Starting phenix.real_space_refine
on Wed Mar  4 08:44:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g6q_29778/03_2026/8g6q_29778_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g6q_29778/03_2026/8g6q_29778.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g6q_29778/03_2026/8g6q_29778.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g6q_29778/03_2026/8g6q_29778.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g6q_29778/03_2026/8g6q_29778_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g6q_29778/03_2026/8g6q_29778_neut.cif"
  }
  resolution = 3.41
  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=   0.001 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     288      5.49       5
     S      13      5.16       5
     C    6947      2.51       5
     N    2331      2.21       5
     O    2906      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 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: 12485
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 795
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2952
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 582
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   LEU K  73 " occ=0.63
      ... (6 atoms not shown)
      pdb=" CD2 LEU K  73 " occ=0.63
  Time building chain proxies: 2.66, per 1000 atoms: 0.21
  Number of scatterers: 12485
  At special positions: 0
  Unit cell: (125.13, 83.42, 118.34, 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      13     16.00
     P     288     15.00
     O    2906      8.00
     N    2331      7.00
     C    6947      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: 0.97
  Conformation dependent library (CDL) restraints added in 388.8 milliseconds
  

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1546

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 10 sheets defined
      69.1% alpha, 4.2% beta
      140 base pairs and 252 stacking pairs defined.
    Time for finding SS restraints: 1.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.988A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.576A  pdb=" N   GLY A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.578A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 50 through 76
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.654A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 22
      removed outlier: 3.600A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 3.598A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.807A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.806A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 121
      removed outlier: 3.640A  pdb=" N   ALA D 121 " --> pdb=" O   LYS D 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.630A  pdb=" N   LEU E  48 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.540A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.565A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.675A  pdb=" N   GLY F  41 " --> pdb=" O   LEU F  37 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.644A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
      removed outlier: 3.537A  pdb=" N   ALA G  21 " --> pdb=" O   ARG G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 72
      removed outlier: 3.577A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.748A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 121
      removed outlier: 3.880A  pdb=" N   ALA H 121 " --> pdb=" O   LYS H 117 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 22 through 34
    Processing helix  chain 'K' and resid 55 through 60
      removed outlier: 3.702A  pdb=" N   TYR K  59 " --> pdb=" O   THR K  55 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.913A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.657A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.257A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 7.033A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.062A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.972A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (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 12 through 16

    415 hydrogen bonds defined for protein.
    1233 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      357 hydrogen bonds
      714 hydrogen bond angles
      0 basepair planarities
      140 basepair parallelities
      252 stacking parallelities
  Total time for adding SS restraints: 2.29

  Time building geometry restraints manager: 1.30 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2851
        1.34 -     1.46: 4008
        1.46 -     1.58: 5834
        1.58 -     1.70: 576
        1.70 -     1.82: 24
  Bond restraints: 13293
  Sorted by residual:
  bond pdb=" N   ALA E 114 "
       pdb=" CA  ALA E 114 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.40e-02 5.10e+03 4.38e+00
  bond pdb=" P    DG J  12 "
       pdb=" OP2  DG J  12 "
    ideal  model  delta    sigma   weight residual
    1.480  1.519 -0.039 2.00e-02 2.50e+03 3.82e+00
  bond pdb=" P    DT J  13 "
       pdb=" OP2  DT J  13 "
    ideal  model  delta    sigma   weight residual
    1.480  1.517 -0.037 2.00e-02 2.50e+03 3.51e+00
  bond pdb=" P    DT J  14 "
       pdb=" OP2  DT J  14 "
    ideal  model  delta    sigma   weight residual
    1.480  1.517 -0.037 2.00e-02 2.50e+03 3.39e+00
  bond pdb=" P    DT J  13 "
       pdb=" OP1  DT J  13 "
    ideal  model  delta    sigma   weight residual
    1.480  1.516 -0.036 2.00e-02 2.50e+03 3.32e+00
  ... (remaining 13288 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 18787
        1.96 -     3.91: 366
        3.91 -     5.87: 40
        5.87 -     7.83: 3
        7.83 -     9.78: 3
  Bond angle restraints: 19199
  Sorted by residual:
  angle pdb=" C3'  DT J  13 "
        pdb=" O3'  DT J  13 "
        pdb=" P    DT J  14 "
      ideal   model   delta    sigma   weight residual
     120.20  113.76    6.44 1.50e+00 4.44e-01 1.84e+01
  angle pdb=" C3'  DC J  11 "
        pdb=" O3'  DC J  11 "
        pdb=" P    DG J  12 "
      ideal   model   delta    sigma   weight residual
     120.20  114.93    5.27 1.50e+00 4.44e-01 1.23e+01
  angle pdb=" N   ASN D  81 "
        pdb=" CA  ASN D  81 "
        pdb=" C   ASN D  81 "
      ideal   model   delta    sigma   weight residual
     112.25  107.80    4.45 1.36e+00 5.41e-01 1.07e+01
  angle pdb=" C3'  DG J  12 "
        pdb=" O3'  DG J  12 "
        pdb=" P    DT J  13 "
      ideal   model   delta    sigma   weight residual
     120.20  115.50    4.70 1.50e+00 4.44e-01 9.83e+00
  angle pdb=" CA  ASN D  81 "
        pdb=" CB  ASN D  81 "
        pdb=" CG  ASN D  81 "
      ideal   model   delta    sigma   weight residual
     112.60  115.72   -3.12 1.00e+00 1.00e+00 9.71e+00
  ... (remaining 19194 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.03: 5833
       35.03 -    70.06: 1405
       70.06 -   105.09: 23
      105.09 -   140.12: 5
      140.12 -   175.15: 1
  Dihedral angle restraints: 7267
    sinusoidal: 4874
      harmonic: 2393
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   44.85  175.15     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" CA  ILE K  44 "
           pdb=" C   ILE K  44 "
           pdb=" N   PHE K  45 "
           pdb=" CA  PHE K  45 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.20   18.80     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" C4'  DC J  34 "
           pdb=" C3'  DC J  34 "
           pdb=" O3'  DC J  34 "
           pdb=" P    DT J  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   86.57  133.43     1      3.50e+01 8.16e-04 1.32e+01
  ... (remaining 7264 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 2143
       0.094 -    0.188: 46
       0.188 -    0.281: 2
       0.281 -    0.375: 0
       0.375 -    0.469: 3
  Chirality restraints: 2194
  Sorted by residual:
  chirality pdb=" P    DG J  12 "
            pdb=" OP1  DG J  12 "
            pdb=" OP2  DG J  12 "
            pdb=" O5'  DG J  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.81   -0.47 2.00e-01 2.50e+01 5.50e+00
  chirality pdb=" P    DT J  13 "
            pdb=" OP1  DT J  13 "
            pdb=" OP2  DT J  13 "
            pdb=" O5'  DT J  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.81   -0.46 2.00e-01 2.50e+01 5.36e+00
  chirality pdb=" P    DT J  14 "
            pdb=" OP1  DT J  14 "
            pdb=" OP2  DT J  14 "
            pdb=" O5'  DT J  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.80   -0.45 2.00e-01 2.50e+01 5.07e+00
  ... (remaining 2191 not shown)

  Planarity restraints: 1427
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN D  81 "   -0.011 2.00e-02 2.50e+03   2.26e-02 5.13e+00
        pdb=" C   ASN D  81 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ASN D  81 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LYS D  82 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  40 "    0.007 2.00e-02 2.50e+03   1.14e-02 2.92e+00
        pdb=" N1   DC J  40 "   -0.012 2.00e-02 2.50e+03
        pdb=" C2   DC J  40 "    0.023 2.00e-02 2.50e+03
        pdb=" O2   DC J  40 "   -0.013 2.00e-02 2.50e+03
        pdb=" N3   DC J  40 "   -0.007 2.00e-02 2.50e+03
        pdb=" C4   DC J  40 "    0.013 2.00e-02 2.50e+03
        pdb=" N4   DC J  40 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DC J  40 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DC J  40 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  68 "    0.008 2.00e-02 2.50e+03   1.11e-02 2.75e+00
        pdb=" N1   DC J  68 "   -0.007 2.00e-02 2.50e+03
        pdb=" C2   DC J  68 "    0.024 2.00e-02 2.50e+03
        pdb=" O2   DC J  68 "   -0.017 2.00e-02 2.50e+03
        pdb=" N3   DC J  68 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DC J  68 "    0.007 2.00e-02 2.50e+03
        pdb=" N4   DC J  68 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DC J  68 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6   DC J  68 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1424 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 639
        2.71 -     3.26: 10948
        3.26 -     3.81: 22761
        3.81 -     4.35: 26747
        4.35 -     4.90: 39308
  Nonbonded interactions: 100403
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 129 "
            pdb=" NH1 ARG A 129 "
     model   vdw
     2.164 3.120
  nonbonded pdb=" N   GLU F  52 "
            pdb=" OE1 GLU F  52 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" N   GLU H 102 "
            pdb=" OE1 GLU H 102 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" O   TYR C  39 "
            pdb=" OG  SER D  75 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" N   GLU B  52 "
            pdb=" OE1 GLU B  52 "
     model   vdw
     2.257 3.120
  ... (remaining 100398 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 39 through 135)
  selection = (chain 'E' and (resid 39 through 134 or (resid 135 and (name N or name CA or nam \ 
e C or name O or name CB ))))
}
ncs_group {
  reference = (chain 'B' and resid 25 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 16 through 118)
}
ncs_group {
  reference = (chain 'D' and resid 29 through 121)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.63 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     13.070
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
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      :  0.003   0.039  13293  Z= 0.163
  Angle     :  0.608   9.784  19199  Z= 0.352
  Chirality :  0.037   0.469   2194
  Planarity :  0.004   0.033   1427
  Dihedral  : 27.964 175.148   5721
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 28.47 %
    Favored  : 71.39 %
  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:  2.17 (0.30), residues: 807
  helix:  2.70 (0.23), residues: 523
  sheet: -0.32 (1.11), residues: 24
  loop : -1.13 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  35 
 TYR   0.013   0.001   TYR A  54 
 PHE   0.007   0.001   PHE D  62 
 HIS   0.005   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (13293)
  covalent geometry    : angle       0.60830 (19199)
  hydrogen bonds       : bond        0.10486 (  772)
  hydrogen bonds       : angle       3.96643 ( 1947)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7835 (ttp-170)
REVERT: B   91 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8538 (tttt)
REVERT: C   64 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8407 (tm-30)
REVERT: C   99 ARG cc_start: 0.7172 (mtt180) cc_final: 0.5961 (mtp85)
REVERT: E   64 LYS cc_start: 0.7944 (mttt) cc_final: 0.7521 (tmtt)
REVERT: E   73 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8793 (tm-30)
REVERT: K    1 MET cc_start: 0.4568 (tmm) cc_final: 0.2265 (pmm)
REVERT: K   60 ASN cc_start: 0.8614 (m-40) cc_final: 0.8287 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 159
  average time/residue: 0.1354
  time to fit residues: 28.9470
Evaluate side-chains
  133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
E  55 GLN
F  75 HIS
** K  31 GLN ** 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 = 0.3724 r_free = 0.3724 target = 0.099877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.067542 restraints weight = 33100.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 2.70
r_work: 0.2868 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2870
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2870 r_free = 0.2870    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2870 r_free = 0.2870    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2870
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.0932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13293  Z= 0.171
  Angle     :  0.566   6.028  19199  Z= 0.335
  Chirality :  0.033   0.166   2194
  Planarity :  0.004   0.045   1427
  Dihedral  : 29.989 176.013   4085
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 28.03 %
    Favored  : 70.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.17 (0.31), residues: 807
  helix:  2.75 (0.22), residues: 529
  sheet: -0.41 (1.12), residues: 24
  loop : -1.37 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  35 
 TYR   0.010   0.001   TYR G  50 
 PHE   0.008   0.001   PHE H  67 
 HIS   0.012   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (13293)
  covalent geometry    : angle       0.56584 (19199)
  hydrogen bonds       : bond        0.05201 (  772)
  hydrogen bonds       : angle       3.24234 ( 1947)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 137
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7648 (pp)
REVERT: A  129 ARG cc_start: 0.8757 (tpt90) cc_final: 0.8364 (tpt170)
REVERT: B   35 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.8203 (ttp-170)
REVERT: C   64 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8623 (tm-30)
REVERT: C   99 ARG cc_start: 0.7491 (mtt180) cc_final: 0.6381 (mtp85)
REVERT: E   64 LYS cc_start: 0.7934 (mttt) cc_final: 0.7658 (tmtt)
REVERT: G   64 GLU cc_start: 0.8100 (tt0) cc_final: 0.7823 (tm-30)
REVERT: H   82 LYS cc_start: 0.9195 (tptp) cc_final: 0.8960 (tptp)
REVERT: K    1 MET cc_start: 0.4498 (tmm) cc_final: 0.3460 (ppp)
  outliers start: 9
  outliers final: 3
  residues processed: 145
  average time/residue: 0.1267
  time to fit residues: 24.8933
Evaluate side-chains
  133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 129
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue    5 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 98 optimal weight:   10.0000
   chunk 96 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   chunk 89 optimal weight:    8.9990
   chunk 53 optimal weight:    0.8980
   chunk 39 optimal weight:    0.2980
   chunk 21 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D  81 ASN
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.101506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.069166 restraints weight = 33602.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 2.75
r_work: 0.2908 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13293  Z= 0.149
  Angle     :  0.534   5.470  19199  Z= 0.320
  Chirality :  0.032   0.165   2194
  Planarity :  0.004   0.046   1427
  Dihedral  : 29.774 176.288   4085
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 25.72 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.30), residues: 807
  helix:  2.71 (0.22), residues: 535
  sheet: -0.35 (1.10), residues: 24
  loop : -1.34 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  35 
 TYR   0.008   0.001   TYR D  37 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (13293)
  covalent geometry    : angle       0.53442 (19199)
  hydrogen bonds       : bond        0.04420 (  772)
  hydrogen bonds       : angle       3.03708 ( 1947)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7558 (pp)
REVERT: A  129 ARG cc_start: 0.8826 (tpt90) cc_final: 0.8363 (tpt170)
REVERT: B   35 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8272 (ttp-170)
REVERT: C   64 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8606 (tm-30)
REVERT: C   99 ARG cc_start: 0.7504 (mtt180) cc_final: 0.6492 (mtp85)
REVERT: G   64 GLU cc_start: 0.8021 (tt0) cc_final: 0.7811 (tm-30)
REVERT: H   31 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7083 (ptpp)
REVERT: H   48 ASP cc_start: 0.9112 (p0) cc_final: 0.8903 (p0)
REVERT: H   73 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8601 (tp30)
REVERT: K    1 MET cc_start: 0.4822 (tmm) cc_final: 0.2429 (pmm)
  outliers start: 21
  outliers final: 9
  residues processed: 157
  average time/residue: 0.1191
  time to fit residues: 25.7261
Evaluate side-chains
  139 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain K residue    5 VAL
Chi-restraints excluded: chain K residue   70 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0370
   chunk 97 optimal weight:    8.9990
   chunk 44 optimal weight:    0.0970
   chunk 101 optimal weight:    8.9990
   chunk 61 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    1.5460

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

Flipped N/Q/H residues before XYZ refinement:
D  81 ASN
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.099673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.067103 restraints weight = 33199.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 2.72
r_work: 0.2854 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2857
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2857
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13293  Z= 0.176
  Angle     :  0.554   6.815  19199  Z= 0.329
  Chirality :  0.033   0.150   2194
  Planarity :  0.004   0.047   1427
  Dihedral  : 29.776 177.619   4085
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 27.17 %
    Favored  : 69.36 %
  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:  2.23 (0.31), residues: 807
  helix:  2.76 (0.22), residues: 534
  sheet: -0.40 (1.07), residues: 24
  loop : -1.33 (0.38), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  35 
 TYR   0.009   0.001   TYR D  37 
 PHE   0.008   0.001   PHE B  61 
 HIS   0.010   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (13293)
  covalent geometry    : angle       0.55448 (19199)
  hydrogen bonds       : bond        0.05256 (  772)
  hydrogen bonds       : angle       3.16632 ( 1947)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7580 (pp)
REVERT: A   97 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8867 (mm-30)
REVERT: B   35 ARG cc_start: 0.8492 (ttm-80) cc_final: 0.8123 (ttp80)
REVERT: C   64 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8651 (tm-30)
REVERT: C   99 ARG cc_start: 0.7509 (mtt180) cc_final: 0.6517 (mtp-110)
REVERT: G   64 GLU cc_start: 0.8087 (tt0) cc_final: 0.7862 (tm-30)
REVERT: H   48 ASP cc_start: 0.9108 (p0) cc_final: 0.8860 (p0)
REVERT: H   73 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8584 (tp30)
REVERT: K    1 MET cc_start: 0.4635 (tmm) cc_final: 0.1522 (pmm)
  outliers start: 24
  outliers final: 15
  residues processed: 156
  average time/residue: 0.1224
  time to fit residues: 26.2160
Evaluate side-chains
  145 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue    5 VAL
Chi-restraints excluded: chain K residue   66 THR
Chi-restraints excluded: chain K residue   70 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 98 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 78 optimal weight:    7.9990
   chunk 27 optimal weight:    8.9990
   chunk 42 optimal weight:    4.9990
   chunk 94 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
D  64 ASN
D  81 ASN
E 125 GLN
G  38 ASN
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.095894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.063003 restraints weight = 33356.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 2.69
r_work: 0.2758 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037  13293  Z= 0.273
  Angle     :  0.639   6.039  19199  Z= 0.374
  Chirality :  0.038   0.158   2194
  Planarity :  0.005   0.049   1427
  Dihedral  : 29.871 178.153   4085
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 26.59 %
    Favored  : 68.50 %
  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:  1.67 (0.30), residues: 807
  helix:  2.35 (0.22), residues: 533
  sheet: -0.47 (1.09), residues: 19
  loop : -1.60 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  29 
 TYR   0.026   0.002   TYR H  80 
 PHE   0.009   0.002   PHE E  67 
 HIS   0.010   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00631 (13293)
  covalent geometry    : angle       0.63871 (19199)
  hydrogen bonds       : bond        0.07396 (  772)
  hydrogen bonds       : angle       3.60252 ( 1947)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 124
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: B   35 ARG cc_start: 0.8524 (ttm-80) cc_final: 0.8222 (mtm180)
REVERT: C   64 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8695 (tm-30)
REVERT: C   99 ARG cc_start: 0.7585 (mtt180) cc_final: 0.6665 (mtp85)
REVERT: D   81 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7856 (t0)
REVERT: H   31 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7194 (ptpp)
REVERT: H   73 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8520 (tm-30)
REVERT: H   82 LYS cc_start: 0.9335 (tptp) cc_final: 0.9075 (tptp)
REVERT: K    1 MET cc_start: 0.5203 (tmm) cc_final: 0.2234 (pmm)
  outliers start: 34
  outliers final: 20
  residues processed: 153
  average time/residue: 0.1218
  time to fit residues: 25.7155
Evaluate side-chains
  141 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   81 ASN
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue    5 VAL
Chi-restraints excluded: chain K residue   15 LEU
Chi-restraints excluded: chain K residue   70 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 84 optimal weight:   10.0000
   chunk 103 optimal weight:    6.9990
   chunk 4 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9980
   chunk 86 optimal weight:    8.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
D  81 ASN
E 125 GLN
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.099580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.067144 restraints weight = 32939.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 2.71
r_work: 0.2859 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2860
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2860
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13293  Z= 0.157
  Angle     :  0.571   8.630  19199  Z= 0.337
  Chirality :  0.033   0.148   2194
  Planarity :  0.004   0.048   1427
  Dihedral  : 29.795 177.672   4085
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 29.05 %
    Favored  : 67.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.31), residues: 807
  helix:  2.76 (0.22), residues: 531
  sheet: -0.53 (1.04), residues: 24
  loop : -1.44 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  83 
 TYR   0.019   0.001   TYR D  80 
 PHE   0.011   0.001   PHE H  67 
 HIS   0.009   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (13293)
  covalent geometry    : angle       0.57119 (19199)
  hydrogen bonds       : bond        0.04857 (  772)
  hydrogen bonds       : angle       3.16947 ( 1947)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8835 (tpt90) cc_final: 0.8501 (tpt170)
REVERT: B   35 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8170 (mtm180)
REVERT: C   64 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8594 (tm-30)
REVERT: C   99 ARG cc_start: 0.7507 (mtt180) cc_final: 0.6652 (mtp85)
REVERT: H   31 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7161 (ptpp)
REVERT: H   73 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8540 (tp30)
REVERT: K    1 MET cc_start: 0.4956 (tmm) cc_final: 0.2048 (pmm)
  outliers start: 24
  outliers final: 17
  residues processed: 149
  average time/residue: 0.1243
  time to fit residues: 25.4560
Evaluate side-chains
  146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   80 TYR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue    5 VAL
Chi-restraints excluded: chain K residue   59 TYR
Chi-restraints excluded: chain K residue   70 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 80 optimal weight:   10.0000
   chunk 79 optimal weight:    7.9990
   chunk 64 optimal weight:    7.9990
   chunk 40 optimal weight:    0.7980
   chunk 85 optimal weight:   10.0000
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
D  81 ASN
E 125 GLN
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.099535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.067085 restraints weight = 33160.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 2.73
r_work: 0.2856 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2857
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2857
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13293  Z= 0.162
  Angle     :  0.565   8.749  19199  Z= 0.335
  Chirality :  0.033   0.147   2194
  Planarity :  0.004   0.047   1427
  Dihedral  : 29.774 179.314   4085
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 27.89 %
    Favored  : 68.35 %
  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:  2.15 (0.31), residues: 807
  helix:  2.73 (0.22), residues: 532
  sheet: -0.48 (1.04), residues: 24
  loop : -1.41 (0.39), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 128 
 TYR   0.027   0.002   TYR D  80 
 PHE   0.010   0.001   PHE H  67 
 HIS   0.009   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (13293)
  covalent geometry    : angle       0.56514 (19199)
  hydrogen bonds       : bond        0.04923 (  772)
  hydrogen bonds       : angle       3.17577 ( 1947)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8885 (tpt90) cc_final: 0.8495 (tpt170)
REVERT: B   35 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.8194 (mtm180)
REVERT: C   64 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8629 (tm-30)
REVERT: C   99 ARG cc_start: 0.7532 (mtt180) cc_final: 0.6672 (mtp85)
REVERT: H   31 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7209 (ptpp)
REVERT: H   73 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8587 (tp30)
REVERT: K    1 MET cc_start: 0.5126 (tmm) cc_final: 0.2058 (pmm)
  outliers start: 26
  outliers final: 20
  residues processed: 155
  average time/residue: 0.1271
  time to fit residues: 27.0992
Evaluate side-chains
  152 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue    5 VAL
Chi-restraints excluded: chain K residue   59 TYR
Chi-restraints excluded: chain K residue   70 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 76 optimal weight:    8.9990
   chunk 97 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 92 optimal weight:    7.9990
   chunk 59 optimal weight:    0.0170
   chunk 105 optimal weight:    9.9990
   chunk 79 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0870
   overall best weight:    2.4202

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

Flipped N/Q/H residues before XYZ refinement:
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.097229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.064776 restraints weight = 32863.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 2.68
r_work: 0.2796 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2798
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2798 r_free = 0.2798    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2798 r_free = 0.2798    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2798
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13293  Z= 0.220
  Angle     :  0.615   9.386  19199  Z= 0.361
  Chirality :  0.036   0.169   2194
  Planarity :  0.004   0.047   1427
  Dihedral  : 29.814 179.969   4085
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 27.89 %
    Favored  : 68.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.92 (0.31), residues: 807
  helix:  2.59 (0.22), residues: 533
  sheet: -0.53 (1.01), residues: 24
  loop : -1.61 (0.38), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  29 
 TYR   0.019   0.002   TYR B  88 
 PHE   0.009   0.001   PHE B  61 
 HIS   0.009   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 (13293)
  covalent geometry    : angle       0.61456 (19199)
  hydrogen bonds       : bond        0.06322 (  772)
  hydrogen bonds       : angle       3.43397 ( 1947)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.8236 (mtm180)
REVERT: C   64 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8639 (tm-30)
REVERT: C   92 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8164 (tt0)
REVERT: C   99 ARG cc_start: 0.7567 (mtt180) cc_final: 0.6663 (mtp85)
REVERT: E  125 GLN cc_start: 0.8603 (mt0) cc_final: 0.8344 (mt0)
REVERT: H   31 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7210 (ptpp)
REVERT: H   73 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8583 (tp30)
REVERT: K    1 MET cc_start: 0.5376 (tmm) cc_final: 0.2363 (pmm)
  outliers start: 27
  outliers final: 20
  residues processed: 154
  average time/residue: 0.1237
  time to fit residues: 26.2172
Evaluate side-chains
  147 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue    5 VAL
Chi-restraints excluded: chain K residue   59 TYR
Chi-restraints excluded: chain K residue   70 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0000
   chunk 58 optimal weight:    5.9990
   chunk 83 optimal weight:   10.0000
   chunk 12 optimal weight:    0.6980
   chunk 87 optimal weight:    7.9990
   chunk 40 optimal weight:    0.6980
   chunk 78 optimal weight:    7.9990
   chunk 24 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.100616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.068613 restraints weight = 32807.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 2.70
r_work: 0.2891 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2893
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2893
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13293  Z= 0.158
  Angle     :  0.582   9.395  19199  Z= 0.342
  Chirality :  0.034   0.204   2194
  Planarity :  0.004   0.047   1427
  Dihedral  : 29.750 179.921   4085
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 28.03 %
    Favored  : 68.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.10 (0.30), residues: 807
  helix:  2.66 (0.22), residues: 533
  sheet: -0.37 (1.04), residues: 24
  loop : -1.38 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  76 
 TYR   0.027   0.002   TYR B  88 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.010   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (13293)
  covalent geometry    : angle       0.58226 (19199)
  hydrogen bonds       : bond        0.04445 (  772)
  hydrogen bonds       : angle       3.21335 ( 1947)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8846 (tpt90) cc_final: 0.8574 (tpt170)
REVERT: B   35 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.8184 (mtm180)
REVERT: C   64 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8619 (tm-30)
REVERT: C   92 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7719 (tt0)
REVERT: C   99 ARG cc_start: 0.7587 (mtt180) cc_final: 0.6863 (mtp-110)
REVERT: G   95 LYS cc_start: 0.8316 (ttpt) cc_final: 0.8087 (tmmt)
REVERT: H   31 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7096 (ptpp)
REVERT: H   73 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8530 (tp30)
REVERT: K    1 MET cc_start: 0.5259 (tmm) cc_final: 0.2346 (pmm)
  outliers start: 26
  outliers final: 22
  residues processed: 158
  average time/residue: 0.1197
  time to fit residues: 26.1092
Evaluate side-chains
  153 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain K residue    5 VAL
Chi-restraints excluded: chain K residue   59 TYR
Chi-restraints excluded: chain K residue   70 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 81 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 2 optimal weight:    0.4980
   chunk 15 optimal weight:    0.0980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.101021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.069077 restraints weight = 33206.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 2.73
r_work: 0.2903 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2904
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2904
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13293  Z= 0.157
  Angle     :  0.598  11.343  19199  Z= 0.349
  Chirality :  0.035   0.390   2194
  Planarity :  0.004   0.047   1427
  Dihedral  : 29.730 178.490   4085
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 29.62 %
    Favored  : 67.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.30), residues: 807
  helix:  2.69 (0.22), residues: 533
  sheet: -0.37 (1.06), residues: 24
  loop : -1.41 (0.38), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 129 
 TYR   0.043   0.002   TYR D  80 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.008   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (13293)
  covalent geometry    : angle       0.59789 (19199)
  hydrogen bonds       : bond        0.04427 (  772)
  hydrogen bonds       : angle       3.25802 ( 1947)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8830 (tpt90) cc_final: 0.8516 (tpt170)
REVERT: B   35 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.8164 (mtm180)
REVERT: C   64 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8604 (tm-30)
REVERT: C   92 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7903 (tt0)
REVERT: C   99 ARG cc_start: 0.7497 (mtt180) cc_final: 0.6506 (mtp-110)
REVERT: G   64 GLU cc_start: 0.8252 (tt0) cc_final: 0.8023 (tm-30)
REVERT: G   95 LYS cc_start: 0.8302 (ttpt) cc_final: 0.8059 (tmmt)
REVERT: H   31 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7087 (ptpp)
REVERT: H   32 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7941 (mm-30)
REVERT: K    1 MET cc_start: 0.5109 (tmm) cc_final: 0.2207 (pmm)
  outliers start: 20
  outliers final: 18
  residues processed: 152
  average time/residue: 0.1216
  time to fit residues: 25.7060
Evaluate side-chains
  153 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain K residue    5 VAL
Chi-restraints excluded: chain K residue   59 TYR
Chi-restraints excluded: chain K residue   70 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 86 optimal weight:   10.0000
   chunk 45 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 83 optimal weight:    8.9990
   chunk 89 optimal weight:    8.9990
   chunk 26 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0020
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.101333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.069308 restraints weight = 33211.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 2.73
r_work: 0.2908 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13293  Z= 0.157
  Angle     :  0.592  11.315  19199  Z= 0.346
  Chirality :  0.034   0.231   2194
  Planarity :  0.004   0.047   1427
  Dihedral  : 29.710 178.589   4085
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 29.62 %
    Favored  : 67.77 %
  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:  2.13 (0.31), residues: 807
  helix:  2.68 (0.22), residues: 534
  sheet: -0.18 (1.08), residues: 24
  loop : -1.40 (0.38), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 129 
 TYR   0.036   0.002   TYR B  88 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.008   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (13293)
  covalent geometry    : angle       0.59245 (19199)
  hydrogen bonds       : bond        0.04346 (  772)
  hydrogen bonds       : angle       3.24104 ( 1947)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2496.08 seconds
wall clock time: 43 minutes 21.05 seconds (2601.05 seconds total)