Starting phenix.real_space_refine
on Wed Mar  4 15:20:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ccq_30339/03_2026/7ccq_30339.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ccq_30339/03_2026/7ccq_30339.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ccq_30339/03_2026/7ccq_30339.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ccq_30339/03_2026/7ccq_30339.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ccq_30339/03_2026/7ccq_30339.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ccq_30339/03_2026/7ccq_30339.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     294      5.49       5
     S      29      5.16       5
     C    8443      2.51       5
     N    2743      2.21       5
     O    3348      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 14857
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 784
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "B"
      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: "C"
      Number of atoms: 787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 787
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
    Chain: "D"
      Number of atoms: 720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 720
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 633
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 789
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 4, 'TRANS': 97}
    Chain: "H"
      Number of atoms: 725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "K"
      Number of atoms: 2958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2958
          Classifications: {'peptide': 361}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 348}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "I"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Time building chain proxies: 3.73, per 1000 atoms: 0.25
  Number of scatterers: 14857
  At special positions: 0
  Unit cell: (125, 113, 139, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      29     16.00
     P     294     15.00
     O    3348      8.00
     N    2743      7.00
     C    8443      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: 1.22
  Conformation dependent library (CDL) restraints added in 593.1 milliseconds
  

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2074

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 14 sheets defined
      66.2% alpha, 6.0% beta
      134 base pairs and 240 stacking pairs defined.
    Time for finding SS restraints: 2.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.596A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.607A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    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
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.730A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.157A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.677A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.531A  pdb=" N   SER D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.238A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.531A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
    Processing helix  chain 'K' and resid 161 through 176
    Processing helix  chain 'K' and resid 178 through 198
      removed outlier: 4.309A  pdb=" N   ALA K 182 " --> pdb=" O   ASP K 178 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLY K 184 " --> pdb=" O   SER K 180 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS K 198 " --> pdb=" O   LEU K 194 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 200 through 204
      removed outlier: 3.875A  pdb=" N   ARG K 204 " --> pdb=" O   SER K 201 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 260 through 266
      removed outlier: 3.663A  pdb=" N   GLN K 264 " --> pdb=" O   ASN K 260 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 272 through 289
      removed outlier: 4.354A  pdb=" N   ASN K 289 " --> pdb=" O   LYS K 285 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 331 through 335
    Processing helix  chain 'K' and resid 345 through 354
    Processing helix  chain 'K' and resid 379 through 389
    Processing helix  chain 'K' and resid 405 through 424
    Processing helix  chain 'K' and resid 425 through 427
      No H-bonds generated for 'chain 'K' and resid 425 through 427'
    Processing helix  chain 'K' and resid 434 through 449
      removed outlier: 3.911A  pdb=" N   VAL K 438 " --> pdb=" O   SER K 434 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 452 through 458
      removed outlier: 3.853A  pdb=" N   ASP K 456 " --> pdb=" O   SER K 453 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   ARG K 457 " --> pdb=" O   GLN K 454 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   LYS K 458 " --> pdb=" O   TRP K 455 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 459 through 477
    Processing helix  chain 'K' and resid 497 through 513
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.030A  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
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 5.959A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.264A  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 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.859A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.737A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 6.991A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 206 through 208
      removed outlier: 3.518A  pdb=" N   PHE K 230 " --> pdb=" O   THR K 321 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 206 through 208
      removed outlier: 3.518A  pdb=" N   PHE K 230 " --> pdb=" O   THR K 321 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU K 311 " --> pdb=" O   ILE K 297 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE K 297 " --> pdb=" O   LEU K 311 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'K' and resid 237 through 241
    Processing sheet with id=AB5, first strand: chain 'K' and resid 324 through 326
      removed outlier: 3.893A  pdb=" N   TYR K 358 " --> pdb=" O   SER K 378 " (cutoff:3.500A)

    550 hydrogen bonds defined for protein.
    1617 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      336 hydrogen bonds
      668 hydrogen bond angles
      0 basepair planarities
      134 basepair parallelities
      240 stacking parallelities
  Total time for adding SS restraints: 4.10

  Time building geometry restraints manager: 1.72 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2815
        1.33 -     1.45: 4992
        1.45 -     1.57: 7290
        1.57 -     1.69: 584
        1.69 -     1.81: 44
  Bond restraints: 15725
  Sorted by residual:
  bond pdb=" C3'  DC J   4 "
       pdb=" O3'  DC J   4 "
    ideal  model  delta    sigma   weight residual
    1.422  1.347  0.075 3.00e-02 1.11e+03 6.18e+00
  bond pdb=" C3'  DC J   6 "
       pdb=" O3'  DC J   6 "
    ideal  model  delta    sigma   weight residual
    1.422  1.350  0.072 3.00e-02 1.11e+03 5.81e+00
  bond pdb=" C3'  DG I   8 "
       pdb=" O3'  DG I   8 "
    ideal  model  delta    sigma   weight residual
    1.422  1.355  0.067 3.00e-02 1.11e+03 5.05e+00
  bond pdb=" O5'  DC I -28 "
       pdb=" C5'  DC I -28 "
    ideal  model  delta    sigma   weight residual
    1.423  1.357  0.066 3.00e-02 1.11e+03 4.86e+00
  bond pdb=" C3'  DG I  -4 "
       pdb=" O3'  DG I  -4 "
    ideal  model  delta    sigma   weight residual
    1.422  1.356  0.066 3.00e-02 1.11e+03 4.78e+00
  ... (remaining 15720 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 20788
        1.90 -     3.81: 1519
        3.81 -     5.71: 126
        5.71 -     7.61: 30
        7.61 -     9.52: 10
  Bond angle restraints: 22473
  Sorted by residual:
  angle pdb=" O5'  DT I  31 "
        pdb=" C5'  DT I  31 "
        pdb=" C4'  DT I  31 "
      ideal   model   delta    sigma   weight residual
     110.80  103.62    7.18 1.50e+00 4.44e-01 2.29e+01
  angle pdb=" O4'  DG I -35 "
        pdb=" C1'  DG I -35 "
        pdb=" N9   DG I -35 "
      ideal   model   delta    sigma   weight residual
     108.40  101.73    6.67 1.50e+00 4.44e-01 1.98e+01
  angle pdb=" O4'  DG I  -8 "
        pdb=" C1'  DG I  -8 "
        pdb=" N9   DG I  -8 "
      ideal   model   delta    sigma   weight residual
     108.40  102.10    6.30 1.50e+00 4.44e-01 1.76e+01
  angle pdb=" C4'  DC I -26 "
        pdb=" C3'  DC I -26 "
        pdb=" O3'  DC I -26 "
      ideal   model   delta    sigma   weight residual
     110.00  104.17    5.83 1.50e+00 4.44e-01 1.51e+01
  angle pdb=" O4'  DA I  -3 "
        pdb=" C1'  DA I  -3 "
        pdb=" N9   DA I  -3 "
      ideal   model   delta    sigma   weight residual
     108.40  102.60    5.80 1.50e+00 4.44e-01 1.50e+01
  ... (remaining 22468 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.00: 7258
       32.00 -    63.99: 1432
       63.99 -    95.99: 42
       95.99 -   127.98: 1
      127.98 -   159.98: 2
  Dihedral angle restraints: 8735
    sinusoidal: 5530
      harmonic: 3205
  Sorted by residual:
  dihedral pdb=" CA  PRO D 103 "
           pdb=" C   PRO D 103 "
           pdb=" N   GLY D 104 "
           pdb=" CA  GLY D 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.37  -31.63     0      5.00e+00 4.00e-02 4.00e+01
  dihedral pdb=" CA  PRO K 361 "
           pdb=" C   PRO K 361 "
           pdb=" N   LYS K 362 "
           pdb=" CA  LYS K 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.94   28.06     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  ILE K 312 "
           pdb=" C   ILE K 312 "
           pdb=" N   SER K 313 "
           pdb=" CA  SER K 313 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.05   25.95     0      5.00e+00 4.00e-02 2.69e+01
  ... (remaining 8732 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 2126
       0.084 -    0.169: 383
       0.169 -    0.253: 22
       0.253 -    0.337: 1
       0.337 -    0.421: 4
  Chirality restraints: 2536
  Sorted by residual:
  chirality pdb=" C1'  DC I -27 "
            pdb=" O4'  DC I -27 "
            pdb=" C2'  DC I -27 "
            pdb=" N1   DC I -27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.05    0.42 2.00e-01 2.50e+01 4.44e+00
  chirality pdb=" C1'  DT J  13 "
            pdb=" O4'  DT J  13 "
            pdb=" C2'  DT J  13 "
            pdb=" N1   DT J  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.07    0.40 2.00e-01 2.50e+01 3.93e+00
  chirality pdb=" C1'  DT I  31 "
            pdb=" O4'  DT I  31 "
            pdb=" C2'  DT I  31 "
            pdb=" N1   DT I  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.10    0.37 2.00e-01 2.50e+01 3.40e+00
  ... (remaining 2533 not shown)

  Planarity restraints: 1830
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  31 "    0.052 2.00e-02 2.50e+03   5.17e-02 6.69e+01
        pdb=" N1   DT I  31 "   -0.131 2.00e-02 2.50e+03
        pdb=" C2   DT I  31 "    0.079 2.00e-02 2.50e+03
        pdb=" O2   DT I  31 "   -0.012 2.00e-02 2.50e+03
        pdb=" N3   DT I  31 "   -0.008 2.00e-02 2.50e+03
        pdb=" C4   DT I  31 "   -0.001 2.00e-02 2.50e+03
        pdb=" O4   DT I  31 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5   DT I  31 "    0.007 2.00e-02 2.50e+03
        pdb=" C7   DT I  31 "    0.017 2.00e-02 2.50e+03
        pdb=" C6   DT I  31 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  -2 "   -0.048 2.00e-02 2.50e+03   4.15e-02 3.88e+01
        pdb=" N1   DC I  -2 "    0.102 2.00e-02 2.50e+03
        pdb=" C2   DC I  -2 "   -0.050 2.00e-02 2.50e+03
        pdb=" O2   DC I  -2 "    0.013 2.00e-02 2.50e+03
        pdb=" N3   DC I  -2 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DC I  -2 "    0.001 2.00e-02 2.50e+03
        pdb=" N4   DC I  -2 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5   DC I  -2 "   -0.011 2.00e-02 2.50e+03
        pdb=" C6   DC I  -2 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  44 "   -0.026 2.00e-02 2.50e+03   3.57e-02 3.18e+01
        pdb=" N1   DT I  44 "    0.087 2.00e-02 2.50e+03
        pdb=" C2   DT I  44 "   -0.063 2.00e-02 2.50e+03
        pdb=" O2   DT I  44 "    0.011 2.00e-02 2.50e+03
        pdb=" N3   DT I  44 "    0.009 2.00e-02 2.50e+03
        pdb=" C4   DT I  44 "    0.002 2.00e-02 2.50e+03
        pdb=" O4   DT I  44 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DT I  44 "   -0.006 2.00e-02 2.50e+03
        pdb=" C7   DT I  44 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6   DT I  44 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1827 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2684
        2.77 -     3.30: 12926
        3.30 -     3.83: 29462
        3.83 -     4.37: 33969
        4.37 -     4.90: 49238
  Nonbonded interactions: 128279
  Sorted by model distance:
  nonbonded pdb=" N2   DG I  21 "
            pdb=" O2   DC J -21 "
     model   vdw
     2.235 2.496
  nonbonded pdb=" OH  TYR H  40 "
            pdb=" OP1  DG I  48 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" NH2 ARG C  32 "
            pdb=" OE1 GLU D  35 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" OH  TYR K 249 "
            pdb=" OG  SER K 333 "
     model   vdw
     2.331 3.040
  nonbonded pdb=" O   TYR C  39 "
            pdb=" OG  SER D  78 "
     model   vdw
     2.331 3.040
  ... (remaining 128274 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'
  selection = (chain 'E' and resid 40 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 24 through 101)
  selection = (chain 'F' and resid 24 through 101)
}
ncs_group {
  reference = (chain 'C' and resid 16 through 116)
  selection = (chain 'G' and resid 16 through 116)
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 32 through 123)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     17.940
  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:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.093  15725  Z= 0.435
  Angle     :  1.033   9.515  22473  Z= 0.606
  Chirality :  0.063   0.421   2536
  Planarity :  0.009   0.063   1830
  Dihedral  : 24.879 159.981   6661
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.89 (0.20), residues: 1081
  helix: -1.61 (0.15), residues: 699
  sheet: -2.19 (0.58), residues: 46
  loop : -2.16 (0.30), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F  45 
 TYR   0.050   0.004   TYR F  98 
 PHE   0.028   0.004   PHE C  25 
 TRP   0.013   0.003   TRP K 375 
 HIS   0.010   0.003   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.01007 (15725)
  covalent geometry    : angle       1.03334 (22473)
  hydrogen bonds       : bond        0.13252 (  884)
  hydrogen bonds       : angle       5.22451 ( 2285)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 337
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.8909 (mt) cc_final: 0.8285 (mt)
REVERT: A   52 ARG cc_start: 0.8806 (mtt90) cc_final: 0.8192 (mtm-85)
REVERT: A   54 TYR cc_start: 0.8594 (m-80) cc_final: 0.8291 (m-80)
REVERT: A   60 LEU cc_start: 0.8571 (mt) cc_final: 0.8318 (mt)
REVERT: A   76 GLN cc_start: 0.8404 (tp40) cc_final: 0.8083 (tm-30)
REVERT: A   79 LYS cc_start: 0.8130 (tttp) cc_final: 0.7800 (tttm)
REVERT: A   93 GLN cc_start: 0.8955 (tt0) cc_final: 0.8103 (tt0)
REVERT: B   80 THR cc_start: 0.9007 (m) cc_final: 0.8282 (p)
REVERT: C   18 SER cc_start: 0.9263 (m) cc_final: 0.8939 (p)
REVERT: C   57 TYR cc_start: 0.8928 (t80) cc_final: 0.8185 (t80)
REVERT: C   64 GLU cc_start: 0.8292 (tt0) cc_final: 0.8022 (tt0)
REVERT: C   75 LYS cc_start: 0.9270 (mmtp) cc_final: 0.8823 (mmmt)
REVERT: C   94 ASN cc_start: 0.8956 (t0) cc_final: 0.8433 (t0)
REVERT: C   95 LYS cc_start: 0.9027 (tppt) cc_final: 0.8671 (tptm)
REVERT: D   34 LYS cc_start: 0.8855 (mppt) cc_final: 0.8238 (mmmt)
REVERT: D   42 TYR cc_start: 0.8022 (t80) cc_final: 0.7797 (t80)
REVERT: D   45 LEU cc_start: 0.9503 (tp) cc_final: 0.9279 (tp)
REVERT: D   71 GLU cc_start: 0.8269 (tp30) cc_final: 0.7852 (tp30)
REVERT: D   86 ARG cc_start: 0.8149 (mmt90) cc_final: 0.7852 (mtt-85)
REVERT: E   70 LEU cc_start: 0.9373 (tp) cc_final: 0.9128 (tt)
REVERT: E   94 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8080 (mm-30)
REVERT: F   34 ILE cc_start: 0.9611 (mt) cc_final: 0.9339 (mt)
REVERT: F   59 LYS cc_start: 0.8730 (tttm) cc_final: 0.8444 (tttp)
REVERT: F   88 TYR cc_start: 0.8578 (m-80) cc_final: 0.8138 (m-80)
REVERT: G   38 ASN cc_start: 0.8359 (m110) cc_final: 0.7674 (m-40)
REVERT: G   39 TYR cc_start: 0.8766 (m-80) cc_final: 0.7635 (m-80)
REVERT: G   75 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8647 (mttm)
REVERT: G   95 LYS cc_start: 0.8998 (tttt) cc_final: 0.8623 (mtpt)
REVERT: H   34 LYS cc_start: 0.8443 (mttt) cc_final: 0.7969 (mmtm)
REVERT: K  208 LEU cc_start: 0.8089 (tp) cc_final: 0.6982 (pt)
REVERT: K  256 ASN cc_start: 0.7519 (t0) cc_final: 0.7291 (t0)
REVERT: K  351 GLN cc_start: 0.8898 (tt0) cc_final: 0.8678 (tm-30)
REVERT: K  432 LYS cc_start: 0.4770 (mmtm) cc_final: 0.4435 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 337
  average time/residue: 0.1801
  time to fit residues: 80.3197
Evaluate side-chains
  208 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:   20.0000
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  76 GLN
A 108 ASN
C  24 GLN
D  47 GLN
D  84 ASN
E  68 GLN
E 125 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  67 ASN
** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 260 ASN
K 449 ASN
K 466 ASN
K 494 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.098758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.066426 restraints weight = 48644.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.067983 restraints weight = 25662.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.068910 restraints weight = 18581.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.069423 restraints weight = 15956.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.069620 restraints weight = 14849.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  15725  Z= 0.239
  Angle     :  0.663   7.393  22473  Z= 0.382
  Chirality :  0.039   0.163   2536
  Planarity :  0.005   0.050   1830
  Dihedral  : 29.906 161.577   4426
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  8.76 %
    Favored  : 89.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.24), residues: 1081
  helix:  0.35 (0.17), residues: 715
  sheet: -1.31 (0.67), residues: 46
  loop : -1.63 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  95 
 TYR   0.023   0.002   TYR F  98 
 PHE   0.014   0.002   PHE A  67 
 TRP   0.007   0.001   TRP K 375 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 (15725)
  covalent geometry    : angle       0.66252 (22473)
  hydrogen bonds       : bond        0.05146 (  884)
  hydrogen bonds       : angle       3.78138 ( 2285)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 233
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8446 (t0) cc_final: 0.8156 (t0)
REVERT: A   87 SER cc_start: 0.9238 (p) cc_final: 0.8986 (t)
REVERT: B   80 THR cc_start: 0.9177 (m) cc_final: 0.8617 (p)
REVERT: C   18 SER cc_start: 0.9270 (m) cc_final: 0.8918 (p)
REVERT: C   57 TYR cc_start: 0.8943 (t80) cc_final: 0.8733 (t80)
REVERT: C   75 LYS cc_start: 0.9310 (mmtp) cc_final: 0.8878 (mmmt)
REVERT: C   94 ASN cc_start: 0.8933 (t0) cc_final: 0.8450 (t0)
REVERT: D   33 ARG cc_start: 0.8271 (ptp-170) cc_final: 0.7997 (ptp-170)
REVERT: D   34 LYS cc_start: 0.8778 (mppt) cc_final: 0.8111 (mmmt)
REVERT: D   71 GLU cc_start: 0.8423 (tp30) cc_final: 0.8024 (tp30)
REVERT: D   86 ARG cc_start: 0.8128 (mmt90) cc_final: 0.7903 (mtt-85)
REVERT: E   90 MET cc_start: 0.8283 (mmp) cc_final: 0.8023 (mtm)
REVERT: E   93 GLN cc_start: 0.8592 (tt0) cc_final: 0.8278 (tt0)
REVERT: E   94 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8094 (mm-30)
REVERT: E  106 ASP cc_start: 0.8045 (m-30) cc_final: 0.7704 (m-30)
REVERT: E  107 THR cc_start: 0.9448 (m) cc_final: 0.8958 (t)
REVERT: F   59 LYS cc_start: 0.8737 (tttm) cc_final: 0.8457 (tttp)
REVERT: F   88 TYR cc_start: 0.8607 (m-80) cc_final: 0.7684 (m-80)
REVERT: G   38 ASN cc_start: 0.8302 (m110) cc_final: 0.7680 (m-40)
REVERT: G   39 TYR cc_start: 0.8710 (m-80) cc_final: 0.7727 (m-80)
REVERT: G   75 LYS cc_start: 0.9029 (mmtm) cc_final: 0.8724 (mttm)
REVERT: G   95 LYS cc_start: 0.8985 (tttt) cc_final: 0.8528 (mtmt)
REVERT: H   34 LYS cc_start: 0.8303 (mttt) cc_final: 0.7865 (mmtm)
REVERT: H   47 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8314 (tm-30)
REVERT: H   83 TYR cc_start: 0.8366 (m-10) cc_final: 0.8067 (m-10)
REVERT: K  208 LEU cc_start: 0.8108 (tp) cc_final: 0.6937 (pt)
REVERT: K  236 ARG cc_start: 0.8108 (ptt90) cc_final: 0.7898 (ptt90)
REVERT: K  432 LYS cc_start: 0.4573 (mmtm) cc_final: 0.4335 (tptt)
  outliers start: 19
  outliers final: 10
  residues processed: 245
  average time/residue: 0.1388
  time to fit residues: 47.9894
Evaluate side-chains
  221 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 211
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain E residue   79 LYS
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   90 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 125 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 23 optimal weight:    0.6980
   chunk 126 optimal weight:    4.9990
   chunk 129 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 118 optimal weight:    7.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN
F  75 HIS
K 390 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.100271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.068090 restraints weight = 48539.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.069651 restraints weight = 25617.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.070645 restraints weight = 18496.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.071102 restraints weight = 15772.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.071210 restraints weight = 14695.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.3232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  15725  Z= 0.164
  Angle     :  0.592   6.932  22473  Z= 0.342
  Chirality :  0.035   0.151   2536
  Planarity :  0.004   0.042   1830
  Dihedral  : 29.598 162.752   4426
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.50 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.25), residues: 1081
  helix:  1.41 (0.18), residues: 700
  sheet: -0.99 (0.75), residues: 39
  loop : -1.33 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  79 
 TYR   0.040   0.002   TYR D  83 
 PHE   0.018   0.001   PHE K 253 
 TRP   0.007   0.001   TRP K 375 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (15725)
  covalent geometry    : angle       0.59197 (22473)
  hydrogen bonds       : bond        0.04114 (  884)
  hydrogen bonds       : angle       3.40610 ( 2285)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 243
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8423 (t0) cc_final: 0.8090 (t0)
REVERT: A   87 SER cc_start: 0.9128 (p) cc_final: 0.8893 (t)
REVERT: A  115 LYS cc_start: 0.9198 (mtmm) cc_final: 0.8985 (mtmt)
REVERT: B   35 ARG cc_start: 0.9066 (ttm-80) cc_final: 0.8789 (mtp-110)
REVERT: B   80 THR cc_start: 0.9203 (m) cc_final: 0.8650 (p)
REVERT: B   84 MET cc_start: 0.8676 (tpp) cc_final: 0.8245 (tpp)
REVERT: C   18 SER cc_start: 0.9208 (m) cc_final: 0.8894 (p)
REVERT: C   41 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7325 (mm-30)
REVERT: C   57 TYR cc_start: 0.9101 (t80) cc_final: 0.8782 (t80)
REVERT: C   75 LYS cc_start: 0.9251 (mmtp) cc_final: 0.8826 (mmmt)
REVERT: C   94 ASN cc_start: 0.8740 (t0) cc_final: 0.8330 (t0)
REVERT: D   33 ARG cc_start: 0.8230 (ptp-170) cc_final: 0.8011 (ptp-170)
REVERT: D   34 LYS cc_start: 0.8712 (mppt) cc_final: 0.8050 (mmmt)
REVERT: D   71 GLU cc_start: 0.8363 (tp30) cc_final: 0.7979 (tp30)
REVERT: D   83 TYR cc_start: 0.7585 (m-10) cc_final: 0.7308 (m-80)
REVERT: E   94 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7875 (mm-30)
REVERT: E  106 ASP cc_start: 0.8009 (m-30) cc_final: 0.7705 (m-30)
REVERT: F   59 LYS cc_start: 0.8689 (tttm) cc_final: 0.8344 (tttp)
REVERT: F   88 TYR cc_start: 0.8461 (m-10) cc_final: 0.7622 (m-80)
REVERT: G   38 ASN cc_start: 0.8111 (m110) cc_final: 0.7897 (m-40)
REVERT: G   39 TYR cc_start: 0.8669 (m-80) cc_final: 0.7984 (m-80)
REVERT: G   75 LYS cc_start: 0.9009 (mmtm) cc_final: 0.8662 (mttm)
REVERT: G   90 ASP cc_start: 0.8755 (t0) cc_final: 0.8366 (t0)
REVERT: G   91 GLU cc_start: 0.7321 (pm20) cc_final: 0.7094 (pm20)
REVERT: G   92 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7870 (mt-10)
REVERT: G   95 LYS cc_start: 0.8866 (tttt) cc_final: 0.8421 (mtpt)
REVERT: H   34 LYS cc_start: 0.8232 (mttt) cc_final: 0.7899 (mppt)
REVERT: H   47 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8228 (tm-30)
REVERT: H   59 MET cc_start: 0.8849 (tpp) cc_final: 0.8453 (tpp)
REVERT: H   71 GLU cc_start: 0.8765 (tp30) cc_final: 0.8480 (tp30)
REVERT: H   83 TYR cc_start: 0.8155 (m-10) cc_final: 0.7717 (m-10)
REVERT: K  208 LEU cc_start: 0.7985 (tp) cc_final: 0.6980 (pt)
REVERT: K  432 LYS cc_start: 0.4564 (mmtm) cc_final: 0.4234 (tptt)
  outliers start: 17
  outliers final: 7
  residues processed: 252
  average time/residue: 0.1420
  time to fit residues: 50.3426
Evaluate side-chains
  215 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 208
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain K residue  410 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 91 optimal weight:    8.9990
   chunk 108 optimal weight:    6.9990
   chunk 131 optimal weight:    4.9990
   chunk 92 optimal weight:    5.9990
   chunk 101 optimal weight:    8.9990
   chunk 95 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 118 optimal weight:    8.9990
   chunk 93 optimal weight:    7.9990
   chunk 79 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
B  75 HIS
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
E 113 HIS
K 217 HIS
** K 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 451 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.094009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.060972 restraints weight = 49558.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.062413 restraints weight = 26767.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.063262 restraints weight = 19483.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.063730 restraints weight = 16794.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.063925 restraints weight = 15637.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.3904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.094  15725  Z= 0.474
  Angle     :  0.824   9.249  22473  Z= 0.456
  Chirality :  0.048   0.247   2536
  Planarity :  0.006   0.077   1830
  Dihedral  : 30.609 162.487   4426
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 15.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 13.50 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.24), residues: 1081
  helix:  0.91 (0.18), residues: 710
  sheet: -0.75 (0.79), residues: 39
  loop : -1.53 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  86 
 TYR   0.027   0.003   TYR G  50 
 PHE   0.016   0.003   PHE K 471 
 TRP   0.009   0.002   TRP K 343 
 HIS   0.008   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.01068 (15725)
  covalent geometry    : angle       0.82403 (22473)
  hydrogen bonds       : bond        0.06893 (  884)
  hydrogen bonds       : angle       4.16276 ( 2285)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 209
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8519 (tttm) cc_final: 0.8304 (tttp)
REVERT: A   81 ASP cc_start: 0.8692 (t0) cc_final: 0.8433 (t0)
REVERT: A  115 LYS cc_start: 0.9308 (mtmm) cc_final: 0.9089 (mtmt)
REVERT: B   44 LYS cc_start: 0.9095 (mtpt) cc_final: 0.8720 (ttmm)
REVERT: B   84 MET cc_start: 0.8888 (tpp) cc_final: 0.8554 (tpp)
REVERT: C   18 SER cc_start: 0.9314 (m) cc_final: 0.9095 (p)
REVERT: C   75 LYS cc_start: 0.9351 (mmtp) cc_final: 0.8983 (mmmt)
REVERT: C   95 LYS cc_start: 0.9069 (tptt) cc_final: 0.8867 (tptm)
REVERT: C  100 VAL cc_start: 0.9574 (t) cc_final: 0.9219 (p)
REVERT: D   34 LYS cc_start: 0.8871 (mppt) cc_final: 0.8105 (mmmt)
REVERT: D   71 GLU cc_start: 0.8524 (tp30) cc_final: 0.8176 (tp30)
REVERT: D   79 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7828 (mtm-85)
REVERT: E   76 GLN cc_start: 0.8832 (pt0) cc_final: 0.8348 (pp30)
REVERT: E  106 ASP cc_start: 0.8090 (m-30) cc_final: 0.7724 (m-30)
REVERT: E  107 THR cc_start: 0.9445 (m) cc_final: 0.9233 (t)
REVERT: F   59 LYS cc_start: 0.8842 (tttm) cc_final: 0.8578 (tttp)
REVERT: F   88 TYR cc_start: 0.8686 (m-10) cc_final: 0.7869 (m-80)
REVERT: F   98 TYR cc_start: 0.9247 (m-10) cc_final: 0.8937 (m-10)
REVERT: G   39 TYR cc_start: 0.8998 (m-80) cc_final: 0.8357 (m-80)
REVERT: G   95 LYS cc_start: 0.9111 (tttt) cc_final: 0.8660 (mtpt)
REVERT: H   34 LYS cc_start: 0.8328 (mttt) cc_final: 0.7864 (mppt)
REVERT: H   47 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8509 (tm-30)
REVERT: H   71 GLU cc_start: 0.8856 (tp30) cc_final: 0.8471 (tp30)
REVERT: H   83 TYR cc_start: 0.8501 (m-10) cc_final: 0.7846 (m-10)
REVERT: K  208 LEU cc_start: 0.8286 (tp) cc_final: 0.7038 (pt)
REVERT: K  229 MET cc_start: 0.7792 (mmp) cc_final: 0.7574 (mmp)
REVERT: K  236 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7717 (ptt90)
REVERT: K  428 LYS cc_start: 0.2397 (mttm) cc_final: 0.2106 (mmmt)
REVERT: K  432 LYS cc_start: 0.5280 (mmtm) cc_final: 0.4777 (tptt)
  outliers start: 36
  outliers final: 25
  residues processed: 229
  average time/residue: 0.1464
  time to fit residues: 47.1095
Evaluate side-chains
  222 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 196
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   79 LYS
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  111 VAL
Chi-restraints excluded: chain K residue  181 THR
Chi-restraints excluded: chain K residue  236 ARG
Chi-restraints excluded: chain K residue  322 LEU
Chi-restraints excluded: chain K residue  354 LEU
Chi-restraints excluded: chain K residue  410 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 107 optimal weight:    6.9990
   chunk 76 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 81 optimal weight:   10.0000
   chunk 117 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
D  47 GLN
D  95 GLN
E  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.098387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.067147 restraints weight = 48922.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.068623 restraints weight = 27270.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.069900 restraints weight = 18041.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.069728 restraints weight = 16098.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.069686 restraints weight = 15841.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.4029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15725  Z= 0.162
  Angle     :  0.608   9.810  22473  Z= 0.350
  Chirality :  0.036   0.135   2536
  Planarity :  0.004   0.040   1830
  Dihedral  : 30.013 165.269   4426
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.56 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.25), residues: 1081
  helix:  1.56 (0.18), residues: 712
  sheet: -0.98 (0.77), residues: 39
  loop : -1.34 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 236 
 TYR   0.045   0.002   TYR D  83 
 PHE   0.016   0.001   PHE E  67 
 TRP   0.008   0.001   TRP K 375 
 HIS   0.005   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (15725)
  covalent geometry    : angle       0.60787 (22473)
  hydrogen bonds       : bond        0.04156 (  884)
  hydrogen bonds       : angle       3.42406 ( 2285)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 223
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8450 (t0) cc_final: 0.8159 (t0)
REVERT: B   80 THR cc_start: 0.9131 (m) cc_final: 0.8627 (p)
REVERT: C   18 SER cc_start: 0.9250 (m) cc_final: 0.8954 (p)
REVERT: C   75 LYS cc_start: 0.9277 (mmtp) cc_final: 0.8903 (mmmt)
REVERT: C   94 ASN cc_start: 0.8837 (t0) cc_final: 0.8473 (t0)
REVERT: C  100 VAL cc_start: 0.9584 (t) cc_final: 0.9301 (p)
REVERT: D   33 ARG cc_start: 0.8184 (ptp-170) cc_final: 0.7902 (ptp-170)
REVERT: D   34 LYS cc_start: 0.8739 (mppt) cc_final: 0.8007 (mmmt)
REVERT: D   71 GLU cc_start: 0.8499 (tp30) cc_final: 0.8139 (tp30)
REVERT: D   79 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7649 (mtm180)
REVERT: E   94 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8319 (mm-30)
REVERT: E  106 ASP cc_start: 0.8051 (m-30) cc_final: 0.7793 (m-30)
REVERT: E  107 THR cc_start: 0.9408 (m) cc_final: 0.8860 (t)
REVERT: E  125 GLN cc_start: 0.8867 (mt0) cc_final: 0.8615 (mt0)
REVERT: F   44 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8483 (mtpt)
REVERT: F   59 LYS cc_start: 0.8751 (tttm) cc_final: 0.8431 (tttp)
REVERT: F   88 TYR cc_start: 0.8509 (m-10) cc_final: 0.7824 (m-80)
REVERT: F   98 TYR cc_start: 0.9323 (m-10) cc_final: 0.9072 (m-10)
REVERT: G   38 ASN cc_start: 0.7928 (m-40) cc_final: 0.7667 (m-40)
REVERT: G   39 TYR cc_start: 0.8752 (m-80) cc_final: 0.8250 (m-80)
REVERT: G   57 TYR cc_start: 0.8476 (t80) cc_final: 0.8091 (t80)
REVERT: G   95 LYS cc_start: 0.8928 (tttt) cc_final: 0.8472 (mtpt)
REVERT: H   34 LYS cc_start: 0.8251 (mttt) cc_final: 0.7830 (mppt)
REVERT: H   47 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8307 (tm-30)
REVERT: H   71 GLU cc_start: 0.8799 (tp30) cc_final: 0.8395 (tp30)
REVERT: H   83 TYR cc_start: 0.8319 (m-10) cc_final: 0.7958 (m-10)
REVERT: K  208 LEU cc_start: 0.8125 (tp) cc_final: 0.7007 (pt)
REVERT: K  236 ARG cc_start: 0.7741 (ptt90) cc_final: 0.7522 (ptt90)
REVERT: K  428 LYS cc_start: 0.1925 (mttm) cc_final: 0.1722 (mmmt)
REVERT: K  432 LYS cc_start: 0.5207 (mmtm) cc_final: 0.4777 (tptt)
  outliers start: 19
  outliers final: 13
  residues processed: 233
  average time/residue: 0.1370
  time to fit residues: 45.9250
Evaluate side-chains
  222 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 209
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue  298 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 109 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 99 optimal weight:    0.3980
   chunk 121 optimal weight:   10.0000
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
C 110 ASN
H 109 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.098874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.066674 restraints weight = 48427.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.068092 restraints weight = 26064.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 75)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.069082 restraints weight = 19108.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.069558 restraints weight = 16273.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.069762 restraints weight = 15122.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.4264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15725  Z= 0.169
  Angle     :  0.604  10.718  22473  Z= 0.345
  Chirality :  0.035   0.182   2536
  Planarity :  0.004   0.041   1830
  Dihedral  : 29.743 165.667   4426
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.77 %
    Favored  : 80.17 %
  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:  1.33 (0.25), residues: 1081
  helix:  1.88 (0.18), residues: 708
  sheet: -0.70 (0.91), residues: 29
  loop : -1.11 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  35 
 TYR   0.054   0.002   TYR D  83 
 PHE   0.012   0.001   PHE E  67 
 TRP   0.006   0.001   TRP K 375 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (15725)
  covalent geometry    : angle       0.60359 (22473)
  hydrogen bonds       : bond        0.04075 (  884)
  hydrogen bonds       : angle       3.34640 ( 2285)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 219
  time to evaluate  : 0.429 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.8491 (t0) cc_final: 0.8203 (t0)
REVERT: B   80 THR cc_start: 0.9128 (m) cc_final: 0.8597 (p)
REVERT: C   18 SER cc_start: 0.9292 (m) cc_final: 0.8995 (p)
REVERT: C   75 LYS cc_start: 0.9257 (mmtp) cc_final: 0.8913 (mmmt)
REVERT: C   94 ASN cc_start: 0.8791 (t0) cc_final: 0.8511 (t0)
REVERT: C  100 VAL cc_start: 0.9657 (t) cc_final: 0.9346 (p)
REVERT: D   33 ARG cc_start: 0.8153 (ptp-170) cc_final: 0.7897 (ptp-170)
REVERT: D   34 LYS cc_start: 0.8620 (mppt) cc_final: 0.7973 (mmmt)
REVERT: D   71 GLU cc_start: 0.8480 (tp30) cc_final: 0.8099 (tp30)
REVERT: D   76 GLU cc_start: 0.8733 (tp30) cc_final: 0.8483 (tp30)
REVERT: E   67 PHE cc_start: 0.8848 (t80) cc_final: 0.8624 (t80)
REVERT: E  106 ASP cc_start: 0.8094 (m-30) cc_final: 0.7833 (m-30)
REVERT: E  125 GLN cc_start: 0.8899 (mt0) cc_final: 0.8643 (mt0)
REVERT: F   44 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8531 (mtpt)
REVERT: F   59 LYS cc_start: 0.8774 (tttm) cc_final: 0.8412 (tttp)
REVERT: F   88 TYR cc_start: 0.8613 (m-10) cc_final: 0.7781 (m-80)
REVERT: F   98 TYR cc_start: 0.9324 (m-10) cc_final: 0.8986 (m-10)
REVERT: G   39 TYR cc_start: 0.8715 (m-80) cc_final: 0.8206 (m-80)
REVERT: G   57 TYR cc_start: 0.8197 (t80) cc_final: 0.7983 (t80)
REVERT: G   95 LYS cc_start: 0.8892 (tttt) cc_final: 0.8448 (mtpt)
REVERT: H   34 LYS cc_start: 0.8274 (mttt) cc_final: 0.7840 (mppt)
REVERT: H   47 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8355 (tm-30)
REVERT: H   71 GLU cc_start: 0.8811 (tp30) cc_final: 0.8501 (tp30)
REVERT: H   83 TYR cc_start: 0.8318 (m-10) cc_final: 0.7754 (m-10)
REVERT: K  208 LEU cc_start: 0.8051 (tp) cc_final: 0.6999 (pt)
REVERT: K  236 ARG cc_start: 0.7842 (ptt90) cc_final: 0.7549 (ptt90)
REVERT: K  428 LYS cc_start: 0.2155 (mttm) cc_final: 0.1938 (mmmt)
REVERT: K  432 LYS cc_start: 0.5083 (mmtm) cc_final: 0.4652 (tptt)
  outliers start: 29
  outliers final: 17
  residues processed: 233
  average time/residue: 0.1287
  time to fit residues: 43.8208
Evaluate side-chains
  224 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 207
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue  181 THR
Chi-restraints excluded: chain K residue  298 MET
Chi-restraints excluded: chain K residue  374 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 83 optimal weight:    0.0570
   chunk 50 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 119 optimal weight:   10.0000
   chunk 61 optimal weight:    0.7980
   chunk 95 optimal weight:    9.9990
   chunk 93 optimal weight:    9.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    1.2902

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

Flipped N/Q/H residues before XYZ refinement:
C 110 ASN
D  47 GLN
K 217 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.098977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.066666 restraints weight = 48740.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.068229 restraints weight = 26191.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.069121 restraints weight = 18970.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.069539 restraints weight = 16270.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.069543 restraints weight = 15161.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.4457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15725  Z= 0.176
  Angle     :  0.600   8.969  22473  Z= 0.344
  Chirality :  0.035   0.165   2536
  Planarity :  0.004   0.041   1830
  Dihedral  : 29.640 166.169   4426
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.19 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.25), residues: 1081
  helix:  1.91 (0.18), residues: 708
  sheet: -0.78 (0.91), residues: 29
  loop : -1.04 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  35 
 TYR   0.044   0.002   TYR D  83 
 PHE   0.010   0.001   PHE K 357 
 TRP   0.006   0.001   TRP K 375 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (15725)
  covalent geometry    : angle       0.59950 (22473)
  hydrogen bonds       : bond        0.04081 (  884)
  hydrogen bonds       : angle       3.32231 ( 2285)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 214
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8495 (t0) cc_final: 0.8200 (t0)
REVERT: B   80 THR cc_start: 0.9140 (m) cc_final: 0.8628 (p)
REVERT: B   84 MET cc_start: 0.8279 (tpp) cc_final: 0.7489 (tpp)
REVERT: C   18 SER cc_start: 0.9297 (m) cc_final: 0.8985 (p)
REVERT: C   64 GLU cc_start: 0.8420 (tt0) cc_final: 0.7804 (tt0)
REVERT: C   75 LYS cc_start: 0.9211 (mmtp) cc_final: 0.8874 (mmmt)
REVERT: C   94 ASN cc_start: 0.8798 (t0) cc_final: 0.8506 (t0)
REVERT: C  100 VAL cc_start: 0.9651 (t) cc_final: 0.9319 (p)
REVERT: D   33 ARG cc_start: 0.8155 (ptp-170) cc_final: 0.7917 (ptp-170)
REVERT: D   34 LYS cc_start: 0.8610 (mppt) cc_final: 0.7952 (mmmt)
REVERT: D   42 TYR cc_start: 0.7623 (t80) cc_final: 0.7198 (t80)
REVERT: D   71 GLU cc_start: 0.8460 (tp30) cc_final: 0.8126 (tp30)
REVERT: D   76 GLU cc_start: 0.8817 (tp30) cc_final: 0.8616 (tp30)
REVERT: E   76 GLN cc_start: 0.8647 (pt0) cc_final: 0.7931 (pp30)
REVERT: E  106 ASP cc_start: 0.8193 (m-30) cc_final: 0.7933 (m-30)
REVERT: E  125 GLN cc_start: 0.8902 (mt0) cc_final: 0.8621 (mt0)
REVERT: F   44 LYS cc_start: 0.8773 (ttmt) cc_final: 0.8543 (mtpt)
REVERT: F   59 LYS cc_start: 0.8757 (tttm) cc_final: 0.8381 (tttp)
REVERT: F   88 TYR cc_start: 0.8661 (m-10) cc_final: 0.7805 (m-10)
REVERT: F   98 TYR cc_start: 0.9302 (m-10) cc_final: 0.9004 (m-10)
REVERT: G   39 TYR cc_start: 0.8770 (m-80) cc_final: 0.8270 (m-80)
REVERT: G   95 LYS cc_start: 0.8898 (tttt) cc_final: 0.8417 (mtpt)
REVERT: H   34 LYS cc_start: 0.8272 (mttt) cc_final: 0.7841 (mppt)
REVERT: H   47 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8386 (tm-30)
REVERT: H   71 GLU cc_start: 0.8824 (tp30) cc_final: 0.8504 (tp30)
REVERT: K  208 LEU cc_start: 0.8112 (tp) cc_final: 0.7077 (pt)
REVERT: K  428 LYS cc_start: 0.2230 (mttm) cc_final: 0.2017 (mmmt)
REVERT: K  432 LYS cc_start: 0.5022 (mmtm) cc_final: 0.4596 (tptt)
  outliers start: 29
  outliers final: 21
  residues processed: 226
  average time/residue: 0.1230
  time to fit residues: 40.5915
Evaluate side-chains
  225 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 204
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain K residue  181 THR
Chi-restraints excluded: chain K residue  217 HIS
Chi-restraints excluded: chain K residue  298 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 130 optimal weight:    5.9990
   chunk 59 optimal weight:    0.5980
   chunk 88 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 115 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   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
K 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.099549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.067387 restraints weight = 48871.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.068927 restraints weight = 26264.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.069711 restraints weight = 19015.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.070326 restraints weight = 16427.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.070427 restraints weight = 15209.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.4612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15725  Z= 0.164
  Angle     :  0.598   9.571  22473  Z= 0.343
  Chirality :  0.035   0.165   2536
  Planarity :  0.004   0.042   1830
  Dihedral  : 29.533 166.751   4426
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 18.99 %
    Favored  : 78.69 %
  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:  1.45 (0.25), residues: 1081
  helix:  1.99 (0.19), residues: 702
  sheet: -0.87 (0.91), residues: 29
  loop : -1.03 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  35 
 TYR   0.045   0.002   TYR D  83 
 PHE   0.025   0.001   PHE E  67 
 TRP   0.008   0.001   TRP K 375 
 HIS   0.006   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (15725)
  covalent geometry    : angle       0.59837 (22473)
  hydrogen bonds       : bond        0.04009 (  884)
  hydrogen bonds       : angle       3.32406 ( 2285)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 224
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8485 (t0) cc_final: 0.8197 (t0)
REVERT: B   35 ARG cc_start: 0.9072 (ttm-80) cc_final: 0.8783 (mtp-110)
REVERT: B   80 THR cc_start: 0.9127 (m) cc_final: 0.8623 (p)
REVERT: C   18 SER cc_start: 0.9303 (m) cc_final: 0.8984 (p)
REVERT: C   74 LYS cc_start: 0.9178 (tttt) cc_final: 0.8787 (tppt)
REVERT: C   75 LYS cc_start: 0.9149 (mmtp) cc_final: 0.8849 (mmmt)
REVERT: C   94 ASN cc_start: 0.8780 (t0) cc_final: 0.8497 (t0)
REVERT: D   34 LYS cc_start: 0.8547 (mppt) cc_final: 0.7943 (mmmt)
REVERT: D   71 GLU cc_start: 0.8450 (tp30) cc_final: 0.8102 (tp30)
REVERT: E   76 GLN cc_start: 0.8661 (pt0) cc_final: 0.7932 (pp30)
REVERT: E  106 ASP cc_start: 0.8135 (m-30) cc_final: 0.7932 (m-30)
REVERT: E  125 GLN cc_start: 0.8911 (mt0) cc_final: 0.8649 (mt0)
REVERT: F   44 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8566 (mtpt)
REVERT: F   59 LYS cc_start: 0.8729 (tttm) cc_final: 0.8370 (tttp)
REVERT: G   39 TYR cc_start: 0.8760 (m-80) cc_final: 0.8364 (m-80)
REVERT: G   95 LYS cc_start: 0.8872 (tttt) cc_final: 0.8391 (mtpt)
REVERT: H   34 LYS cc_start: 0.8275 (mttt) cc_final: 0.7841 (mppt)
REVERT: H   47 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8395 (tm-30)
REVERT: H   71 GLU cc_start: 0.8800 (tp30) cc_final: 0.8578 (tp30)
REVERT: K  208 LEU cc_start: 0.8054 (tp) cc_final: 0.7049 (pt)
REVERT: K  236 ARG cc_start: 0.7464 (ptt90) cc_final: 0.6873 (ptt90)
REVERT: K  432 LYS cc_start: 0.4883 (mmtm) cc_final: 0.4475 (tptt)
  outliers start: 22
  outliers final: 17
  residues processed: 236
  average time/residue: 0.1203
  time to fit residues: 41.9251
Evaluate side-chains
  227 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 210
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   83 TYR
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue  181 THR
Chi-restraints excluded: chain K residue  298 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 109 optimal weight:    5.9990
   chunk 90 optimal weight:    9.9990
   chunk 110 optimal weight:    5.9990
   chunk 129 optimal weight:    5.9990
   chunk 93 optimal weight:    0.0170
   chunk 94 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 117 optimal weight:    5.9990
   chunk 112 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   overall best weight:    1.9622

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
F  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.098222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.066218 restraints weight = 48967.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.067557 restraints weight = 27419.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.068381 restraints weight = 20294.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.068675 restraints weight = 17615.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.068952 restraints weight = 16637.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.4669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  15725  Z= 0.214
  Angle     :  0.631  10.410  22473  Z= 0.359
  Chirality :  0.037   0.181   2536
  Planarity :  0.004   0.041   1830
  Dihedral  : 29.650 166.953   4426
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.41 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.25), residues: 1081
  helix:  1.84 (0.19), residues: 709
  sheet: -0.71 (1.00), residues: 24
  loop : -1.02 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  35 
 TYR   0.089   0.003   TYR D  83 
 PHE   0.036   0.001   PHE E  67 
 TRP   0.007   0.001   TRP K 455 
 HIS   0.008   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 (15725)
  covalent geometry    : angle       0.63062 (22473)
  hydrogen bonds       : bond        0.04369 (  884)
  hydrogen bonds       : angle       3.42945 ( 2285)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 209
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8531 (t0) cc_final: 0.8242 (t0)
REVERT: B   80 THR cc_start: 0.9172 (m) cc_final: 0.8681 (p)
REVERT: C   18 SER cc_start: 0.9334 (m) cc_final: 0.9056 (p)
REVERT: C   74 LYS cc_start: 0.9224 (tttt) cc_final: 0.8774 (tppt)
REVERT: C   75 LYS cc_start: 0.9206 (mmtp) cc_final: 0.8907 (mmmt)
REVERT: C   94 ASN cc_start: 0.8825 (t0) cc_final: 0.8445 (t0)
REVERT: D   34 LYS cc_start: 0.8526 (mppt) cc_final: 0.7905 (mmmt)
REVERT: D   71 GLU cc_start: 0.8535 (tp30) cc_final: 0.8159 (tp30)
REVERT: D   76 GLU cc_start: 0.8930 (tp30) cc_final: 0.8708 (tp30)
REVERT: D   93 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8641 (mm-30)
REVERT: D  105 GLU cc_start: 0.7674 (tp30) cc_final: 0.7456 (tp30)
REVERT: E   76 GLN cc_start: 0.8696 (pt0) cc_final: 0.7955 (pp30)
REVERT: E  125 GLN cc_start: 0.8943 (mt0) cc_final: 0.8663 (mt0)
REVERT: F   44 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8539 (mtpt)
REVERT: F   59 LYS cc_start: 0.8762 (tttm) cc_final: 0.8382 (tttp)
REVERT: F   88 TYR cc_start: 0.8519 (m-10) cc_final: 0.8302 (m-80)
REVERT: G   39 TYR cc_start: 0.8883 (m-80) cc_final: 0.8531 (m-80)
REVERT: G   74 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8835 (mttp)
REVERT: G   95 LYS cc_start: 0.8944 (tttt) cc_final: 0.8438 (mtpt)
REVERT: G  110 ASN cc_start: 0.8151 (m-40) cc_final: 0.7869 (m-40)
REVERT: H   34 LYS cc_start: 0.8288 (mttt) cc_final: 0.7817 (mppt)
REVERT: H   47 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8450 (tm-30)
REVERT: H   71 GLU cc_start: 0.8888 (tp30) cc_final: 0.8634 (tp30)
REVERT: K  208 LEU cc_start: 0.8116 (tp) cc_final: 0.7100 (pt)
REVERT: K  432 LYS cc_start: 0.5164 (mmtm) cc_final: 0.4751 (tptt)
  outliers start: 25
  outliers final: 21
  residues processed: 221
  average time/residue: 0.1280
  time to fit residues: 41.4096
Evaluate side-chains
  226 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 204
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   83 TYR
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain K residue  181 THR
Chi-restraints excluded: chain K residue  217 HIS
Chi-restraints excluded: chain K residue  298 MET
Chi-restraints excluded: chain K residue  320 ILE
Chi-restraints excluded: chain K residue  322 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 112 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 115 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 130 optimal weight:    5.9990
   chunk 87 optimal weight:    8.9990
   chunk 116 optimal weight:    5.9990
   chunk 84 optimal weight:    6.9990
   chunk 121 optimal weight:   10.0000
   chunk 33 optimal weight:    0.8980
   overall best weight:    3.9586

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C  73 ASN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.095217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.062237 restraints weight = 49240.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.063632 restraints weight = 27532.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.064500 restraints weight = 20369.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.064909 restraints weight = 17570.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.065081 restraints weight = 16454.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.4794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.065  15725  Z= 0.350
  Angle     :  0.735  10.707  22473  Z= 0.413
  Chirality :  0.043   0.268   2536
  Planarity :  0.005   0.049   1830
  Dihedral  : 30.192 166.766   4426
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 15.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 19.62 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.25), residues: 1081
  helix:  1.44 (0.18), residues: 709
  sheet: -0.98 (0.87), residues: 34
  loop : -1.19 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  35 
 TYR   0.108   0.004   TYR D  83 
 PHE   0.043   0.002   PHE E  67 
 TRP   0.010   0.002   TRP K 455 
 HIS   0.012   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00790 (15725)
  covalent geometry    : angle       0.73492 (22473)
  hydrogen bonds       : bond        0.05949 (  884)
  hydrogen bonds       : angle       3.85262 ( 2285)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 202
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8533 (t0) cc_final: 0.8323 (t0)
REVERT: B   25 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.8079 (t0)
REVERT: C   18 SER cc_start: 0.9264 (m) cc_final: 0.9024 (p)
REVERT: C   74 LYS cc_start: 0.9259 (tttt) cc_final: 0.8805 (tppt)
REVERT: C   75 LYS cc_start: 0.9258 (mmtp) cc_final: 0.9012 (mmmt)
REVERT: D   34 LYS cc_start: 0.8615 (mppt) cc_final: 0.7876 (mmmt)
REVERT: D   61 ILE cc_start: 0.9701 (mm) cc_final: 0.9399 (mt)
REVERT: D   71 GLU cc_start: 0.8511 (tp30) cc_final: 0.8185 (tp30)
REVERT: D  105 GLU cc_start: 0.7845 (tp30) cc_final: 0.7624 (tp30)
REVERT: E  120 MET cc_start: 0.8964 (mtp) cc_final: 0.8419 (mtp)
REVERT: F   59 LYS cc_start: 0.8843 (tttm) cc_final: 0.8555 (tttp)
REVERT: F   88 TYR cc_start: 0.8612 (m-10) cc_final: 0.8248 (m-80)
REVERT: G   39 TYR cc_start: 0.8949 (m-80) cc_final: 0.8654 (m-80)
REVERT: G   74 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8815 (mttp)
REVERT: G   95 LYS cc_start: 0.9006 (tttt) cc_final: 0.8609 (mtpt)
REVERT: G  110 ASN cc_start: 0.8156 (m-40) cc_final: 0.7833 (m-40)
REVERT: H   34 LYS cc_start: 0.8330 (mttt) cc_final: 0.7884 (mppt)
REVERT: H   47 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8453 (tm-30)
REVERT: K  208 LEU cc_start: 0.8249 (tp) cc_final: 0.6995 (pt)
REVERT: K  432 LYS cc_start: 0.5574 (mmtm) cc_final: 0.5221 (tptt)
  outliers start: 24
  outliers final: 20
  residues processed: 215
  average time/residue: 0.1310
  time to fit residues: 40.9052
Evaluate side-chains
  216 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 194
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   83 TYR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain K residue  181 THR
Chi-restraints excluded: chain K residue  298 MET
Chi-restraints excluded: chain K residue  320 ILE
Chi-restraints excluded: chain K residue  322 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0570
   chunk 39 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 102 optimal weight:    7.9990
   chunk 71 optimal weight:    7.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
E 108 ASN
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.099540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.067429 restraints weight = 48826.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.068928 restraints weight = 26832.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.069855 restraints weight = 19658.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.070262 restraints weight = 16907.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.070518 restraints weight = 15805.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.5004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15725  Z= 0.161
  Angle     :  0.638   9.430  22473  Z= 0.364
  Chirality :  0.035   0.147   2536
  Planarity :  0.004   0.044   1830
  Dihedral  : 29.529 170.130   4426
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 20.46 %
    Favored  : 77.43 %
  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:  1.27 (0.25), residues: 1081
  helix:  1.79 (0.19), residues: 707
  sheet: -1.01 (1.15), residues: 22
  loop : -1.01 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG K 236 
 TYR   0.104   0.003   TYR D  83 
 PHE   0.032   0.001   PHE E  67 
 TRP   0.008   0.001   TRP K 375 
 HIS   0.009   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (15725)
  covalent geometry    : angle       0.63817 (22473)
  hydrogen bonds       : bond        0.04178 (  884)
  hydrogen bonds       : angle       3.42159 ( 2285)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2734.40 seconds
wall clock time: 47 minutes 50.31 seconds (2870.31 seconds total)