Starting phenix.real_space_refine
on Wed Mar  4 11:57:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d20_30552/03_2026/7d20_30552.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d20_30552/03_2026/7d20_30552.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d20_30552/03_2026/7d20_30552.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d20_30552/03_2026/7d20_30552.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d20_30552/03_2026/7d20_30552.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d20_30552/03_2026/7d20_30552.map"
  }
  resolution = 3.0
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1358 atoms to isotropic.
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     272      5.49       5
     S      14      5.16       5
     C    7237      2.51       5
     N    2397      2.21       5
     O    2916      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 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: 12836
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 732
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
    Chain: "E"
      Number of atoms: 749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 749
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "B"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 824
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 729
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "F"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 699
          Classifications: {'peptide': 87}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 85}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "G"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "I"
      Number of atoms: 2768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 2768
          Classifications: {'DNA': 136}
          Link IDs: {'rna3p': 135}
    Chain: "J"
      Number of atoms: 2808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 2808
          Classifications: {'DNA': 136}
          Link IDs: {'rna3p': 135}
    Chain: "K"
      Number of atoms: 1330
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 166, 1330
          Classifications: {'peptide': 166}
          Link IDs: {'PTRANS': 3, 'TRANS': 162}
    Chain: "H"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
  Time building chain proxies: 2.81, per 1000 atoms: 0.22
  Number of scatterers: 12836
  At special positions: 0
  Unit cell: (118.65, 99.75, 116.55, 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      14     16.00
     P     272     15.00
     O    2916      8.00
     N    2397      7.00
     C    7237      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: 1.00
  Conformation dependent library (CDL) restraints added in 378.7 milliseconds
  

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1694

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 12 sheets defined
      61.9% alpha, 6.0% beta
      132 base pairs and 237 stacking pairs defined.
    Time for finding SS restraints: 2.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 56
      removed outlier: 3.758A  pdb=" N   LYS A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 75
    Processing helix  chain 'A' and resid 87 through 114
      removed outlier: 4.010A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 127
      removed outlier: 3.854A  pdb=" N   VAL A 126 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 132
      removed outlier: 3.592A  pdb=" N   ARG A 131 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 78
      removed outlier: 3.575A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL E  76 " --> pdb=" O   ARG E  72 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LYS E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 110
      removed outlier: 3.833A  pdb=" N   LEU E  92 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 134
      removed outlier: 3.620A  pdb=" N   ARG E 133 " --> pdb=" O   ALA E 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.581A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.606A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.397A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.569A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (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
      removed outlier: 3.616A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 124
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.618A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.524A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.568A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'K' and resid 194 through 213
    Processing helix  chain 'K' and resid 254 through 264
      removed outlier: 3.885A  pdb=" N   GLU K 259 " --> pdb=" O   ALA K 255 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ALA K 260 " --> pdb=" O   LYS K 256 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLN K 264 " --> pdb=" O   ALA K 260 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 340 through 347
    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 sheet with id=AA1, first strand: chain 'A' and resid 120 through 121
    Processing sheet with id=AA2, first strand: chain 'E' and resid 85 through 86
      removed outlier: 7.260A  pdb=" N   ASN E  85 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'E' and resid 120 through 121
    Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.401A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA7, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.913A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.034A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB1, first strand: chain 'K' and resid 218 through 223
      removed outlier: 3.931A  pdb=" N   GLY K 227 " --> pdb=" O   ILE K 223 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'K' and resid 241 through 244
      removed outlier: 7.160A  pdb=" N   LEU K 320 " --> pdb=" O   VAL K 242 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   GLU K 244 " --> pdb=" O   LEU K 318 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   LEU K 318 " --> pdb=" O   GLU K 244 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   VAL K 315 " --> pdb=" O   ILE K 312 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 248 through 250
      removed outlier: 3.685A  pdb=" N   CYS K 283 " --> pdb=" O   ILE K 250 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   PHE K 275 " --> pdb=" O   TYR K 282 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1248 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      341 hydrogen bonds
      682 hydrogen bond angles
      0 basepair planarities
      132 basepair parallelities
      237 stacking parallelities
  Total time for adding SS restraints: 2.60

  Time building geometry restraints manager: 1.38 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: 2145
        1.33 -     1.45: 4532
        1.45 -     1.57: 6382
        1.57 -     1.69: 542
        1.69 -     1.81: 22
  Bond restraints: 13623
  Sorted by residual:
  bond pdb=" CA  ALA B  76 "
       pdb=" C   ALA B  76 "
    ideal  model  delta    sigma   weight residual
    1.523  1.468  0.055 1.80e-02 3.09e+03 9.40e+00
  bond pdb=" CB  ILE F  46 "
       pdb=" CG2 ILE F  46 "
    ideal  model  delta    sigma   weight residual
    1.521  1.450  0.071 3.30e-02 9.18e+02 4.68e+00
  bond pdb=" CB  THR E 113 "
       pdb=" CG2 THR E 113 "
    ideal  model  delta    sigma   weight residual
    1.521  1.454  0.067 3.30e-02 9.18e+02 4.09e+00
  bond pdb=" CB  VAL B  70 "
       pdb=" CG1 VAL B  70 "
    ideal  model  delta    sigma   weight residual
    1.521  1.458  0.063 3.30e-02 9.18e+02 3.66e+00
  bond pdb=" CB  ILE B  50 "
       pdb=" CG2 ILE B  50 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.43e+00
  ... (remaining 13618 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.49: 19534
        5.49 -    10.97: 18
       10.97 -    16.46: 0
       16.46 -    21.95: 1
       21.95 -    27.43: 1
  Bond angle restraints: 19554
  Sorted by residual:
  angle pdb=" O3'  DG J  20 "
        pdb=" P    DG J  21 "
        pdb=" OP1  DG J  21 "
      ideal   model   delta    sigma   weight residual
     108.00   80.57   27.43 3.00e+00 1.11e-01 8.36e+01
  angle pdb=" N   VAL E 119 "
        pdb=" CA  VAL E 119 "
        pdb=" C   VAL E 119 "
      ideal   model   delta    sigma   weight residual
     113.71  106.10    7.61 9.50e-01 1.11e+00 6.41e+01
  angle pdb=" O3'  DG J  20 "
        pdb=" P    DG J  21 "
        pdb=" OP2  DG J  21 "
      ideal   model   delta    sigma   weight residual
     108.00   87.00   21.00 3.00e+00 1.11e-01 4.90e+01
  angle pdb=" O3'  DG J  20 "
        pdb=" P    DG J  21 "
        pdb=" O5'  DG J  21 "
      ideal   model   delta    sigma   weight residual
     104.00   98.12    5.88 1.50e+00 4.44e-01 1.54e+01
  angle pdb=" OP1  DG J  21 "
        pdb=" P    DG J  21 "
        pdb=" OP2  DG J  21 "
      ideal   model   delta    sigma   weight residual
     120.00  130.43  -10.43 3.00e+00 1.11e-01 1.21e+01
  ... (remaining 19549 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.94: 5845
       32.94 -    65.88: 1564
       65.88 -    98.82: 53
       98.82 -   131.76: 1
      131.76 -   164.71: 1
  Dihedral angle restraints: 7464
    sinusoidal: 4830
      harmonic: 2634
  Sorted by residual:
  dihedral pdb=" CA  THR E 113 "
           pdb=" C   THR E 113 "
           pdb=" N   LEU E 114 "
           pdb=" CA  LEU E 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.65   29.35     0      5.00e+00 4.00e-02 3.45e+01
  dihedral pdb=" CA  ILE F  29 "
           pdb=" C   ILE F  29 "
           pdb=" N   THR F  30 "
           pdb=" CA  THR F  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.25  -19.75     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  PRO H 103 "
           pdb=" C   PRO H 103 "
           pdb=" N   GLY H 104 "
           pdb=" CA  GLY H 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.33  -19.67     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 7461 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.405: 2211
       0.405 -    0.809: 0
       0.809 -    1.214: 0
       1.214 -    1.619: 0
       1.619 -    2.023: 1
  Chirality restraints: 2212
  Sorted by residual:
  chirality pdb=" P    DG J  21 "
            pdb=" OP1  DG J  21 "
            pdb=" OP2  DG J  21 "
            pdb=" O5'  DG J  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35    0.32    2.02 2.00e-01 2.50e+01 1.02e+02
  chirality pdb=" CB  ILE D  54 "
            pdb=" CA  ILE D  54 "
            pdb=" CG1 ILE D  54 "
            pdb=" CG2 ILE D  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.27e-01
  chirality pdb=" CA  ILE F  29 "
            pdb=" N   ILE F  29 "
            pdb=" C   ILE F  29 "
            pdb=" CB  ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.74e-01
  ... (remaining 2209 not shown)

  Planarity restraints: 1531
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  26 "    0.029 2.00e-02 2.50e+03   1.24e-02 4.61e+00
        pdb=" N9   DG I  26 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8   DG I  26 "   -0.006 2.00e-02 2.50e+03
        pdb=" N7   DG I  26 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5   DG I  26 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DG I  26 "    0.003 2.00e-02 2.50e+03
        pdb=" O6   DG I  26 "    0.011 2.00e-02 2.50e+03
        pdb=" N1   DG I  26 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  26 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I  26 "   -0.007 2.00e-02 2.50e+03
        pdb=" N3   DG I  26 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DG I  26 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "    0.030 2.00e-02 2.50e+03   1.29e-02 4.55e+00
        pdb=" N9   DA I -35 "   -0.027 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "    0.011 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "   -0.007 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  24 "   -0.002 2.00e-02 2.50e+03   1.32e-02 3.91e+00
        pdb=" N1   DC J  24 "    0.004 2.00e-02 2.50e+03
        pdb=" C2   DC J  24 "   -0.031 2.00e-02 2.50e+03
        pdb=" O2   DC J  24 "    0.018 2.00e-02 2.50e+03
        pdb=" N3   DC J  24 "    0.008 2.00e-02 2.50e+03
        pdb=" C4   DC J  24 "   -0.012 2.00e-02 2.50e+03
        pdb=" N4   DC J  24 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DC J  24 "    0.005 2.00e-02 2.50e+03
        pdb=" C6   DC J  24 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1528 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.38: 38
        2.38 -     3.01: 6761
        3.01 -     3.64: 21719
        3.64 -     4.27: 34416
        4.27 -     4.90: 50373
  Nonbonded interactions: 113307
  Sorted by model distance:
  nonbonded pdb=" OXT GLY B 102 "
            pdb=" ND2 ASN H  67 "
     model   vdw
     1.752 3.120
  nonbonded pdb=" OG1 THR A  79 "
            pdb=" O   VAL A  82 "
     model   vdw
     2.039 3.040
  nonbonded pdb=" O   ALA K 255 "
            pdb=" OH  TYR K 274 "
     model   vdw
     2.088 3.040
  nonbonded pdb=" OD2 ASP D  68 "
            pdb=" OH  TYR F  98 "
     model   vdw
     2.121 3.040
  nonbonded pdb=" OH  TYR B  98 "
            pdb=" OD2 ASP H  68 "
     model   vdw
     2.132 3.040
  ... (remaining 113302 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 46 through 134)
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 23 through 102)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 12 through 118)
}
ncs_group {
  reference = (chain 'D' and resid 33 through 124)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     14.440
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.071  13623  Z= 0.397
  Angle     :  0.811  27.433  19554  Z= 0.464
  Chirality :  0.061   2.023   2212
  Planarity :  0.004   0.039   1531
  Dihedral  : 28.627 164.706   5770
  Min Nonbonded Distance : 1.752

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  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: -3.29 (0.23), residues: 896
  helix: -1.58 (0.18), residues: 561
  sheet: -3.38 (0.76), residues: 26
  loop : -3.03 (0.29), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 118 
 TYR   0.015   0.002   TYR K 274 
 PHE   0.027   0.002   PHE G  25 
 TRP   0.006   0.002   TRP K 349 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00926 (13623)
  covalent geometry    : angle       0.81094 (19554)
  hydrogen bonds       : bond        0.10803 (  764)
  hydrogen bonds       : angle       4.82231 ( 1930)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.8397 (tttt) cc_final: 0.7808 (tttp)
REVERT: E   53 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7983 (ttmm)
REVERT: E   59 HIS cc_start: 0.7451 (m-70) cc_final: 0.6808 (m170)
REVERT: E  131 ARG cc_start: 0.8275 (tmt-80) cc_final: 0.8042 (ttp80)
REVERT: B   44 LYS cc_start: 0.8510 (tttt) cc_final: 0.8292 (tttt)
REVERT: C   15 LYS cc_start: 0.8510 (pttm) cc_final: 0.8252 (pttt)
REVERT: C   36 LYS cc_start: 0.8870 (ptmm) cc_final: 0.8542 (ptpt)
REVERT: C   50 TYR cc_start: 0.8890 (t80) cc_final: 0.8543 (t80)
REVERT: C   75 LYS cc_start: 0.8255 (mttp) cc_final: 0.8021 (mtpp)
REVERT: C   90 ASP cc_start: 0.7868 (t0) cc_final: 0.7547 (t0)
REVERT: C   95 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8407 (mtpp)
REVERT: C  104 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8291 (mm110)
REVERT: D   51 ASP cc_start: 0.7960 (p0) cc_final: 0.7621 (p0)
REVERT: D   76 GLU cc_start: 0.8022 (tp30) cc_final: 0.7530 (tp30)
REVERT: D   85 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8761 (mtmm)
REVERT: G   19 SER cc_start: 0.9475 (t) cc_final: 0.9121 (p)
REVERT: K  218 MET cc_start: 0.5989 (mpp) cc_final: 0.5753 (mpp)
REVERT: K  310 HIS cc_start: 0.7529 (t70) cc_final: 0.6996 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.9425
  time to fit residues: 160.3558
Evaluate side-chains
  119 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   50.0000
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:   50.0000
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 115 HIS
E  59 HIS
E 115 HIS
B  27 GLN
D  47 GLN
D  49 HIS
D  84 ASN
D  95 GLN
F  18 HIS
F  75 HIS
G  31 HIS
** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.163014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.098903 restraints weight = 20646.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.45
r_work: 0.2990 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13623  Z= 0.156
  Angle     :  0.665  26.798  19554  Z= 0.368
  Chirality :  0.056   2.030   2212
  Planarity :  0.004   0.035   1531
  Dihedral  : 31.003 164.574   3983
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.21 %
    Favored  : 82.54 %
  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: -0.82 (0.27), residues: 896
  helix:  0.38 (0.21), residues: 573
  sheet: -2.66 (0.68), residues: 41
  loop : -2.07 (0.33), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  92 
 TYR   0.014   0.002   TYR D  40 
 PHE   0.010   0.001   PHE A  67 
 TRP   0.005   0.001   TRP A  86 
 HIS   0.005   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (13623)
  covalent geometry    : angle       0.66500 (19554)
  hydrogen bonds       : bond        0.03640 (  764)
  hydrogen bonds       : angle       3.24824 ( 1930)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.7539 (tttt) cc_final: 0.7043 (tttm)
REVERT: E   53 LYS cc_start: 0.7494 (ttmt) cc_final: 0.7283 (ttmm)
REVERT: E   59 HIS cc_start: 0.7114 (m90) cc_final: 0.6278 (m90)
REVERT: E   83 ASP cc_start: 0.8811 (m-30) cc_final: 0.7651 (p0)
REVERT: E  131 ARG cc_start: 0.8254 (ttt-90) cc_final: 0.7697 (ttp-110)
REVERT: B   77 LYS cc_start: 0.8904 (mttt) cc_final: 0.8613 (mtmt)
REVERT: C   15 LYS cc_start: 0.7555 (pttm) cc_final: 0.7337 (pttt)
REVERT: C   19 SER cc_start: 0.9027 (t) cc_final: 0.8552 (p)
REVERT: C   36 LYS cc_start: 0.8093 (ptmm) cc_final: 0.7823 (ptpt)
REVERT: C   75 LYS cc_start: 0.7535 (mttp) cc_final: 0.7302 (mtpp)
REVERT: C   92 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7084 (mt-10)
REVERT: C   95 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7886 (mtpp)
REVERT: C   99 ARG cc_start: 0.7654 (mtt180) cc_final: 0.6667 (mmt-90)
REVERT: D   47 GLN cc_start: 0.8327 (mt0) cc_final: 0.8077 (mt0)
REVERT: D   85 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8418 (mtmm)
REVERT: F   84 MET cc_start: 0.7412 (mmm) cc_final: 0.6931 (mmt)
REVERT: G   19 SER cc_start: 0.9244 (t) cc_final: 0.9015 (p)
REVERT: G   36 LYS cc_start: 0.8519 (pptt) cc_final: 0.7949 (pttt)
REVERT: G   90 ASP cc_start: 0.7890 (t0) cc_final: 0.7487 (t0)
REVERT: G   92 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7901 (mt-10)
REVERT: K  310 HIS cc_start: 0.7194 (t70) cc_final: 0.6599 (t-90)
  outliers start: 17
  outliers final: 5
  residues processed: 150
  average time/residue: 0.8046
  time to fit residues: 128.6728
Evaluate side-chains
  125 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 120
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue  113 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 78 optimal weight:   10.0000
   chunk 105 optimal weight:    4.9990
   chunk 108 optimal weight:    3.9990
   chunk 53 optimal weight:    0.4980
   chunk 67 optimal weight:    7.9990
   chunk 97 optimal weight:    8.9990
   chunk 104 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0870
   chunk 100 optimal weight:   30.0000
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
E  95 GLN
B  27 GLN
F  27 GLN
F  93 GLN
G 110 ASN
** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.164235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.100666 restraints weight = 20794.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 2.42
r_work: 0.3036 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13623  Z= 0.145
  Angle     :  0.635  26.822  19554  Z= 0.351
  Chirality :  0.055   2.005   2212
  Planarity :  0.004   0.036   1531
  Dihedral  : 30.646 166.955   3983
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.93 %
    Favored  : 79.63 %
  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:  0.55 (0.28), residues: 896
  helix:  1.36 (0.21), residues: 576
  sheet: -2.32 (0.67), residues: 44
  loop : -1.28 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  71 
 TYR   0.016   0.001   TYR D  40 
 PHE   0.007   0.001   PHE C  25 
 TRP   0.004   0.001   TRP K 349 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (13623)
  covalent geometry    : angle       0.63463 (19554)
  hydrogen bonds       : bond        0.03338 (  764)
  hydrogen bonds       : angle       2.95864 ( 1930)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.7395 (tttt) cc_final: 0.6931 (tttp)
REVERT: A   92 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6725 (tp)
REVERT: E   59 HIS cc_start: 0.6911 (m90) cc_final: 0.6236 (m90)
REVERT: E   83 ASP cc_start: 0.8781 (m-30) cc_final: 0.7619 (p0)
REVERT: E  131 ARG cc_start: 0.8276 (ttt-90) cc_final: 0.7776 (ttp-110)
REVERT: B   74 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8126 (mt-10)
REVERT: C   19 SER cc_start: 0.9106 (t) cc_final: 0.8634 (p)
REVERT: C   36 LYS cc_start: 0.8069 (ptmm) cc_final: 0.7747 (ptpt)
REVERT: C   72 ASP cc_start: 0.8144 (m-30) cc_final: 0.7935 (m-30)
REVERT: C   90 ASP cc_start: 0.6911 (t0) cc_final: 0.6347 (t0)
REVERT: C   92 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7222 (mt-10)
REVERT: C   95 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7811 (mtpp)
REVERT: C   99 ARG cc_start: 0.7573 (mtt180) cc_final: 0.6604 (mmt-90)
REVERT: C  104 GLN cc_start: 0.8120 (tp40) cc_final: 0.7453 (mm110)
REVERT: D   42 TYR cc_start: 0.7325 (t80) cc_final: 0.7069 (t80)
REVERT: D   85 LYS cc_start: 0.8654 (mtpt) cc_final: 0.8330 (mtmm)
REVERT: F   21 VAL cc_start: 0.5754 (OUTLIER) cc_final: 0.5390 (p)
REVERT: F   84 MET cc_start: 0.7380 (mmm) cc_final: 0.7060 (mmt)
REVERT: G   19 SER cc_start: 0.9243 (t) cc_final: 0.9022 (p)
REVERT: G   36 LYS cc_start: 0.8132 (pptt) cc_final: 0.7816 (pttt)
REVERT: G   90 ASP cc_start: 0.7987 (t0) cc_final: 0.7564 (t0)
REVERT: G   92 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7672 (mt-10)
REVERT: H   46 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.6883 (mppt)
REVERT: H  105 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7066 (mm-30)
  outliers start: 26
  outliers final: 9
  residues processed: 146
  average time/residue: 0.7146
  time to fit residues: 111.8683
Evaluate side-chains
  126 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain K residue  307 THR
Chi-restraints excluded: chain H residue   46 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:   40.0000
   chunk 89 optimal weight:    6.9990
   chunk 71 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 74 optimal weight:   20.0000
   chunk 80 optimal weight:    6.9990
   chunk 76 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   50.0000
   chunk 107 optimal weight:    3.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
E 127 GLN
B  27 GLN
B  93 GLN
F  25 ASN
F  27 GLN
G  73 ASN
** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 310 HIS
** H  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.158818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.093533 restraints weight = 20872.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 2.39
r_work: 0.2923 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.068  13623  Z= 0.338
  Angle     :  0.736  27.152  19554  Z= 0.397
  Chirality :  0.059   1.965   2212
  Planarity :  0.005   0.044   1531
  Dihedral  : 31.500 169.536   3983
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 19.84 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.23 (0.28), residues: 896
  helix:  1.10 (0.21), residues: 576
  sheet: -2.46 (0.67), residues: 44
  loop : -1.35 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG D  92 
 TYR   0.015   0.002   TYR H  40 
 PHE   0.021   0.002   PHE G  25 
 TRP   0.006   0.002   TRP A  86 
 HIS   0.004   0.001   HIS E 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00790 (13623)
  covalent geometry    : angle       0.73621 (19554)
  hydrogen bonds       : bond        0.04313 (  764)
  hydrogen bonds       : angle       3.31872 ( 1930)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 135
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7029 (tt0) cc_final: 0.6799 (tt0)
REVERT: A   53 LYS cc_start: 0.7611 (tttt) cc_final: 0.7119 (tttp)
REVERT: A   92 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6900 (tp)
REVERT: E   59 HIS cc_start: 0.7218 (m90) cc_final: 0.6653 (m90)
REVERT: E   63 ARG cc_start: 0.7105 (mmp-170) cc_final: 0.6766 (mmp80)
REVERT: E  131 ARG cc_start: 0.8358 (ttt-90) cc_final: 0.7695 (ttp-110)
REVERT: C   15 LYS cc_start: 0.7402 (pttt) cc_final: 0.7118 (pmtt)
REVERT: C   19 SER cc_start: 0.9039 (t) cc_final: 0.8513 (p)
REVERT: C   29 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.5883 (ttp-170)
REVERT: C   36 LYS cc_start: 0.8191 (ptmm) cc_final: 0.7900 (ptpt)
REVERT: C   72 ASP cc_start: 0.7963 (m-30) cc_final: 0.7748 (m-30)
REVERT: C   90 ASP cc_start: 0.7045 (t0) cc_final: 0.6423 (t0)
REVERT: C   92 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7165 (mt-10)
REVERT: C   95 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7890 (mtpp)
REVERT: D   85 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8399 (mtmm)
REVERT: D  108 LYS cc_start: 0.6863 (mmtt) cc_final: 0.6435 (mmtt)
REVERT: F   21 VAL cc_start: 0.5883 (OUTLIER) cc_final: 0.5550 (p)
REVERT: F   84 MET cc_start: 0.7266 (mmm) cc_final: 0.6790 (mmp)
REVERT: G   19 SER cc_start: 0.9230 (t) cc_final: 0.8965 (p)
REVERT: G   36 LYS cc_start: 0.8224 (pptt) cc_final: 0.7868 (pttt)
REVERT: G   92 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7931 (mt-10)
REVERT: K  310 HIS cc_start: 0.7435 (t70) cc_final: 0.6741 (t70)
REVERT: H  105 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7608 (tp30)
  outliers start: 32
  outliers final: 14
  residues processed: 157
  average time/residue: 0.8253
  time to fit residues: 137.8066
Evaluate side-chains
  139 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   29 ARG
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain K residue  307 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 87 optimal weight:   20.0000
   chunk 53 optimal weight:    0.2980
   chunk 63 optimal weight:   10.0000
   chunk 82 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 84 optimal weight:    8.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
E 127 GLN
C  38 ASN
F  27 GLN
G 104 GLN
** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  49 HIS
H  84 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.161404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.096415 restraints weight = 20543.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 2.41
r_work: 0.2968 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6950
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13623  Z= 0.190
  Angle     :  0.653  27.031  19554  Z= 0.356
  Chirality :  0.056   1.997   2212
  Planarity :  0.004   0.054   1531
  Dihedral  : 31.032 168.855   3983
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 21.83 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.28), residues: 896
  helix:  1.47 (0.21), residues: 575
  sheet: -2.24 (0.70), residues: 44
  loop : -1.05 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C  71 
 TYR   0.014   0.001   TYR H  40 
 PHE   0.009   0.001   PHE G  25 
 TRP   0.005   0.001   TRP K 349 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (13623)
  covalent geometry    : angle       0.65266 (19554)
  hydrogen bonds       : bond        0.03526 (  764)
  hydrogen bonds       : angle       3.01120 ( 1930)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.6957 (tt0) cc_final: 0.6697 (tt0)
REVERT: A   53 LYS cc_start: 0.7437 (tttt) cc_final: 0.7009 (tttp)
REVERT: E   59 HIS cc_start: 0.6992 (m90) cc_final: 0.6360 (m90)
REVERT: E   63 ARG cc_start: 0.6936 (mmp-170) cc_final: 0.6630 (mmp80)
REVERT: E   83 ASP cc_start: 0.8748 (m-30) cc_final: 0.7675 (p0)
REVERT: E  131 ARG cc_start: 0.8316 (ttt-90) cc_final: 0.7739 (ttp-110)
REVERT: B   74 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8143 (mt-10)
REVERT: C   15 LYS cc_start: 0.7200 (pttt) cc_final: 0.6941 (pttm)
REVERT: C   19 SER cc_start: 0.9066 (t) cc_final: 0.8590 (p)
REVERT: C   36 LYS cc_start: 0.8088 (ptmm) cc_final: 0.7847 (ptpt)
REVERT: C   90 ASP cc_start: 0.6815 (t0) cc_final: 0.6184 (t0)
REVERT: C   92 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7153 (mt-10)
REVERT: C   95 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7967 (mtpp)
REVERT: D   85 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8377 (mtmm)
REVERT: D  105 GLU cc_start: 0.7686 (tp30) cc_final: 0.7470 (tp30)
REVERT: F   21 VAL cc_start: 0.6086 (OUTLIER) cc_final: 0.5785 (p)
REVERT: G   19 SER cc_start: 0.9252 (t) cc_final: 0.9014 (p)
REVERT: G   36 LYS cc_start: 0.8045 (pptt) cc_final: 0.7732 (pttt)
REVERT: G   90 ASP cc_start: 0.7997 (t0) cc_final: 0.7581 (t0)
REVERT: K  310 HIS cc_start: 0.7344 (t70) cc_final: 0.6668 (t70)
  outliers start: 25
  outliers final: 16
  residues processed: 144
  average time/residue: 0.7816
  time to fit residues: 120.0185
Evaluate side-chains
  130 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain K residue  307 THR
Chi-restraints excluded: chain H residue  113 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 86 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 63 optimal weight:   20.0000
   chunk 4 optimal weight:    0.6980
   chunk 93 optimal weight:   20.0000
   chunk 10 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 72 optimal weight:    7.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
E 127 GLN
C 104 GLN
F  27 GLN
** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.162145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.097302 restraints weight = 20453.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.40
r_work: 0.3002 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13623  Z= 0.172
  Angle     :  0.642  27.165  19554  Z= 0.349
  Chirality :  0.055   2.004   2212
  Planarity :  0.004   0.057   1531
  Dihedral  : 30.946 171.128   3983
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 21.83 %
    Favored  : 75.00 %
  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:  1.08 (0.28), residues: 896
  helix:  1.71 (0.21), residues: 575
  sheet: -2.02 (0.74), residues: 44
  loop : -0.91 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG C  71 
 TYR   0.024   0.001   TYR B  88 
 PHE   0.008   0.001   PHE G  25 
 TRP   0.004   0.001   TRP K 349 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (13623)
  covalent geometry    : angle       0.64189 (19554)
  hydrogen bonds       : bond        0.03439 (  764)
  hydrogen bonds       : angle       2.92528 ( 1930)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7027 (tt0) cc_final: 0.6761 (tt0)
REVERT: A   53 LYS cc_start: 0.7269 (tttt) cc_final: 0.6884 (tttp)
REVERT: E   59 HIS cc_start: 0.7152 (m90) cc_final: 0.6468 (m90)
REVERT: E   60 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7935 (mt)
REVERT: E   63 ARG cc_start: 0.6845 (mmp-170) cc_final: 0.6545 (mmp80)
REVERT: E   83 ASP cc_start: 0.8760 (m-30) cc_final: 0.7755 (p0)
REVERT: E  131 ARG cc_start: 0.8296 (ttt-90) cc_final: 0.7722 (ttp-110)
REVERT: B   74 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7994 (mt-10)
REVERT: C   15 LYS cc_start: 0.6924 (pttt) cc_final: 0.6711 (pttm)
REVERT: C   19 SER cc_start: 0.9062 (t) cc_final: 0.8598 (p)
REVERT: C   36 LYS cc_start: 0.7919 (ptmm) cc_final: 0.7684 (ptpt)
REVERT: C   72 ASP cc_start: 0.8155 (m-30) cc_final: 0.7939 (m-30)
REVERT: C   90 ASP cc_start: 0.6797 (t0) cc_final: 0.6149 (t0)
REVERT: C   92 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7192 (mt-10)
REVERT: C   95 LYS cc_start: 0.8308 (ttmt) cc_final: 0.7977 (mtpp)
REVERT: D   85 LYS cc_start: 0.8689 (mtpt) cc_final: 0.8384 (mtmm)
REVERT: D   93 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6590 (mm-30)
REVERT: D  105 GLU cc_start: 0.7719 (tp30) cc_final: 0.7479 (tp30)
REVERT: F   21 VAL cc_start: 0.6070 (OUTLIER) cc_final: 0.5768 (p)
REVERT: G   19 SER cc_start: 0.9239 (t) cc_final: 0.9000 (p)
REVERT: G   36 LYS cc_start: 0.7964 (pptt) cc_final: 0.7691 (pttt)
REVERT: G   90 ASP cc_start: 0.7789 (t0) cc_final: 0.7416 (t0)
REVERT: K  218 MET cc_start: 0.3920 (pmm) cc_final: 0.3705 (pmm)
REVERT: K  310 HIS cc_start: 0.7308 (t70) cc_final: 0.6652 (t70)
REVERT: H   99 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7732 (mtp180)
REVERT: H  105 GLU cc_start: 0.7401 (tp30) cc_final: 0.7043 (tp30)
  outliers start: 24
  outliers final: 12
  residues processed: 141
  average time/residue: 0.7735
  time to fit residues: 116.2240
Evaluate side-chains
  125 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain K residue  307 THR
Chi-restraints excluded: chain H residue   99 ARG
Chi-restraints excluded: chain H residue  112 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 75 optimal weight:   30.0000
   chunk 15 optimal weight:    0.0570
   chunk 18 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 76 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 82 optimal weight:    7.9990
   chunk 85 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    1.3504

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

Flipped N/Q/H residues before XYZ refinement:
E  89 GLN
E 127 GLN
B  25 ASN
C  24 GLN
C  38 ASN
D  47 GLN
F  27 GLN
** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.163326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.098543 restraints weight = 20516.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.42
r_work: 0.3011 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13623  Z= 0.157
  Angle     :  0.632  27.109  19554  Z= 0.342
  Chirality :  0.055   1.999   2212
  Planarity :  0.004   0.052   1531
  Dihedral  : 30.702 172.455   3983
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 23.15 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.28), residues: 896
  helix:  1.89 (0.21), residues: 582
  sheet: -2.02 (0.72), residues: 44
  loop : -0.69 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C  71 
 TYR   0.025   0.001   TYR B  88 
 PHE   0.010   0.001   PHE A  78 
 TRP   0.004   0.001   TRP K 349 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (13623)
  covalent geometry    : angle       0.63171 (19554)
  hydrogen bonds       : bond        0.03343 (  764)
  hydrogen bonds       : angle       2.85799 ( 1930)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.7074 (tt0) cc_final: 0.6805 (tt0)
REVERT: A   53 LYS cc_start: 0.7266 (tttt) cc_final: 0.6898 (tttp)
REVERT: E   83 ASP cc_start: 0.8748 (m-30) cc_final: 0.7915 (p0)
REVERT: E  131 ARG cc_start: 0.8274 (ttt-90) cc_final: 0.7715 (ttp-110)
REVERT: B   74 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8027 (mt-10)
REVERT: C   19 SER cc_start: 0.9071 (t) cc_final: 0.8611 (p)
REVERT: C   36 LYS cc_start: 0.8049 (ptmm) cc_final: 0.7816 (ptpt)
REVERT: C   72 ASP cc_start: 0.8049 (m-30) cc_final: 0.7834 (m-30)
REVERT: C   90 ASP cc_start: 0.6837 (t0) cc_final: 0.6176 (t0)
REVERT: C   92 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7291 (mt-10)
REVERT: C   95 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8011 (mtpp)
REVERT: D   85 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8428 (mtmm)
REVERT: D   93 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6640 (mm-30)
REVERT: D  108 LYS cc_start: 0.6668 (mmtt) cc_final: 0.6273 (mmtt)
REVERT: F   21 VAL cc_start: 0.5982 (OUTLIER) cc_final: 0.5675 (p)
REVERT: G   19 SER cc_start: 0.9233 (t) cc_final: 0.8999 (p)
REVERT: G   23 LEU cc_start: 0.8145 (mt) cc_final: 0.7944 (mp)
REVERT: G   36 LYS cc_start: 0.7987 (pptt) cc_final: 0.7729 (pttt)
REVERT: G   90 ASP cc_start: 0.7802 (t0) cc_final: 0.7349 (t0)
REVERT: K  310 HIS cc_start: 0.7287 (t70) cc_final: 0.6667 (t70)
REVERT: H   99 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7691 (mtp180)
REVERT: H  105 GLU cc_start: 0.7261 (tp30) cc_final: 0.6841 (tp30)
REVERT: H  113 GLU cc_start: 0.7827 (tp30) cc_final: 0.7453 (tp30)
  outliers start: 21
  outliers final: 14
  residues processed: 138
  average time/residue: 0.7535
  time to fit residues: 111.2326
Evaluate side-chains
  131 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain K residue  307 THR
Chi-restraints excluded: chain H residue   99 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 57 optimal weight:    0.8980
   chunk 75 optimal weight:   30.0000
   chunk 91 optimal weight:   10.0000
   chunk 84 optimal weight:    8.9990
   chunk 18 optimal weight:    0.4980
   chunk 28 optimal weight:    4.9990
   chunk 79 optimal weight:    7.9990
   chunk 105 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 44 optimal weight:   20.0000
   overall best weight:    3.4786

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

Flipped N/Q/H residues before XYZ refinement:
E  95 GLN
E 127 GLN
B  27 GLN
F  25 ASN
F  27 GLN
** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.160485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.094829 restraints weight = 20388.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.40
r_work: 0.2944 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  13623  Z= 0.264
  Angle     :  0.693  27.371  19554  Z= 0.371
  Chirality :  0.057   1.989   2212
  Planarity :  0.004   0.060   1531
  Dihedral  : 31.124 173.872   3983
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 23.41 %
    Favored  : 73.15 %
  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:  1.09 (0.28), residues: 896
  helix:  1.65 (0.21), residues: 575
  sheet: -2.03 (0.72), residues: 44
  loop : -0.73 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG C  71 
 TYR   0.035   0.002   TYR B  88 
 PHE   0.013   0.002   PHE G  25 
 TRP   0.005   0.001   TRP K 349 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00615 (13623)
  covalent geometry    : angle       0.69344 (19554)
  hydrogen bonds       : bond        0.03910 (  764)
  hydrogen bonds       : angle       3.08878 ( 1930)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7032 (tt0) cc_final: 0.6790 (tt0)
REVERT: A   53 LYS cc_start: 0.7310 (tttt) cc_final: 0.6930 (tttp)
REVERT: E   59 HIS cc_start: 0.7026 (m-70) cc_final: 0.6802 (m90)
REVERT: E   60 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8012 (mt)
REVERT: E   63 ARG cc_start: 0.6989 (mmp-170) cc_final: 0.6684 (mmp80)
REVERT: E   83 ASP cc_start: 0.8758 (m-30) cc_final: 0.7927 (p0)
REVERT: E  131 ARG cc_start: 0.8331 (ttt-90) cc_final: 0.7744 (ttp-110)
REVERT: C   19 SER cc_start: 0.9035 (t) cc_final: 0.8510 (p)
REVERT: C   36 LYS cc_start: 0.8053 (ptmm) cc_final: 0.7817 (ptpt)
REVERT: C   90 ASP cc_start: 0.6796 (t0) cc_final: 0.6163 (t0)
REVERT: C   92 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7209 (mt-10)
REVERT: C   95 LYS cc_start: 0.8287 (ttmt) cc_final: 0.7990 (mtpp)
REVERT: D   85 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8440 (mtmm)
REVERT: D   93 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6716 (mm-30)
REVERT: D  105 GLU cc_start: 0.7725 (tp30) cc_final: 0.7402 (tp30)
REVERT: D  108 LYS cc_start: 0.6727 (mmtt) cc_final: 0.6295 (mmtt)
REVERT: F   21 VAL cc_start: 0.6059 (OUTLIER) cc_final: 0.5755 (p)
REVERT: G   19 SER cc_start: 0.9202 (t) cc_final: 0.8957 (p)
REVERT: G   36 LYS cc_start: 0.8035 (pptt) cc_final: 0.7735 (pttt)
REVERT: G   90 ASP cc_start: 0.7797 (t0) cc_final: 0.7594 (t0)
REVERT: K  310 HIS cc_start: 0.7228 (t70) cc_final: 0.6575 (t70)
REVERT: H   99 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7726 (mtp180)
REVERT: H  105 GLU cc_start: 0.7631 (tp30) cc_final: 0.7218 (tp30)
  outliers start: 26
  outliers final: 14
  residues processed: 140
  average time/residue: 0.7754
  time to fit residues: 116.0052
Evaluate side-chains
  135 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain K residue  307 THR
Chi-restraints excluded: chain H residue   99 ARG
Chi-restraints excluded: chain H residue  112 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 105 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 84 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 101 optimal weight:   20.0000
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
E 127 GLN
B  27 GLN
C  38 ASN
F  27 GLN
** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.162679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.097464 restraints weight = 20480.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.40
r_work: 0.2988 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.3268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13623  Z= 0.168
  Angle     :  0.651  27.200  19554  Z= 0.349
  Chirality :  0.055   1.999   2212
  Planarity :  0.004   0.063   1531
  Dihedral  : 30.813 173.385   3983
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 23.81 %
    Favored  : 72.62 %
  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:  1.37 (0.28), residues: 896
  helix:  1.87 (0.21), residues: 575
  sheet: -1.95 (0.72), residues: 44
  loop : -0.62 (0.38), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG C  71 
 TYR   0.028   0.002   TYR B  88 
 PHE   0.008   0.001   PHE G  25 
 TRP   0.004   0.001   TRP A  47 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (13623)
  covalent geometry    : angle       0.65067 (19554)
  hydrogen bonds       : bond        0.03429 (  764)
  hydrogen bonds       : angle       2.90566 ( 1930)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7043 (tt0) cc_final: 0.6774 (tt0)
REVERT: A   53 LYS cc_start: 0.7258 (tttt) cc_final: 0.6877 (tttp)
REVERT: E   59 HIS cc_start: 0.6771 (m-70) cc_final: 0.6504 (m90)
REVERT: E   60 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7895 (mt)
REVERT: E   63 ARG cc_start: 0.6857 (mmp-170) cc_final: 0.6570 (mmp80)
REVERT: E   83 ASP cc_start: 0.8670 (m-30) cc_final: 0.7931 (p0)
REVERT: E  131 ARG cc_start: 0.8233 (ttt-90) cc_final: 0.7647 (ttp-110)
REVERT: B   74 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8045 (mt-10)
REVERT: C   19 SER cc_start: 0.9047 (t) cc_final: 0.8574 (p)
REVERT: C   36 LYS cc_start: 0.8066 (ptmm) cc_final: 0.7813 (ptpt)
REVERT: C   90 ASP cc_start: 0.6779 (t0) cc_final: 0.6118 (t0)
REVERT: C   92 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7277 (mt-10)
REVERT: C   95 LYS cc_start: 0.8331 (ttmt) cc_final: 0.8025 (mtpp)
REVERT: D   85 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8401 (mtmm)
REVERT: D  105 GLU cc_start: 0.7672 (tp30) cc_final: 0.7351 (tp30)
REVERT: D  108 LYS cc_start: 0.6704 (mmtt) cc_final: 0.6296 (mmtt)
REVERT: F   21 VAL cc_start: 0.6009 (OUTLIER) cc_final: 0.5707 (p)
REVERT: G   19 SER cc_start: 0.9223 (t) cc_final: 0.8995 (p)
REVERT: G   23 LEU cc_start: 0.8155 (mt) cc_final: 0.7948 (mp)
REVERT: G   36 LYS cc_start: 0.8014 (pptt) cc_final: 0.7755 (pttt)
REVERT: G   90 ASP cc_start: 0.7777 (t0) cc_final: 0.7285 (t0)
REVERT: K  310 HIS cc_start: 0.7266 (t70) cc_final: 0.6650 (t70)
REVERT: H   99 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7719 (mtp180)
REVERT: H  105 GLU cc_start: 0.7453 (tp30) cc_final: 0.7059 (tp30)
REVERT: H  113 GLU cc_start: 0.7785 (tp30) cc_final: 0.7391 (tp30)
  outliers start: 27
  outliers final: 17
  residues processed: 138
  average time/residue: 0.6947
  time to fit residues: 102.7926
Evaluate side-chains
  132 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain K residue  307 THR
Chi-restraints excluded: chain H residue   99 ARG
Chi-restraints excluded: chain H residue  112 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 100 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 101 optimal weight:    9.9990
   chunk 63 optimal weight:   20.0000
   chunk 76 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
B  27 GLN
D  47 GLN
F  27 GLN
** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.162551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.097302 restraints weight = 20659.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.40
r_work: 0.2997 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6916
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.171  13623  Z= 0.215
  Angle     :  0.845  59.200  19554  Z= 0.482
  Chirality :  0.056   1.999   2212
  Planarity :  0.004   0.059   1531
  Dihedral  : 30.811 173.435   3983
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 25.00 %
    Favored  : 72.09 %
  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:  1.35 (0.28), residues: 896
  helix:  1.86 (0.21), residues: 575
  sheet: -1.94 (0.72), residues: 44
  loop : -0.65 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG C  71 
 TYR   0.030   0.002   TYR C  39 
 PHE   0.008   0.001   PHE G  25 
 TRP   0.004   0.001   TRP A  47 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (13623)
  covalent geometry    : angle       0.84499 (19554)
  hydrogen bonds       : bond        0.03434 (  764)
  hydrogen bonds       : angle       2.91693 ( 1930)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7036 (tt0) cc_final: 0.6795 (tt0)
REVERT: A   53 LYS cc_start: 0.7254 (tttt) cc_final: 0.6874 (tttp)
REVERT: E   59 HIS cc_start: 0.6772 (m-70) cc_final: 0.6503 (m90)
REVERT: E   60 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7891 (mt)
REVERT: E   63 ARG cc_start: 0.6851 (mmp-170) cc_final: 0.6566 (mmp80)
REVERT: E   83 ASP cc_start: 0.8666 (m-30) cc_final: 0.7924 (p0)
REVERT: E  131 ARG cc_start: 0.8229 (ttt-90) cc_final: 0.7642 (ttp-110)
REVERT: B   74 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8036 (mt-10)
REVERT: C   19 SER cc_start: 0.9046 (t) cc_final: 0.8572 (p)
REVERT: C   36 LYS cc_start: 0.8026 (ptmm) cc_final: 0.7776 (ptpt)
REVERT: C   38 ASN cc_start: 0.8300 (m-40) cc_final: 0.7744 (p0)
REVERT: C   90 ASP cc_start: 0.6765 (t0) cc_final: 0.6128 (t0)
REVERT: C   92 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7267 (mt-10)
REVERT: C   95 LYS cc_start: 0.8324 (ttmt) cc_final: 0.8019 (mtpp)
REVERT: D   85 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8396 (mtmm)
REVERT: D   93 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6678 (mm-30)
REVERT: D  105 GLU cc_start: 0.7659 (tp30) cc_final: 0.7336 (tp30)
REVERT: D  108 LYS cc_start: 0.6691 (mmtt) cc_final: 0.6288 (mmtt)
REVERT: F   21 VAL cc_start: 0.6007 (OUTLIER) cc_final: 0.5696 (p)
REVERT: G   19 SER cc_start: 0.9221 (t) cc_final: 0.8994 (p)
REVERT: G   23 LEU cc_start: 0.8152 (mt) cc_final: 0.7947 (mp)
REVERT: G   36 LYS cc_start: 0.8006 (pptt) cc_final: 0.7750 (pttt)
REVERT: G   41 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8526 (mp0)
REVERT: G   90 ASP cc_start: 0.7781 (t0) cc_final: 0.7266 (t0)
REVERT: K  310 HIS cc_start: 0.7286 (t70) cc_final: 0.6662 (t70)
REVERT: H   99 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7719 (mtp180)
REVERT: H  105 GLU cc_start: 0.7433 (tp30) cc_final: 0.6991 (tp30)
REVERT: H  113 GLU cc_start: 0.7780 (tp30) cc_final: 0.7387 (tp30)
  outliers start: 22
  outliers final: 16
  residues processed: 129
  average time/residue: 0.7934
  time to fit residues: 109.2191
Evaluate side-chains
  131 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain K residue  307 THR
Chi-restraints excluded: chain H residue   99 ARG
Chi-restraints excluded: chain H residue  112 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 65 optimal weight:   10.0000
   chunk 105 optimal weight:    2.9990
   chunk 101 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 108 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 75 optimal weight:   30.0000
   chunk 58 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
D  47 GLN
F  27 GLN
** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.162595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.097353 restraints weight = 20503.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.40
r_work: 0.2985 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.171  13623  Z= 0.215
  Angle     :  0.845  59.200  19554  Z= 0.482
  Chirality :  0.056   1.999   2212
  Planarity :  0.004   0.059   1531
  Dihedral  : 30.811 173.435   3983
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 25.00 %
    Favored  : 72.22 %
  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:  1.35 (0.28), residues: 896
  helix:  1.86 (0.21), residues: 575
  sheet: -1.94 (0.72), residues: 44
  loop : -0.65 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG C  71 
 TYR   0.030   0.002   TYR C  39 
 PHE   0.008   0.001   PHE G  25 
 TRP   0.004   0.001   TRP A  47 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (13623)
  covalent geometry    : angle       0.84499 (19554)
  hydrogen bonds       : bond        0.03434 (  764)
  hydrogen bonds       : angle       2.91693 ( 1930)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4754.41 seconds
wall clock time: 81 minutes 25.35 seconds (4885.35 seconds total)