Starting phenix.real_space_refine
on Wed Jul 30 10:47:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g6q_29778/07_2025/8g6q_29778_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g6q_29778/07_2025/8g6q_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_29778/07_2025/8g6q_29778.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g6q_29778/07_2025/8g6q_29778.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g6q_29778/07_2025/8g6q_29778_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g6q_29778/07_2025/8g6q_29778_neut.cif"
  }
  resolution = 3.41
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.09, per 1000 atoms: 0.65
  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: 2.97
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 5.87
  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: 4.71

  Time building geometry restraints manager: 3.56 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:             1.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     34.740
  Find NCS groups from input model:        0.290
  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:             0.010
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.890
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.005   0.001   HIS A 113 
 PHE   0.007   0.001   PHE D  62 
 TYR   0.013   0.001   TYR A  54 
 ARG   0.008   0.000   ARG B  35 

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

*********************** 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  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7836 (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: 0.5960 (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: 0.8794 (tm-30)
REVERT: G   95 LYS cc_start: 0.8244 (tmmt) cc_final: 0.7748 (tmmt)
REVERT: K    1 MET cc_start: 0.4568 (tmm) cc_final: 0.2263 (pmm)
REVERT: K   60 ASN cc_start: 0.8614 (m-40) cc_final: 0.8286 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 159
  average time/residue: 0.3389
  time to fit residues: 72.3704
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  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:   10.0000
   chunk 80 optimal weight:    8.9990
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 54 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9980
   chunk 83 optimal weight:   10.0000
   chunk 32 optimal weight:    0.5980
   chunk 50 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 96 optimal weight:    6.9990
   overall best weight:    3.5186

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
B  75 HIS
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  31 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 = 0.3656 r_free = 0.3656 target = 0.095937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.063143 restraints weight = 33108.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 2.66
r_work: 0.2764 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2766
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2766 r_free = 0.2766    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2766 r_free = 0.2766    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2766
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  13293  Z= 0.276
  Angle     :  0.645   5.905  19199  Z= 0.376
  Chirality :  0.037   0.180   2194
  Planarity :  0.005   0.043   1427
  Dihedral  : 30.040 176.477   4085
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 27.46 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.30), residues: 807
  helix:  2.43 (0.22), residues: 525
  sheet: -0.66 (1.06), residues: 24
  loop : -1.57 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.001   HIS B  75 
 PHE   0.011   0.002   PHE H  62 
 TYR   0.015   0.002   TYR G  50 
 ARG   0.005   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07430 (  772)
  hydrogen bonds       : angle       3.58454 ( 1947)
  covalent geometry    : bond        0.00638 (13293)
  covalent geometry    : angle       0.64541 (19199)

*********************** 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
  147 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 1.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7741 (pp)
REVERT: A  129 ARG cc_start: 0.8820 (tpt90) cc_final: 0.8486 (tpt170)
REVERT: B   35 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8133 (ttp-170)
REVERT: B   91 LYS cc_start: 0.9160 (ttpt) cc_final: 0.8947 (ttmt)
REVERT: C   56 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8363 (tt0)
REVERT: C   64 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8644 (tm-30)
REVERT: C   99 ARG cc_start: 0.7516 (mtt180) cc_final: 0.6480 (mtp85)
REVERT: E   64 LYS cc_start: 0.8073 (mttt) cc_final: 0.7847 (tmtt)
REVERT: H   48 ASP cc_start: 0.9083 (p0) cc_final: 0.8870 (p0)
REVERT: H   80 TYR cc_start: 0.7755 (m-10) cc_final: 0.7501 (m-10)
REVERT: K    1 MET cc_start: 0.4869 (tmm) cc_final: 0.3955 (ppp)
REVERT: K   15 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8552 (mm)
  outliers start: 19
  outliers final: 12
  residues processed: 143
  average time/residue: 0.3931
  time to fit residues: 79.0724
Evaluate side-chains
  134 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain K residue    5 VAL
Chi-restraints excluded: chain K residue   15 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 27 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 81 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 29 optimal weight:    0.6980
   chunk 104 optimal weight:    4.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN
E 125 GLN
F  75 HIS
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.099258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.066664 restraints weight = 33147.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 2.71
r_work: 0.2852 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.1323

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= 0.158
  Angle     :  0.547   5.432  19199  Z= 0.328
  Chirality :  0.033   0.146   2194
  Planarity :  0.004   0.046   1427
  Dihedral  : 29.863 175.418   4085
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 27.02 %
    Favored  : 70.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.31), residues: 807
  helix:  2.67 (0.22), residues: 534
  sheet: -0.56 (1.10), residues: 24
  loop : -1.42 (0.38), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D  79 
 PHE   0.012   0.001   PHE H  67 
 TYR   0.010   0.001   TYR D  37 
 ARG   0.004   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04958 (  772)
  hydrogen bonds       : angle       3.12116 ( 1947)
  covalent geometry    : bond        0.00335 (13293)
  covalent geometry    : angle       0.54691 (19199)

*********************** 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
  158 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7671 (pp)
REVERT: A  129 ARG cc_start: 0.8847 (tpt90) cc_final: 0.8387 (tpt170)
REVERT: B   35 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8069 (ttp80)
REVERT: B   91 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8880 (tttt)
REVERT: C   56 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8391 (tt0)
REVERT: C   64 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8589 (tm-30)
REVERT: C   99 ARG cc_start: 0.7474 (mtt180) cc_final: 0.6603 (mtp85)
REVERT: D   81 ASN cc_start: 0.7906 (t0) cc_final: 0.7624 (t0)
REVERT: G   64 GLU cc_start: 0.8114 (tt0) cc_final: 0.7833 (tm-30)
REVERT: H   31 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7111 (ptpp)
REVERT: H   82 LYS cc_start: 0.9222 (tptp) cc_final: 0.8981 (tptp)
REVERT: K    1 MET cc_start: 0.4961 (tmm) cc_final: 0.2055 (pmm)
  outliers start: 20
  outliers final: 10
  residues processed: 156
  average time/residue: 0.3187
  time to fit residues: 67.7417
Evaluate side-chains
  140 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
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   80 TYR
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   70 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   chunk 63 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 90 optimal weight:    6.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.099748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.067366 restraints weight = 33025.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 2.70
r_work: 0.2863 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    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 = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.1377

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= 0.154
  Angle     :  0.540   5.515  19199  Z= 0.324
  Chirality :  0.032   0.150   2194
  Planarity :  0.004   0.047   1427
  Dihedral  : 29.826 176.986   4085
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 27.02 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.31), residues: 807
  helix:  2.76 (0.22), residues: 532
  sheet: -0.62 (1.06), residues: 24
  loop : -1.40 (0.38), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.010   0.001   PHE H  67 
 TYR   0.009   0.001   TYR D  37 
 ARG   0.003   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04834 (  772)
  hydrogen bonds       : angle       3.09372 ( 1947)
  covalent geometry    : bond        0.00328 (13293)
  covalent geometry    : angle       0.53961 (19199)

*********************** 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
  155 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7644 (pp)
REVERT: B   35 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.8085 (ttp80)
REVERT: B   91 LYS cc_start: 0.9095 (ttpt) cc_final: 0.8881 (tttt)
REVERT: C   56 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8398 (tt0)
REVERT: C   64 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8599 (tm-30)
REVERT: C   99 ARG cc_start: 0.7481 (mtt180) cc_final: 0.6658 (mtp-110)
REVERT: D   81 ASN cc_start: 0.7824 (t0) cc_final: 0.7474 (t0)
REVERT: G   64 GLU cc_start: 0.8085 (tt0) cc_final: 0.7875 (tm-30)
REVERT: H   31 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7223 (pttp)
REVERT: H   80 TYR cc_start: 0.7164 (m-10) cc_final: 0.6930 (m-80)
REVERT: H   82 LYS cc_start: 0.9198 (tptp) cc_final: 0.8974 (tptp)
REVERT: K    1 MET cc_start: 0.4801 (tmm) cc_final: 0.1651 (pmm)
  outliers start: 22
  outliers final: 15
  residues processed: 151
  average time/residue: 0.3034
  time to fit residues: 62.7051
Evaluate side-chains
  149 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
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 C residue  100 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   80 TYR
Chi-restraints excluded: chain E residue  118 THR
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   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 8 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 87 optimal weight:    8.9990
   chunk 102 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 71 optimal weight:   10.0000
   chunk 64 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    2.3184

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

Flipped N/Q/H residues before XYZ refinement:
D  64 ASN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  49 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.097305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.064929 restraints weight = 33096.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 2.66
r_work: 0.2797 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2797
-------------------------------------------------------------------------------
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 = 0.79   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 = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2798
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  13293  Z= 0.212
  Angle     :  0.583   5.490  19199  Z= 0.346
  Chirality :  0.035   0.153   2194
  Planarity :  0.004   0.048   1427
  Dihedral  : 29.845 177.713   4085
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 25.87 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.31), residues: 807
  helix:  2.63 (0.22), residues: 531
  sheet: -0.62 (1.04), residues: 24
  loop : -1.51 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS K  68 
 PHE   0.010   0.001   PHE B  61 
 TYR   0.030   0.002   TYR D  80 
 ARG   0.003   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06276 (  772)
  hydrogen bonds       : angle       3.33863 ( 1947)
  covalent geometry    : bond        0.00479 (13293)
  covalent geometry    : angle       0.58294 (19199)

*********************** 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
  162 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8893 (tpt90) cc_final: 0.8479 (tpt170)
REVERT: B   35 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.8190 (mtm180)
REVERT: B   91 LYS cc_start: 0.9177 (ttpt) cc_final: 0.8945 (ttmt)
REVERT: C   64 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8624 (tm-30)
REVERT: C   99 ARG cc_start: 0.7524 (mtt180) cc_final: 0.6599 (mtp85)
REVERT: D   81 ASN cc_start: 0.8215 (t0) cc_final: 0.7959 (t0)
REVERT: D  103 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8567 (mp)
REVERT: E   64 LYS cc_start: 0.8027 (mttt) cc_final: 0.7784 (tmtt)
REVERT: G   64 GLU cc_start: 0.8204 (tt0) cc_final: 0.7913 (tm-30)
REVERT: H   31 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7193 (pttm)
REVERT: H   48 ASP cc_start: 0.9149 (p0) cc_final: 0.8873 (p0)
REVERT: H   82 LYS cc_start: 0.9300 (tptp) cc_final: 0.9046 (tptp)
REVERT: K    1 MET cc_start: 0.5159 (tmm) cc_final: 0.2080 (pmm)
  outliers start: 30
  outliers final: 20
  residues processed: 159
  average time/residue: 0.2954
  time to fit residues: 64.1493
Evaluate side-chains
  144 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   62 ILE
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 E residue   46 VAL
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   43 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 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   67 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 38 optimal weight:    0.2980
   chunk 3 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 80 optimal weight:    8.9990
   chunk 34 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.099472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.067021 restraints weight = 33454.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 2.71
r_work: 0.2852 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    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 = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1671

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= 0.160
  Angle     :  0.554   7.413  19199  Z= 0.330
  Chirality :  0.033   0.153   2194
  Planarity :  0.004   0.047   1427
  Dihedral  : 29.791 177.668   4085
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 27.31 %
    Favored  : 69.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.31), residues: 807
  helix:  2.77 (0.22), residues: 532
  sheet: -0.61 (1.04), residues: 24
  loop : -1.46 (0.38), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D  79 
 PHE   0.011   0.001   PHE H  67 
 TYR   0.029   0.001   TYR H  80 
 ARG   0.002   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04902 (  772)
  hydrogen bonds       : angle       3.11458 ( 1947)
  covalent geometry    : bond        0.00343 (13293)
  covalent geometry    : angle       0.55413 (19199)

*********************** 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
  158 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 1.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8919 (tpt90) cc_final: 0.8442 (tpt170)
REVERT: B   35 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.8193 (mtm180)
REVERT: B   91 LYS cc_start: 0.9120 (ttpt) cc_final: 0.8898 (ttmt)
REVERT: C   64 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8608 (tm-30)
REVERT: C   99 ARG cc_start: 0.7507 (mtt180) cc_final: 0.6772 (mtp-110)
REVERT: D   81 ASN cc_start: 0.7943 (t0) cc_final: 0.7691 (t0)
REVERT: G   64 GLU cc_start: 0.8123 (tt0) cc_final: 0.7893 (tm-30)
REVERT: H   31 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7218 (pttp)
REVERT: H   48 ASP cc_start: 0.9089 (p0) cc_final: 0.8794 (p0)
REVERT: H   82 LYS cc_start: 0.9195 (tptp) cc_final: 0.8971 (tptp)
REVERT: K    1 MET cc_start: 0.5114 (tmm) cc_final: 0.2185 (pmm)
  outliers start: 25
  outliers final: 16
  residues processed: 155
  average time/residue: 0.3868
  time to fit residues: 81.3204
Evaluate side-chains
  146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 C residue  100 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain E residue   46 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 92 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0570
   chunk 94 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 80 optimal weight:    8.9990
   chunk 87 optimal weight:    8.9990
   overall best weight:    1.6104

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

Flipped N/Q/H residues before XYZ refinement:
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3699 r_free = 0.3699 target = 0.098617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.066319 restraints weight = 32993.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 2.68
r_work: 0.2831 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2833
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2833
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13293  Z= 0.180
  Angle     :  0.578   8.516  19199  Z= 0.341
  Chirality :  0.034   0.152   2194
  Planarity :  0.004   0.047   1427
  Dihedral  : 29.794 179.112   4085
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 27.02 %
    Favored  : 69.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.31), residues: 807
  helix:  2.73 (0.22), residues: 532
  sheet: -0.70 (1.00), residues: 24
  loop : -1.49 (0.39), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 113 
 PHE   0.010   0.001   PHE H  67 
 TYR   0.023   0.002   TYR D  80 
 ARG   0.004   0.000   ARG K  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05420 (  772)
  hydrogen bonds       : angle       3.26735 ( 1947)
  covalent geometry    : bond        0.00399 (13293)
  covalent geometry    : angle       0.57765 (19199)

*********************** 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
  157 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8936 (tpt90) cc_final: 0.8437 (tpt170)
REVERT: B   35 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.8203 (mtm180)
REVERT: B   91 LYS cc_start: 0.9122 (ttpt) cc_final: 0.8905 (ttmt)
REVERT: B   95 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8121 (ptp90)
REVERT: C   64 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8598 (tm-30)
REVERT: C   92 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7688 (tt0)
REVERT: C   99 ARG cc_start: 0.7529 (mtt180) cc_final: 0.6626 (mtp85)
REVERT: D   81 ASN cc_start: 0.8034 (t0) cc_final: 0.7780 (t0)
REVERT: E  125 GLN cc_start: 0.8657 (mt0) cc_final: 0.8429 (mt0)
REVERT: G   64 GLU cc_start: 0.8151 (tt0) cc_final: 0.7914 (tm-30)
REVERT: H   31 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7224 (pttp)
REVERT: H   48 ASP cc_start: 0.9138 (p0) cc_final: 0.8842 (p0)
REVERT: H   82 LYS cc_start: 0.9221 (tptp) cc_final: 0.8987 (tptp)
REVERT: K    1 MET cc_start: 0.5102 (tmm) cc_final: 0.1983 (pmm)
  outliers start: 24
  outliers final: 17
  residues processed: 154
  average time/residue: 0.2986
  time to fit residues: 62.2909
Evaluate side-chains
  147 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   95 ARG
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   92 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  114 VAL
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 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 50 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 80 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 105 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 98 optimal weight:   10.0000
   chunk 40 optimal weight:    0.8980
   chunk 100 optimal weight:    0.5980
   chunk 85 optimal weight:   10.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  49 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.100868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.069037 restraints weight = 33085.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 2.71
r_work: 0.2896 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2896
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1820

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= 0.153
  Angle     :  0.569   9.164  19199  Z= 0.334
  Chirality :  0.033   0.146   2194
  Planarity :  0.004   0.046   1427
  Dihedral  : 29.741 179.263   4085
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 27.60 %
    Favored  : 69.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.31), residues: 807
  helix:  2.71 (0.22), residues: 535
  sheet: -0.44 (1.02), residues: 24
  loop : -1.30 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.010   0.001   PHE H  67 
 TYR   0.017   0.001   TYR H  80 
 ARG   0.003   0.000   ARG K  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04398 (  772)
  hydrogen bonds       : angle       3.17402 ( 1947)
  covalent geometry    : bond        0.00325 (13293)
  covalent geometry    : angle       0.56920 (19199)

*********************** 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
  163 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8963 (tpt90) cc_final: 0.8425 (tpt170)
REVERT: B   35 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.8180 (mtm180)
REVERT: B   95 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8121 (ptp90)
REVERT: C   64 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8582 (tm-30)
REVERT: C   92 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7417 (tt0)
REVERT: C   99 ARG cc_start: 0.7544 (mtt180) cc_final: 0.6625 (mtp-110)
REVERT: D   81 ASN cc_start: 0.7860 (t0) cc_final: 0.7603 (t0)
REVERT: H   31 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7110 (ptpp)
REVERT: H   48 ASP cc_start: 0.9108 (p0) cc_final: 0.8833 (p0)
REVERT: K    1 MET cc_start: 0.5217 (tmm) cc_final: 0.2177 (pmm)
  outliers start: 23
  outliers final: 17
  residues processed: 158
  average time/residue: 0.3122
  time to fit residues: 67.3924
Evaluate side-chains
  153 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
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   95 ARG
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   92 GLU
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 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 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 69 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 79 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 81 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0470
   chunk 93 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   overall best weight:    2.2086

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

Flipped N/Q/H residues before XYZ refinement:
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.098065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.065354 restraints weight = 33045.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 2.69
r_work: 0.2808 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2812
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2812
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  13293  Z= 0.211
  Angle     :  0.613   8.873  19199  Z= 0.358
  Chirality :  0.035   0.195   2194
  Planarity :  0.004   0.046   1427
  Dihedral  : 29.782 179.122   4085
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 27.89 %
    Favored  : 68.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.31), residues: 807
  helix:  2.61 (0.23), residues: 534
  sheet: -0.61 (1.02), residues: 24
  loop : -1.53 (0.38), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS B  75 
 PHE   0.009   0.001   PHE B  61 
 TYR   0.032   0.002   TYR D  80 
 ARG   0.002   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05943 (  772)
  hydrogen bonds       : angle       3.37960 ( 1947)
  covalent geometry    : bond        0.00478 (13293)
  covalent geometry    : angle       0.61328 (19199)

*********************** 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
  155 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8989 (tpt90) cc_final: 0.8704 (tpt90)
REVERT: B   35 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.8196 (mtm180)
REVERT: C   64 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8625 (tm-30)
REVERT: C   99 ARG cc_start: 0.7548 (mtt180) cc_final: 0.6623 (mtp85)
REVERT: D   81 ASN cc_start: 0.8172 (t0) cc_final: 0.7937 (t0)
REVERT: E   64 LYS cc_start: 0.7986 (mttt) cc_final: 0.7747 (tmtt)
REVERT: H   31 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7236 (pttp)
REVERT: H   48 ASP cc_start: 0.9122 (p0) cc_final: 0.8824 (p0)
REVERT: H  102 GLU cc_start: 0.6987 (pm20) cc_final: 0.6733 (pm20)
REVERT: K    1 MET cc_start: 0.5220 (tmm) cc_final: 0.2231 (pmm)
  outliers start: 23
  outliers final: 18
  residues processed: 152
  average time/residue: 0.2921
  time to fit residues: 60.2621
Evaluate side-chains
  148 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
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 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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 87 optimal weight:    8.9990
   chunk 58 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 63 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 95 optimal weight:    7.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3699 r_free = 0.3699 target = 0.098663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.066259 restraints weight = 32953.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 2.68
r_work: 0.2830 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13293  Z= 0.187
  Angle     :  0.610   9.610  19199  Z= 0.355
  Chirality :  0.034   0.151   2194
  Planarity :  0.004   0.046   1427
  Dihedral  : 29.782 179.722   4085
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 27.46 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.31), residues: 807
  helix:  2.60 (0.23), residues: 532
  sheet: -0.50 (1.04), residues: 24
  loop : -1.60 (0.38), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS F  75 
 PHE   0.009   0.001   PHE H  67 
 TYR   0.036   0.002   TYR F  88 
 ARG   0.002   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05455 (  772)
  hydrogen bonds       : angle       3.33852 ( 1947)
  covalent geometry    : bond        0.00417 (13293)
  covalent geometry    : angle       0.60997 (19199)

********************** 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: 22
    poor density    : 134
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.9001 (tpt90) cc_final: 0.8719 (tpt90)
REVERT: B   35 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.8180 (mtm180)
REVERT: C   64 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8600 (tm-30)
REVERT: C   99 ARG cc_start: 0.7574 (mtt180) cc_final: 0.6657 (mtp85)
REVERT: D   59 MET cc_start: 0.9171 (tpp) cc_final: 0.8906 (mmm)
REVERT: D   81 ASN cc_start: 0.8117 (t0) cc_final: 0.7885 (t0)
REVERT: G   64 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8204 (tt0)
REVERT: H   31 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7122 (ptpp)
REVERT: H   48 ASP cc_start: 0.9117 (p0) cc_final: 0.8847 (p0)
REVERT: K    1 MET cc_start: 0.5410 (tmm) cc_final: 0.2421 (pmm)
  outliers start: 22
  outliers final: 20
  residues processed: 153
  average time/residue: 0.2974
  time to fit residues: 62.8037
Evaluate side-chains
  150 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
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   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   33 SER
Chi-restraints excluded: chain D residue   99 LEU
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 104 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 95 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9990
   chunk 45 optimal weight:    0.3980
   chunk 96 optimal weight:    6.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3707 r_free = 0.3707 target = 0.099183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.066969 restraints weight = 32988.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.68
r_work: 0.2845 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2845
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2845
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13293  Z= 0.175
  Angle     :  0.602   9.300  19199  Z= 0.351
  Chirality :  0.034   0.151   2194
  Planarity :  0.004   0.046   1427
  Dihedral  : 29.771 178.887   4085
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 28.03 %
    Favored  : 69.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.31), residues: 807
  helix:  2.66 (0.23), residues: 530
  sheet: -0.40 (1.05), residues: 24
  loop : -1.52 (0.38), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS F  75 
 PHE   0.009   0.001   PHE H  67 
 TYR   0.024   0.002   TYR D  80 
 ARG   0.002   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05208 (  772)
  hydrogen bonds       : angle       3.31756 ( 1947)
  covalent geometry    : bond        0.00386 (13293)
  covalent geometry    : angle       0.60199 (19199)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6088.60 seconds
wall clock time: 109 minutes 2.24 seconds (6542.24 seconds total)