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   LEU K 146 " --> pdb=" O   MET K 107 " (cutoff:3.500A)
      removed outlier: 11.009A  pdb=" N   MET K 107 " --> pdb=" O   LEU K 146 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LYS K 117 " --> pdb=" O   ASP K 112 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'K' and resid 208 through 212
      removed outlier: 4.058A  pdb=" N   PHE K 211 " --> pdb=" O   HIS K 284 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   HIS K 284 " --> pdb=" O   PHE K 211 " (cutoff:3.500A)

    522 hydrogen bonds defined for protein.
    1494 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      364 hydrogen bonds
      728 hydrogen bond angles
      0 basepair planarities
      142 basepair parallelities
      245 stacking parallelities
  Total time for adding SS restraints: 3.42

  Time building geometry restraints manager: 1.74 seconds

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

  Histogram of bond lengths:
        1.16 -     1.30: 1794
        1.30 -     1.44: 5928
        1.44 -     1.58: 7861
        1.58 -     1.72: 589
        1.72 -     1.86: 57
  Bond restraints: 16229
  Sorted by residual:
  bond pdb=" C   LYS K  79 "
       pdb=" O   LYS K  79 "
    ideal  model  delta    sigma   weight residual
    1.236  1.158  0.078 1.26e-02 6.30e+03 3.86e+01
  bond pdb=" CA  SER K 161 "
       pdb=" C   SER K 161 "
    ideal  model  delta    sigma   weight residual
    1.524  1.456  0.068 1.32e-02 5.74e+03 2.64e+01
  bond pdb=" CA  LEU K 464 "
       pdb=" C   LEU K 464 "
    ideal  model  delta    sigma   weight residual
    1.524  1.588 -0.065 1.27e-02 6.20e+03 2.59e+01
  bond pdb=" C   ILE K 305 "
       pdb=" O   ILE K 305 "
    ideal  model  delta    sigma   weight residual
    1.242  1.199  0.043 8.60e-03 1.35e+04 2.51e+01
  bond pdb=" CA  TYR K  49 "
       pdb=" C   TYR K  49 "
    ideal  model  delta    sigma   weight residual
    1.526  1.480  0.046 9.70e-03 1.06e+04 2.27e+01
  ... (remaining 16224 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 21514
        1.63 -     3.26: 1362
        3.26 -     4.89: 231
        4.89 -     6.52: 53
        6.52 -     8.15: 15
  Bond angle restraints: 23175
  Sorted by residual:
  angle pdb=" N   THR K 237 "
        pdb=" CA  THR K 237 "
        pdb=" C   THR K 237 "
      ideal   model   delta    sigma   weight residual
     110.53  103.44    7.09 1.32e+00 5.74e-01 2.89e+01
  angle pdb=" N   GLY K 481 "
        pdb=" CA  GLY K 481 "
        pdb=" C   GLY K 481 "
      ideal   model   delta    sigma   weight residual
     114.67  120.35   -5.68 1.10e+00 8.26e-01 2.67e+01
  angle pdb=" N   ASP K 491 "
        pdb=" CA  ASP K 491 "
        pdb=" C   ASP K 491 "
      ideal   model   delta    sigma   weight residual
     111.36  116.61   -5.25 1.09e+00 8.42e-01 2.32e+01
  angle pdb=" N   LEU K 359 "
        pdb=" CA  LEU K 359 "
        pdb=" C   LEU K 359 "
      ideal   model   delta    sigma   weight residual
     111.33  117.03   -5.70 1.21e+00 6.83e-01 2.22e+01
  angle pdb=" N   ILE K 311 "
        pdb=" CA  ILE K 311 "
        pdb=" C   ILE K 311 "
      ideal   model   delta    sigma   weight residual
     110.42  114.71   -4.29 9.60e-01 1.09e+00 2.00e+01
  ... (remaining 23170 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.26: 7495
       35.26 -    70.53: 1455
       70.53 -   105.79: 25
      105.79 -   141.05: 0
      141.05 -   176.32: 1
  Dihedral angle restraints: 8976
    sinusoidal: 5597
      harmonic: 3379
  Sorted by residual:
  dihedral pdb=" C4'  DT I -59 "
           pdb=" C3'  DT I -59 "
           pdb=" O3'  DT I -59 "
           pdb=" P    DC I -58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   43.68  176.32     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  THR K 218 "
           pdb=" C   THR K 218 "
           pdb=" N   SER K 219 "
           pdb=" CA  SER K 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.73   18.27     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" C   PHE K 215 "
           pdb=" N   PHE K 215 "
           pdb=" CA  PHE K 215 "
           pdb=" CB  PHE K 215 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.37    8.77     0      2.50e+00 1.60e-01 1.23e+01
  ... (remaining 8973 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 2227
       0.066 -    0.132: 275
       0.132 -    0.199: 77
       0.199 -    0.265: 19
       0.265 -    0.331: 8
  Chirality restraints: 2606
  Sorted by residual:
  chirality pdb=" CA  PHE K 215 "
            pdb=" N   PHE K 215 "
            pdb=" C   PHE K 215 "
            pdb=" CB  PHE K 215 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CA  THR K 209 "
            pdb=" N   THR K 209 "
            pdb=" C   THR K 209 "
            pdb=" CB  THR K 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.83   -0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CA  TYR K 222 "
            pdb=" N   TYR K 222 "
            pdb=" C   TYR K 222 "
            pdb=" CB  TYR K 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.04e+00
  ... (remaining 2603 not shown)

  Planarity restraints: 1927
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   OH0 K 701 "    0.034 2.00e-02 2.50e+03   1.18e-01 2.09e+02
        pdb=" O   OH0 K 701 "   -0.164 2.00e-02 2.50e+03
        pdb=" C5  OH0 K 701 "   -0.156 2.00e-02 2.50e+03
        pdb=" C6  OH0 K 701 "    0.045 2.00e-02 2.50e+03
        pdb=" C7  OH0 K 701 "    0.112 2.00e-02 2.50e+03
        pdb=" O3  OH0 K 701 "    0.129 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP K 221 "    0.055 2.00e-02 2.50e+03   2.67e-02 1.79e+01
        pdb=" CG  TRP K 221 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP K 221 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP K 221 "   -0.040 2.00e-02 2.50e+03
        pdb=" NE1 TRP K 221 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP K 221 "    0.014 2.00e-02 2.50e+03
        pdb=" CE3 TRP K 221 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ2 TRP K 221 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ3 TRP K 221 "   -0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP K 221 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP K 247 "    0.049 2.00e-02 2.50e+03   2.65e-02 1.75e+01
        pdb=" CG  TRP K 247 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TRP K 247 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TRP K 247 "   -0.015 2.00e-02 2.50e+03
        pdb=" NE1 TRP K 247 "    0.013 2.00e-02 2.50e+03
        pdb=" CE2 TRP K 247 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE3 TRP K 247 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP K 247 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ3 TRP K 247 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP K 247 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1924 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.23: 6
        2.23 -     2.90: 5058
        2.90 -     3.56: 21208
        3.56 -     4.23: 39510
        4.23 -     4.90: 60663
  Nonbonded interactions: 126445
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU K  41 "
            pdb=" NE2 HIS K  45 "
     model   vdw
     1.561 3.120
  nonbonded pdb=" O   OH0 K 701 "
            pdb="FE    FE K 702 "
     model   vdw
     2.037 2.260
  nonbonded pdb=" OD1 ASP K 214 "
            pdb="FE    FE K 702 "
     model   vdw
     2.159 2.260
  nonbonded pdb=" O3  OH0 K 701 "
            pdb="FE    FE K 702 "
     model   vdw
     2.203 2.260
  nonbonded pdb=" NE2 HIS K 212 "
            pdb="FE    FE K 702 "
     model   vdw
     2.208 2.340
  ... (remaining 126440 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 43 through 134)
  selection = (chain 'E' and resid 43 through 134)
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 24 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

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=0.58 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     16.540
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
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      :  0.009   0.093  16229  Z= 0.550
  Angle     :  0.890   8.149  23175  Z= 0.554
  Chirality :  0.055   0.331   2606
  Planarity :  0.007   0.118   1927
  Dihedral  : 26.048 176.319   6798
  Min Nonbonded Distance : 1.561

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  2.41 %
    Favored  : 97.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.25), residues: 1138
  helix:  1.94 (0.21), residues: 645
  sheet:  0.84 (0.64), residues: 63
  loop : -0.99 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.029   0.001   ARG K 339 
 TYR   0.042   0.005   TYR K 222 
 PHE   0.058   0.007   PHE K 215 
 TRP   0.057   0.015   TRP K 247 
 HIS   0.021   0.004   HIS K 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00861 (16229)
  covalent geometry    : angle       0.88987 (23175)
  hydrogen bonds       : bond        0.11749 (  886)
  hydrogen bonds       : angle       4.01512 ( 2222)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 166
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.7756 (t0) cc_final: 0.7396 (t0)
REVERT: D   31 ARG cc_start: 0.4458 (OUTLIER) cc_final: 0.3048 (ttm110)
REVERT: K  120 GLU cc_start: 0.4573 (mt-10) cc_final: 0.4120 (mt-10)
  outliers start: 3
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1654
  time to fit residues: 38.1375
Evaluate side-chains
  139 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   31 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
C  24 GLN
C 104 GLN
F  25 ASN
H  49 HIS
H 109 HIS
K 176 HIS
** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.175751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.136640 restraints weight = 26394.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 2.96
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3731
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3731 r_free = 0.3731    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3731 r_free = 0.3731    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  16229  Z= 0.178
  Angle     :  0.567   6.100  23175  Z= 0.340
  Chirality :  0.037   0.141   2606
  Planarity :  0.005   0.050   1927
  Dihedral  : 29.205 177.931   4485
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  5.92 %
    Favored  : 93.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.25), residues: 1138
  helix:  2.09 (0.20), residues: 666
  sheet:  0.97 (0.64), residues: 66
  loop : -0.85 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  86 
 TYR   0.012   0.001   TYR K 312 
 PHE   0.022   0.002   PHE K  93 
 TRP   0.024   0.002   TRP K 247 
 HIS   0.005   0.001   HIS K 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (16229)
  covalent geometry    : angle       0.56674 (23175)
  hydrogen bonds       : bond        0.06370 (  886)
  hydrogen bonds       : angle       3.30938 ( 2222)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 144
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.7880 (t0) cc_final: 0.7295 (t0)
REVERT: D   31 ARG cc_start: 0.4432 (OUTLIER) cc_final: 0.3414 (ttm110)
REVERT: K   57 MET cc_start: 0.2436 (ttm) cc_final: 0.2160 (ttm)
REVERT: K  123 MET cc_start: 0.4761 (tpt) cc_final: 0.4545 (tpt)
REVERT: K  191 MET cc_start: 0.1444 (mtt) cc_final: 0.0662 (tpt)
REVERT: K  332 MET cc_start: 0.1725 (tpp) cc_final: 0.0929 (tpp)
REVERT: K  466 ASP cc_start: 0.1391 (OUTLIER) cc_final: 0.1125 (p0)
  outliers start: 9
  outliers final: 4
  residues processed: 152
  average time/residue: 0.1739
  time to fit residues: 36.0721
Evaluate side-chains
  131 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 125
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  201 LEU
Chi-restraints excluded: chain K residue  466 ASP
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 124 optimal weight:    9.9990
   chunk 6 optimal weight:    0.6980
   chunk 138 optimal weight:   50.0000
   chunk 56 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 92 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9980
   chunk 136 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
C 104 GLN
K 114 ASN
K 226 GLN
** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 515 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.175541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.133571 restraints weight = 26376.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.98
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3698
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3698 r_free = 0.3698    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3698 r_free = 0.3698    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  16229  Z= 0.167
  Angle     :  0.555   9.348  23175  Z= 0.329
  Chirality :  0.036   0.150   2606
  Planarity :  0.004   0.049   1927
  Dihedral  : 29.260 178.359   4485
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  8.22 %
    Favored  : 90.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.77 (0.25), residues: 1138
  helix:  2.24 (0.20), residues: 669
  sheet:  1.18 (0.63), residues: 66
  loop : -0.70 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  11 
 TYR   0.019   0.001   TYR K 222 
 PHE   0.010   0.001   PHE K 215 
 TRP   0.016   0.002   TRP K 247 
 HIS   0.003   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (16229)
  covalent geometry    : angle       0.55462 (23175)
  hydrogen bonds       : bond        0.06167 (  886)
  hydrogen bonds       : angle       3.18561 ( 2222)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 135
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.7899 (t0) cc_final: 0.7329 (t0)
REVERT: K  191 MET cc_start: 0.1302 (mtt) cc_final: 0.0035 (tpt)
REVERT: K  317 ARG cc_start: 0.1892 (mtm-85) cc_final: 0.1430 (mtp-110)
REVERT: K  332 MET cc_start: 0.1531 (tpp) cc_final: 0.0774 (tpp)
REVERT: K  466 ASP cc_start: 0.1067 (OUTLIER) cc_final: 0.0847 (p0)
  outliers start: 9
  outliers final: 5
  residues processed: 140
  average time/residue: 0.1722
  time to fit residues: 32.9380
Evaluate side-chains
  134 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 128
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue   52 ASN
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  466 ASP
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 114 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 103 optimal weight:    8.9990
   chunk 110 optimal weight:    0.0770
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.7340

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.176552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.137515 restraints weight = 26602.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 2.43
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3747
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3747 r_free = 0.3747    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3747 r_free = 0.3747    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3747
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16229  Z= 0.145
  Angle     :  0.530  12.114  23175  Z= 0.316
  Chirality :  0.035   0.142   2606
  Planarity :  0.004   0.047   1927
  Dihedral  : 29.206 178.124   4481
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 10.13 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.26), residues: 1138
  helix:  2.38 (0.20), residues: 677
  sheet:  1.50 (0.63), residues: 64
  loop : -0.72 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  86 
 TYR   0.021   0.001   TYR K 222 
 PHE   0.015   0.001   PHE K  38 
 TRP   0.013   0.001   TRP K 247 
 HIS   0.003   0.001   HIS K 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (16229)
  covalent geometry    : angle       0.53002 (23175)
  hydrogen bonds       : bond        0.05339 (  886)
  hydrogen bonds       : angle       3.04623 ( 2222)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.7892 (t0) cc_final: 0.7314 (t0)
REVERT: D   52 THR cc_start: 0.8197 (m) cc_final: 0.7897 (m)
REVERT: K  156 MET cc_start: 0.1059 (mtm) cc_final: 0.0718 (ptp)
REVERT: K  191 MET cc_start: 0.1455 (mtt) cc_final: 0.0109 (tpt)
REVERT: K  317 ARG cc_start: 0.2191 (mtm-85) cc_final: 0.1664 (mtp-110)
REVERT: K  332 MET cc_start: 0.1640 (tpp) cc_final: 0.0834 (tpp)
REVERT: K  466 ASP cc_start: 0.1043 (OUTLIER) cc_final: 0.0842 (p0)
  outliers start: 8
  outliers final: 5
  residues processed: 139
  average time/residue: 0.1687
  time to fit residues: 32.2453
Evaluate side-chains
  136 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 130
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue   52 ASN
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  466 ASP
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 13 optimal weight:    0.7980
   chunk 133 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 138 optimal weight:    5.9990
   chunk 53 optimal weight:    0.4980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 121 optimal weight:    9.9990
   chunk 86 optimal weight:    8.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
K 308 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.174427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.133567 restraints weight = 26514.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 2.93
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3691 r_free = 0.3691    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3691 r_free = 0.3691    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  16229  Z= 0.187
  Angle     :  0.571   9.891  23175  Z= 0.337
  Chirality :  0.037   0.150   2606
  Planarity :  0.004   0.046   1927
  Dihedral  : 29.288 179.154   4481
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 11.33 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.25), residues: 1138
  helix:  2.13 (0.20), residues: 678
  sheet:  1.26 (0.61), residues: 64
  loop : -0.97 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  86 
 TYR   0.012   0.001   TYR K 330 
 PHE   0.012   0.002   PHE K 215 
 TRP   0.013   0.002   TRP K 126 
 HIS   0.004   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (16229)
  covalent geometry    : angle       0.57111 (23175)
  hydrogen bonds       : bond        0.06757 (  886)
  hydrogen bonds       : angle       3.16656 ( 2222)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.7952 (t0) cc_final: 0.7378 (t0)
REVERT: K  191 MET cc_start: 0.1436 (mtt) cc_final: 0.0149 (tpt)
REVERT: K  317 ARG cc_start: 0.3122 (mtm-85) cc_final: 0.1402 (ptm-80)
REVERT: K  332 MET cc_start: 0.1733 (tpp) cc_final: 0.0908 (tpp)
REVERT: K  466 ASP cc_start: 0.1052 (OUTLIER) cc_final: 0.0849 (p0)
  outliers start: 9
  outliers final: 6
  residues processed: 137
  average time/residue: 0.1731
  time to fit residues: 32.3608
Evaluate side-chains
  129 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 122
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  199 TYR
Chi-restraints excluded: chain K residue  270 LEU
Chi-restraints excluded: chain K residue  466 ASP
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 132 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    0.2980
   chunk 60 optimal weight:    0.9980
   chunk 105 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 125 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.175178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.136921 restraints weight = 26370.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.99
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3734
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3734 r_free = 0.3734    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3734 r_free = 0.3734    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3734
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16229  Z= 0.160
  Angle     :  0.552   9.050  23175  Z= 0.327
  Chirality :  0.036   0.145   2606
  Planarity :  0.004   0.044   1927
  Dihedral  : 29.262 179.096   4481
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 11.74 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.25), residues: 1138
  helix:  2.31 (0.20), residues: 670
  sheet:  1.21 (0.63), residues: 64
  loop : -0.82 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 339 
 TYR   0.031   0.002   TYR K 130 
 PHE   0.016   0.001   PHE K 257 
 TRP   0.011   0.002   TRP K 221 
 HIS   0.003   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (16229)
  covalent geometry    : angle       0.55169 (23175)
  hydrogen bonds       : bond        0.06087 (  886)
  hydrogen bonds       : angle       3.07092 ( 2222)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.7961 (t0) cc_final: 0.7369 (t0)
REVERT: D   52 THR cc_start: 0.8216 (m) cc_final: 0.7918 (m)
REVERT: K  172 MET cc_start: -0.1770 (mmm) cc_final: -0.2273 (mmp)
REVERT: K  191 MET cc_start: 0.1404 (mtt) cc_final: 0.0513 (tpt)
REVERT: K  317 ARG cc_start: 0.3150 (mtm-85) cc_final: 0.1442 (ptm-80)
REVERT: K  332 MET cc_start: 0.1741 (tpp) cc_final: 0.0939 (tpp)
  outliers start: 12
  outliers final: 10
  residues processed: 133
  average time/residue: 0.1696
  time to fit residues: 30.9617
Evaluate side-chains
  133 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   99 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  199 TYR
Chi-restraints excluded: chain K residue  201 LEU
Chi-restraints excluded: chain K residue  270 LEU
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    0.4980
   chunk 132 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.175546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.137289 restraints weight = 26175.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 3.00
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3739 r_free = 0.3739    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3739 r_free = 0.3739    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3739
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16229  Z= 0.159
  Angle     :  0.538   8.721  23175  Z= 0.320
  Chirality :  0.036   0.142   2606
  Planarity :  0.004   0.045   1927
  Dihedral  : 29.230 178.897   4481
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 12.34 %
    Favored  : 86.66 %
  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 are not related in a simple way.
  whole:  1.86 (0.25), residues: 1138
  helix:  2.41 (0.20), residues: 669
  sheet:  1.23 (0.64), residues: 64
  loop : -0.84 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000  AARG K 152 
 TYR   0.011   0.001   TYR K  49 
 PHE   0.013   0.001   PHE K 257 
 TRP   0.013   0.002   TRP K 221 
 HIS   0.003   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (16229)
  covalent geometry    : angle       0.53755 (23175)
  hydrogen bonds       : bond        0.05777 (  886)
  hydrogen bonds       : angle       3.01436 ( 2222)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.7949 (t0) cc_final: 0.7364 (t0)
REVERT: D   52 THR cc_start: 0.8219 (m) cc_final: 0.7912 (m)
REVERT: K  172 MET cc_start: -0.1696 (mmm) cc_final: -0.1916 (mmp)
REVERT: K  191 MET cc_start: 0.1473 (mtt) cc_final: 0.0282 (tpt)
REVERT: K  317 ARG cc_start: 0.3341 (mtm-85) cc_final: 0.1502 (ptm-80)
REVERT: K  332 MET cc_start: 0.1825 (tpp) cc_final: 0.1139 (mmt)
  outliers start: 10
  outliers final: 10
  residues processed: 133
  average time/residue: 0.1696
  time to fit residues: 30.8431
Evaluate side-chains
  136 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   99 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  199 TYR
Chi-restraints excluded: chain K residue  201 LEU
Chi-restraints excluded: chain K residue  270 LEU
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 124 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 123 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 114 optimal weight:    0.7980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.172924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.134671 restraints weight = 26185.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 3.11
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3698
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3698 r_free = 0.3698    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3698 r_free = 0.3698    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  16229  Z= 0.217
  Angle     :  0.609   8.616  23175  Z= 0.357
  Chirality :  0.039   0.152   2606
  Planarity :  0.005   0.043   1927
  Dihedral  : 29.429 179.434   4481
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 12.34 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.25), residues: 1138
  helix:  2.02 (0.20), residues: 679
  sheet:  1.17 (0.65), residues: 66
  loop : -1.05 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 116 
 TYR   0.020   0.002   TYR K 222 
 PHE   0.027   0.002   PHE K 299 
 TRP   0.014   0.002   TRP K 221 
 HIS   0.005   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 (16229)
  covalent geometry    : angle       0.60948 (23175)
  hydrogen bonds       : bond        0.07683 (  886)
  hydrogen bonds       : angle       3.26748 ( 2222)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.8014 (t0) cc_final: 0.7478 (t0)
REVERT: F   59 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7804 (tttm)
REVERT: K   93 PHE cc_start: 0.2073 (t80) cc_final: 0.0941 (m-80)
REVERT: K  172 MET cc_start: -0.1628 (mmm) cc_final: -0.1910 (mmp)
REVERT: K  191 MET cc_start: 0.1516 (mtt) cc_final: 0.0407 (tpt)
REVERT: K  332 MET cc_start: 0.2000 (tpp) cc_final: 0.1155 (mmt)
  outliers start: 12
  outliers final: 10
  residues processed: 136
  average time/residue: 0.1686
  time to fit residues: 31.7587
Evaluate side-chains
  131 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   99 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  199 TYR
Chi-restraints excluded: chain K residue  201 LEU
Chi-restraints excluded: chain K residue  257 PHE
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 105 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 136 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
K  80 ASN
K 515 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.174313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.136303 restraints weight = 26203.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 3.01
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3724
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3724 r_free = 0.3724    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3724 r_free = 0.3724    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3724
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  16229  Z= 0.171
  Angle     :  0.563   8.369  23175  Z= 0.333
  Chirality :  0.037   0.148   2606
  Planarity :  0.004   0.042   1927
  Dihedral  : 29.338 179.536   4481
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 12.64 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.25), residues: 1138
  helix:  2.23 (0.20), residues: 673
  sheet:  1.21 (0.65), residues: 64
  loop : -0.98 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 317 
 TYR   0.013   0.001   TYR K  49 
 PHE   0.029   0.002   PHE K 299 
 TRP   0.013   0.002   TRP K 221 
 HIS   0.004   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (16229)
  covalent geometry    : angle       0.56306 (23175)
  hydrogen bonds       : bond        0.06314 (  886)
  hydrogen bonds       : angle       3.13601 ( 2222)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.7991 (t0) cc_final: 0.7445 (t0)
REVERT: D   52 THR cc_start: 0.8219 (m) cc_final: 0.7915 (m)
REVERT: K   93 PHE cc_start: 0.2112 (t80) cc_final: 0.1000 (m-80)
REVERT: K  172 MET cc_start: -0.1688 (mmm) cc_final: -0.2051 (mmp)
REVERT: K  191 MET cc_start: 0.1591 (mtt) cc_final: 0.0381 (tpt)
REVERT: K  332 MET cc_start: 0.1953 (tpp) cc_final: 0.1059 (tpp)
  outliers start: 13
  outliers final: 10
  residues processed: 135
  average time/residue: 0.1700
  time to fit residues: 31.6274
Evaluate side-chains
  132 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   99 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  122 THR
Chi-restraints excluded: chain K residue  199 TYR
Chi-restraints excluded: chain K residue  257 PHE
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 121 optimal weight:   10.0000
   chunk 12 optimal weight:    0.2980
   chunk 130 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 122 optimal weight:    1.9990
   chunk 44 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 115 optimal weight:    0.0870
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.175268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.134468 restraints weight = 26382.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.59
r_work: 0.3097 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16229  Z= 0.146
  Angle     :  0.553   8.188  23175  Z= 0.328
  Chirality :  0.036   0.145   2606
  Planarity :  0.004   0.045   1927
  Dihedral  : 29.308 179.495   4481
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 13.14 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.25), residues: 1138
  helix:  2.37 (0.20), residues: 675
  sheet:  1.22 (0.64), residues: 64
  loop : -0.87 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  86 
 TYR   0.016   0.001   TYR K 193 
 PHE   0.028   0.001   PHE K 299 
 TRP   0.064   0.003   TRP K 334 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (16229)
  covalent geometry    : angle       0.55350 (23175)
  hydrogen bonds       : bond        0.05644 (  886)
  hydrogen bonds       : angle       3.08806 ( 2222)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.8231 (t0) cc_final: 0.7585 (t0)
REVERT: D   52 THR cc_start: 0.8420 (m) cc_final: 0.8118 (m)
REVERT: K  172 MET cc_start: 0.0512 (mmm) cc_final: -0.0117 (mmp)
  outliers start: 8
  outliers final: 8
  residues processed: 130
  average time/residue: 0.1620
  time to fit residues: 29.0472
Evaluate side-chains
  133 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   99 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue  119 ILE
Chi-restraints excluded: chain K residue  199 TYR
Chi-restraints excluded: chain K residue  257 PHE
Chi-restraints excluded: chain K residue  480 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 110 optimal weight:    1.9990
   chunk 117 optimal weight:    8.9990
   chunk 100 optimal weight:    7.9990
   chunk 138 optimal weight:    6.9990
   chunk 127 optimal weight:    5.9990
   chunk 119 optimal weight:    1.9990
   chunk 134 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.172767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.132452 restraints weight = 25930.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 2.73
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3667
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3667 r_free = 0.3667    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3667 r_free = 0.3667    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3667
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  16229  Z= 0.225
  Angle     :  0.619   8.390  23175  Z= 0.361
  Chirality :  0.039   0.152   2606
  Planarity :  0.005   0.041   1927
  Dihedral  : 29.457 179.651   4481
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 13.14 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.25), residues: 1138
  helix:  2.03 (0.20), residues: 679
  sheet:  0.94 (0.63), residues: 66
  loop : -1.12 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 116 
 TYR   0.023   0.002   TYR K 222 
 PHE   0.029   0.002   PHE K 299 
 TRP   0.038   0.003   TRP K 334 
 HIS   0.006   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 (16229)
  covalent geometry    : angle       0.61949 (23175)
  hydrogen bonds       : bond        0.07626 (  886)
  hydrogen bonds       : angle       3.28941 ( 2222)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2869.14 seconds
wall clock time: 50 minutes 2.17 seconds (3002.17 seconds total)