Starting phenix.real_space_refine
on Wed Aug  5 13:11:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9r1d_53505/08_2026/9r1d_53505.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9r1d_53505/08_2026/9r1d_53505.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9r1d_53505/08_2026/9r1d_53505.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9r1d_53505/08_2026/9r1d_53505.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9r1d_53505/08_2026/9r1d_53505.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9r1d_53505/08_2026/9r1d_53505.cif"
  }
  resolution = 3.21
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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     230      5.49       5
     S      20      5.16       5
     C    5471      2.51       5
     N    1861      2.21       5
     O    2298      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9880
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 604
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
    Chain: "B"
      Number of atoms: 612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 612
          Classifications: {'peptide': 77}
          Link IDs: {'TRANS': 76}
    Chain: "C"
      Number of atoms: 679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 679
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
    Chain: "D"
      Number of atoms: 685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 685
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
    Chain: "E"
      Number of atoms: 604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 604
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
    Chain: "F"
      Number of atoms: 604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 604
          Classifications: {'peptide': 76}
          Link IDs: {'TRANS': 75}
    Chain: "G"
      Number of atoms: 685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 685
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "H"
      Number of atoms: 692
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 692
          Classifications: {'peptide': 89}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 87}
    Chain: "I"
      Number of atoms: 2375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 2375
          Classifications: {'DNA': 115}
          Link IDs: {'rna3p': 114}
    Chain: "J"
      Number of atoms: 2340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 2340
          Classifications: {'DNA': 115}
          Link IDs: {'rna3p': 114}
  Time building chain proxies: 2.34, per 1000 atoms: 0.24
  Number of scatterers: 9880
  At special positions: 0
  Unit cell: (80.56, 114.48, 117.66, 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      20     16.00
     P     230     15.00
     O    2298      8.00
     N    1861      7.00
     C    5471      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 208.3 milliseconds
  

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1246

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 7 sheets defined
      78.0% alpha, 2.1% beta
      107 base pairs and 185 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 80
    Processing helix  chain 'A' and resid 88 through 117
    Processing helix  chain 'A' and resid 123 through 134
      removed outlier: 3.633A  pdb=" N   ILE A 127 " --> pdb=" O   PHE A 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 27
    Processing helix  chain 'B' and resid 28 through 40
      removed outlier: 3.531A  pdb=" N   ILE B  32 " --> pdb=" O   THR B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 74
      removed outlier: 4.054A  pdb=" N   GLU B  51 " --> pdb=" O   VAL B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 91
      removed outlier: 3.707A  pdb=" N   ARG B  91 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 44 through 73
      removed outlier: 3.755A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 92
    Processing helix  chain 'C' and resid 94 through 99
    Processing helix  chain 'D' and resid 25 through 37
    Processing helix  chain 'D' and resid 43 through 72
      removed outlier: 3.558A  pdb=" N   ILE D  49 " --> pdb=" O   ARG D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 90
      removed outlier: 3.504A  pdb=" N   THR D  84 " --> pdb=" O   ARG D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 91 through 110
      removed outlier: 3.650A  pdb=" N   LYS D  96 " --> pdb=" O   ALA D  92 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   HIS D  97 " --> pdb=" O   ASP D  93 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU D 101 " --> pdb=" O   HIS D  97 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   SER D 110 " --> pdb=" O   VAL D 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 66 through 81
      removed outlier: 3.529A  pdb=" N   LEU E  81 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 88 through 117
    Processing helix  chain 'E' and resid 123 through 135
      removed outlier: 3.606A  pdb=" N   ILE E 127 " --> pdb=" O   PHE E 123 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 23 through 27
    Processing helix  chain 'F' and resid 28 through 39
    Processing helix  chain 'F' and resid 47 through 74
      removed outlier: 4.228A  pdb=" N   GLU F  51 " --> pdb=" O   VAL F  47 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 80 through 91
      removed outlier: 3.704A  pdb=" N   ARG F  91 " --> pdb=" O   ALA F  87 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 44 through 72
      removed outlier: 3.656A  pdb=" N   ALA G  48 " --> pdb=" O   GLY G  44 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 81 through 91
    Processing helix  chain 'G' and resid 94 through 99
    Processing helix  chain 'H' and resid 25 through 37
    Processing helix  chain 'H' and resid 43 through 73
    Processing helix  chain 'H' and resid 78 through 90
      removed outlier: 3.656A  pdb=" N   LEU H  82 " --> pdb=" O   GLY H  78 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 91 through 110
      removed outlier: 4.258A  pdb=" N   HIS H  97 " --> pdb=" O   ASP H  93 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ALA H 100 " --> pdb=" O   LYS H  96 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87
      removed outlier: 6.747A  pdb=" N   ARG A  86 " --> pdb=" O   VAL B  79 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 122
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.916A  pdb=" N   ARG C  42 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 80
    Processing sheet with id=AA5, first strand: chain 'E' and resid 86 through 87
      removed outlier: 6.847A  pdb=" N   ARG E  86 " --> pdb=" O   VAL F  79 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 121 through 122
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.353A  pdb=" N   ARG G  42 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    371 hydrogen bonds defined for protein.
    1101 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      278 hydrogen bonds
      556 hydrogen bond angles
      0 basepair planarities
      107 basepair parallelities
      185 stacking parallelities
  Total time for adding SS restraints: 1.77

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1178
        1.32 -     1.44: 3889
        1.44 -     1.56: 4950
        1.56 -     1.69: 458
        1.69 -     1.81: 36
  Bond restraints: 10511
  Sorted by residual:
  bond pdb=" C2   DG I -33 "
       pdb=" N2   DG I -33 "
    ideal  model  delta    sigma   weight residual
    1.341  1.304  0.037 1.00e-02 1.00e+04 1.40e+01
  bond pdb=" C4'  DG J  48 "
       pdb=" O4'  DG J  48 "
    ideal  model  delta    sigma   weight residual
    1.446  1.409  0.037 1.00e-02 1.00e+04 1.36e+01
  bond pdb=" C5'  DA I -53 "
       pdb=" C4'  DA I -53 "
    ideal  model  delta    sigma   weight residual
    1.512  1.537 -0.025 7.00e-03 2.04e+04 1.27e+01
  bond pdb=" C   PRO D  91 "
       pdb=" O   PRO D  91 "
    ideal  model  delta    sigma   weight residual
    1.235  1.191  0.044 1.30e-02 5.92e+03 1.16e+01
  bond pdb=" C3'  DC J  56 "
       pdb=" C2'  DC J  56 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.11e+01
  ... (remaining 10506 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 13580
        1.61 -     3.22: 1364
        3.22 -     4.83: 181
        4.83 -     6.44: 38
        6.44 -     8.05: 21
  Bond angle restraints: 15184
  Sorted by residual:
  angle pdb=" O5'  DA I -53 "
        pdb=" C5'  DA I -53 "
        pdb=" C4'  DA I -53 "
      ideal   model   delta    sigma   weight residual
     109.40  114.49   -5.09 8.00e-01 1.56e+00 4.05e+01
  angle pdb=" O5'  DG J  48 "
        pdb=" C5'  DG J  48 "
        pdb=" C4'  DG J  48 "
      ideal   model   delta    sigma   weight residual
     109.40  113.93   -4.53 8.00e-01 1.56e+00 3.21e+01
  angle pdb=" O5'  DG J  47 "
        pdb=" C5'  DG J  47 "
        pdb=" C4'  DG J  47 "
      ideal   model   delta    sigma   weight residual
     109.40  113.84   -4.44 8.00e-01 1.56e+00 3.08e+01
  angle pdb=" O4'  DG I  -5 "
        pdb=" C4'  DG I  -5 "
        pdb=" C3'  DG I  -5 "
      ideal   model   delta    sigma   weight residual
     106.00  102.85    3.15 6.00e-01 2.78e+00 2.76e+01
  angle pdb=" O5'  DC J  49 "
        pdb=" C5'  DC J  49 "
        pdb=" C4'  DC J  49 "
      ideal   model   delta    sigma   weight residual
     109.40  113.37   -3.97 8.00e-01 1.56e+00 2.47e+01
  ... (remaining 15179 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.32: 4193
       25.32 -    50.63: 1155
       50.63 -    75.95: 346
       75.95 -   101.26: 3
      101.26 -   126.58: 1
  Dihedral angle restraints: 5698
    sinusoidal: 3779
      harmonic: 1919
  Sorted by residual:
  dihedral pdb=" C4'  DG I  20 "
           pdb=" C3'  DG I  20 "
           pdb=" O3'  DG I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   93.42  126.58     1      3.50e+01 8.16e-04 1.25e+01
  dihedral pdb=" C   ARG D  73 "
           pdb=" N   ARG D  73 "
           pdb=" CA  ARG D  73 "
           pdb=" CB  ARG D  73 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.26    8.66     0      2.50e+00 1.60e-01 1.20e+01
  dihedral pdb=" CA  ILE D  36 "
           pdb=" C   ILE D  36 "
           pdb=" N   ASN D  37 "
           pdb=" CA  ASN D  37 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.02   16.98     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 5695 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.129: 1702
       0.129 -    0.257: 39
       0.257 -    0.386: 2
       0.386 -    0.514: 0
       0.514 -    0.643: 14
  Chirality restraints: 1757
  Sorted by residual:
  chirality pdb=" P    DG I -56 "
            pdb=" OP1  DG I -56 "
            pdb=" OP2  DG I -56 "
            pdb=" O5'  DG I -56 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.98   -0.64 2.00e-01 2.50e+01 1.03e+01
  chirality pdb=" P    DA I -55 "
            pdb=" OP1  DA I -55 "
            pdb=" OP2  DA I -55 "
            pdb=" O5'  DA I -55 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.95   -0.61 2.00e-01 2.50e+01 9.34e+00
  chirality pdb=" P    DC I -54 "
            pdb=" OP1  DC I -54 "
            pdb=" OP2  DC I -54 "
            pdb=" O5'  DC I -54 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.94   -0.61 2.00e-01 2.50e+01 9.24e+00
  ... (remaining 1754 not shown)

  Planarity restraints: 1113
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  73 "    0.117 2.00e-02 2.50e+03   5.88e-02 6.91e+01
        pdb=" CG  TYR B  73 "   -0.068 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  73 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  73 "   -0.050 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  73 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  73 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  73 "    0.013 2.00e-02 2.50e+03
        pdb=" OH  TYR B  73 "    0.060 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I -33 "    0.080 2.00e-02 2.50e+03   4.54e-02 6.17e+01
        pdb=" N9   DG I -33 "   -0.027 2.00e-02 2.50e+03
        pdb=" C8   DG I -33 "    0.018 2.00e-02 2.50e+03
        pdb=" N7   DG I -33 "    0.007 2.00e-02 2.50e+03
        pdb=" C5   DG I -33 "   -0.029 2.00e-02 2.50e+03
        pdb=" C6   DG I -33 "   -0.006 2.00e-02 2.50e+03
        pdb=" O6   DG I -33 "    0.045 2.00e-02 2.50e+03
        pdb=" N1   DG I -33 "    0.009 2.00e-02 2.50e+03
        pdb=" C2   DG I -33 "   -0.036 2.00e-02 2.50e+03
        pdb=" N2   DG I -33 "    0.069 2.00e-02 2.50e+03
        pdb=" N3   DG I -33 "   -0.070 2.00e-02 2.50e+03
        pdb=" C4   DG I -33 "   -0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J  47 "   -0.069 2.00e-02 2.50e+03   2.63e-02 2.07e+01
        pdb=" N9   DG J  47 "    0.032 2.00e-02 2.50e+03
        pdb=" C8   DG J  47 "    0.025 2.00e-02 2.50e+03
        pdb=" N7   DG J  47 "    0.007 2.00e-02 2.50e+03
        pdb=" C5   DG J  47 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DG J  47 "   -0.012 2.00e-02 2.50e+03
        pdb=" O6   DG J  47 "   -0.027 2.00e-02 2.50e+03
        pdb=" N1   DG J  47 "   -0.010 2.00e-02 2.50e+03
        pdb=" C2   DG J  47 "    0.006 2.00e-02 2.50e+03
        pdb=" N2   DG J  47 "    0.006 2.00e-02 2.50e+03
        pdb=" N3   DG J  47 "    0.021 2.00e-02 2.50e+03
        pdb=" C4   DG J  47 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1110 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1204
        2.75 -     3.29: 9082
        3.29 -     3.83: 19330
        3.83 -     4.36: 22215
        4.36 -     4.90: 32442
  Nonbonded interactions: 84273
  Sorted by model distance:
  nonbonded pdb=" O   ASN D  37 "
            pdb=" OG  SER D  38 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O6   DG I  48 "
            pdb=" N1   DG J -49 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" NH2 ARG B  89 "
            pdb=" OD1 ASP H  56 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   ASN D  37 "
            pdb=" OD1 ASN D  37 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" N   ILE G  24 "
            pdb=" OE1 GLU G  56 "
     model   vdw
     2.331 3.120
  ... (remaining 84268 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 23 through 98)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 16 through 104)
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 23 through 110)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.050
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
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      :  0.008   0.044  10511  Z= 0.621
  Angle     :  1.035   8.055  15184  Z= 0.806
  Chirality :  0.075   0.643   1757
  Planarity :  0.006   0.059   1113
  Dihedral  : 26.896 126.577   4452
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.11 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.32), residues: 643
  helix:  1.29 (0.23), residues: 495
  sheet:  None (None), residues: 0
  loop : -1.01 (0.41), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  75 
 TYR   0.117   0.007   TYR B  73 
 PHE   0.030   0.003   PHE D  53 
 TRP   0.005   0.001   TRP H  25 
 HIS   0.004   0.001   HIS D 108 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00773 /  0.62 (10511)
  covalent geometry    : angle       1.03528 /  0.81 (15184)
  hydrogen bonds       : bond        0.11530 /  7.64 (  649)
  hydrogen bonds       : angle       4.93020 /  3.45 ( 1657)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7618 (t0) cc_final: 0.6994 (p0)
REVERT: B   25 ARG cc_start: 0.7670 (ptt90) cc_final: 0.7409 (ptt-90)
REVERT: B   72 GLU cc_start: 0.8449 (tp30) cc_final: 0.8015 (tp30)
REVERT: C   51 MET cc_start: 0.8082 (tpp) cc_final: 0.7648 (tpt)
REVERT: D   73 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7782 (ttm-80)
REVERT: G   92 ASP cc_start: 0.8344 (t0) cc_final: 0.7957 (t0)
REVERT: H   96 LYS cc_start: 0.7921 (tttt) cc_final: 0.7636 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1610
  time to fit residues: 23.1921
Evaluate side-chains
  96 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:   20.0000
   chunk 45 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.7476 > 50:)
   chunk 74 optimal weight:    9.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  39 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 = 0.3938 r_free = 0.3938 target = 0.148939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.100234 restraints weight = 13249.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 2.10
r_work: 0.3100 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.0886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10511  Z= 0.179
  Angle     :  0.651   8.983  15184  Z= 0.382
  Chirality :  0.041   0.188   1757
  Planarity :  0.004   0.029   1113
  Dihedral  : 30.130 126.020   3230
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 12.84 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.21 (0.31), residues: 643
  helix:  2.17 (0.22), residues: 492
  sheet:  None (None), residues: 0
  loop : -0.96 (0.41), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  79 
 TYR   0.025   0.002   TYR B  73 
 PHE   0.024   0.002   PHE F  86 
 TRP   0.007   0.001   TRP D  25 
 HIS   0.003   0.001   HIS C  91 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.18 (10511)
  covalent geometry    : angle       0.65060 /  0.38 (15184)
  hydrogen bonds       : bond        0.04789 /  3.17 (  649)
  hydrogen bonds       : angle       3.01132 /  2.15 ( 1657)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7506 (t0) cc_final: 0.7029 (p0)
REVERT: A   67 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7679 (mtp85)
REVERT: B   25 ARG cc_start: 0.7718 (ptt90) cc_final: 0.7400 (ptt-90)
REVERT: B   72 GLU cc_start: 0.8412 (tp30) cc_final: 0.8091 (tp30)
REVERT: C   51 MET cc_start: 0.7997 (tpp) cc_final: 0.7427 (tpp)
REVERT: D   73 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7850 (ttm-80)
REVERT: E   80 ASN cc_start: 0.8167 (m-40) cc_final: 0.7934 (t0)
REVERT: F   93 LYS cc_start: 0.8377 (mtpp) cc_final: 0.8029 (mtpp)
REVERT: G   92 ASP cc_start: 0.8527 (t70) cc_final: 0.8116 (t0)
REVERT: H   59 GLU cc_start: 0.8565 (tp30) cc_final: 0.8302 (tp30)
REVERT: H   96 LYS cc_start: 0.8017 (tttt) cc_final: 0.7747 (tttm)
  outliers start: 16
  outliers final: 10
  residues processed: 107
  average time/residue: 0.1399
  time to fit residues: 19.3278
Evaluate side-chains
  100 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   94 VAL
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   73 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 59 optimal weight:    0.0980
   chunk 12 optimal weight:    0.0000
   chunk 76 optimal weight:   10.0000
   chunk 44 optimal weight:    0.4980
   chunk 78 optimal weight:    9.9990
   chunk 79 optimal weight:    9.9990
   chunk 28 optimal weight:    0.5980
   chunk 68 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.4184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.150846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.102024 restraints weight = 13151.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.09
r_work: 0.3128 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10511  Z= 0.134
  Angle     :  0.579   8.387  15184  Z= 0.348
  Chirality :  0.038   0.185   1757
  Planarity :  0.003   0.039   1113
  Dihedral  : 30.267 125.221   3230
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.09 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.76 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.71 (0.32), residues: 643
  helix:  2.54 (0.22), residues: 495
  sheet:  None (None), residues: 0
  loop : -0.87 (0.41), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  87 
 TYR   0.021   0.001   TYR C  57 
 PHE   0.017   0.001   PHE H  53 
 TRP   0.006   0.001   TRP D  25 
 HIS   0.002   0.001   HIS C  91 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00206 /  0.13 (10511)
  covalent geometry    : angle       0.57914 /  0.35 (15184)
  hydrogen bonds       : bond        0.04156 /  2.70 (  649)
  hydrogen bonds       : angle       2.78527 /  1.98 ( 1657)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7576 (t0) cc_final: 0.7088 (p0)
REVERT: B   25 ARG cc_start: 0.7655 (ptt90) cc_final: 0.7351 (ptt-90)
REVERT: B   48 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8101 (tt)
REVERT: B   72 GLU cc_start: 0.8340 (tp30) cc_final: 0.8044 (tp30)
REVERT: D   37 ASN cc_start: 0.8441 (t0) cc_final: 0.8060 (t0)
REVERT: D   42 MET cc_start: 0.8120 (ptm) cc_final: 0.7833 (ptm)
REVERT: D   73 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7705 (ttm-80)
REVERT: F   73 TYR cc_start: 0.9048 (t80) cc_final: 0.8813 (t80)
REVERT: F   75 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8449 (ttp-170)
REVERT: F   93 LYS cc_start: 0.8316 (mtpp) cc_final: 0.7974 (mtpp)
REVERT: G   92 ASP cc_start: 0.8621 (t70) cc_final: 0.8155 (t0)
REVERT: H   73 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7513 (mtp85)
REVERT: H   96 LYS cc_start: 0.8006 (tttt) cc_final: 0.7744 (tttm)
  outliers start: 10
  outliers final: 7
  residues processed: 95
  average time/residue: 0.1244
  time to fit residues: 15.3331
Evaluate side-chains
  96 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain F residue   24 VAL
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   75 ARG
Chi-restraints excluded: chain F residue   94 VAL
Chi-restraints excluded: chain F residue   95 LEU
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain H residue   88 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 71 optimal weight:   20.0000
   chunk 27 optimal weight:    4.9990
   chunk 70 optimal weight:    9.9990
   chunk 67 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 61 optimal weight:   30.0000
   chunk 2 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 81 optimal weight:    9.9990
   overall best weight:    2.2984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.144177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.094576 restraints weight = 13347.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 2.09
r_work: 0.3022 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  10511  Z= 0.249
  Angle     :  0.706   8.763  15184  Z= 0.389
  Chirality :  0.043   0.207   1757
  Planarity :  0.004   0.036   1113
  Dihedral  : 30.838 127.784   3230
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.02 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 13.94 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.31), residues: 643
  helix:  1.96 (0.22), residues: 499
  sheet:  None (None), residues: 0
  loop : -1.42 (0.41), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  87 
 TYR   0.020   0.002   TYR F  73 
 PHE   0.020   0.003   PHE H  53 
 TRP   0.010   0.002   TRP H  25 
 HIS   0.006   0.002   HIS F  83 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00544 /  0.25 (10511)
  covalent geometry    : angle       0.70570 /  0.39 (15184)
  hydrogen bonds       : bond        0.05011 /  3.39 (  649)
  hydrogen bonds       : angle       3.01746 /  2.16 ( 1657)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 ASP cc_start: 0.7615 (t0) cc_final: 0.7129 (p0)
REVERT: A  128 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7660 (mt0)
REVERT: B   25 ARG cc_start: 0.7881 (ptt90) cc_final: 0.7544 (ptt-90)
REVERT: B   72 GLU cc_start: 0.8424 (tp30) cc_final: 0.7957 (tp30)
REVERT: D   37 ASN cc_start: 0.8534 (t0) cc_final: 0.8082 (t0)
REVERT: D   42 MET cc_start: 0.8642 (ptm) cc_final: 0.8263 (ptm)
REVERT: E   75 ARG cc_start: 0.6997 (tpp80) cc_final: 0.6442 (mtm-85)
REVERT: F   75 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8473 (ttp-170)
REVERT: G   92 ASP cc_start: 0.8658 (t70) cc_final: 0.8153 (t0)
REVERT: H   48 LYS cc_start: 0.7890 (mttp) cc_final: 0.7595 (mttp)
REVERT: H   96 LYS cc_start: 0.8021 (tttt) cc_final: 0.7758 (tttm)
  outliers start: 22
  outliers final: 16
  residues processed: 108
  average time/residue: 0.1323
  time to fit residues: 18.2916
Evaluate side-chains
  106 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   75 ARG
Chi-restraints excluded: chain F residue   94 VAL
Chi-restraints excluded: chain G residue   32 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue  102 VAL
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain H residue  110 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0370
   chunk 20 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  72 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.148134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.098863 restraints weight = 13266.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 2.11
r_work: 0.3077 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10511  Z= 0.131
  Angle     :  0.578   8.506  15184  Z= 0.338
  Chirality :  0.038   0.188   1757
  Planarity :  0.003   0.025   1113
  Dihedral  : 30.608 128.552   3230
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.40 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 14.50 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.57 (0.32), residues: 643
  helix:  2.44 (0.22), residues: 498
  sheet:  None (None), residues: 0
  loop : -1.04 (0.44), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  71 
 TYR   0.021   0.002   TYR B  73 
 PHE   0.015   0.001   PHE H  53 
 TRP   0.005   0.001   TRP H  25 
 HIS   0.003   0.001   HIS C  91 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00218 /  0.13 (10511)
  covalent geometry    : angle       0.57752 /  0.34 (15184)
  hydrogen bonds       : bond        0.04016 /  2.62 (  649)
  hydrogen bonds       : angle       2.70425 /  1.93 ( 1657)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7523 (t0) cc_final: 0.7122 (p0)
REVERT: B   25 ARG cc_start: 0.7796 (ptt90) cc_final: 0.7458 (ptt-90)
REVERT: B   72 GLU cc_start: 0.8400 (tp30) cc_final: 0.8069 (tp30)
REVERT: D   37 ASN cc_start: 0.8472 (t0) cc_final: 0.7916 (t0)
REVERT: E   75 ARG cc_start: 0.7150 (tpp80) cc_final: 0.6458 (mtm-85)
REVERT: F   75 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8393 (ttp-170)
REVERT: G   92 ASP cc_start: 0.8610 (t70) cc_final: 0.8304 (t0)
REVERT: H   96 LYS cc_start: 0.8004 (tttt) cc_final: 0.7748 (tttm)
  outliers start: 17
  outliers final: 12
  residues processed: 95
  average time/residue: 0.1166
  time to fit residues: 14.4846
Evaluate side-chains
  94 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain F residue   24 VAL
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   75 ARG
Chi-restraints excluded: chain F residue   94 VAL
Chi-restraints excluded: chain F residue   95 LEU
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain H residue   88 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 76 optimal weight:   10.0000
   chunk 67 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 66 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 77 optimal weight:    9.9990
   overall best weight:    1.5386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.146118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.096683 restraints weight = 13359.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.10
r_work: 0.3050 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10511  Z= 0.189
  Angle     :  0.614   8.763  15184  Z= 0.348
  Chirality :  0.038   0.186   1757
  Planarity :  0.003   0.027   1113
  Dihedral  : 30.678 128.768   3230
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.24 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 15.41 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.35 (0.31), residues: 643
  helix:  2.29 (0.22), residues: 501
  sheet:  None (None), residues: 0
  loop : -1.25 (0.43), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  87 
 TYR   0.021   0.002   TYR B  73 
 PHE   0.017   0.002   PHE H  53 
 TRP   0.008   0.001   TRP H  25 
 HIS   0.004   0.001   HIS C  91 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.19 (10511)
  covalent geometry    : angle       0.61356 /  0.35 (15184)
  hydrogen bonds       : bond        0.04267 /  2.84 (  649)
  hydrogen bonds       : angle       2.76812 /  1.97 ( 1657)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7463 (t0) cc_final: 0.7051 (p0)
REVERT: A  115 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8215 (mp)
REVERT: A  128 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7604 (mt0)
REVERT: B   25 ARG cc_start: 0.7815 (ptt90) cc_final: 0.7467 (ptt-90)
REVERT: B   72 GLU cc_start: 0.8390 (tp30) cc_final: 0.7722 (tt0)
REVERT: D   37 ASN cc_start: 0.8488 (t0) cc_final: 0.7905 (t0)
REVERT: E   75 ARG cc_start: 0.7215 (tpp80) cc_final: 0.6475 (mtm-85)
REVERT: F   75 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8396 (ttp-170)
REVERT: G   92 ASP cc_start: 0.8613 (t70) cc_final: 0.8162 (t0)
REVERT: H   96 LYS cc_start: 0.8004 (tttt) cc_final: 0.7741 (tttm)
  outliers start: 19
  outliers final: 11
  residues processed: 92
  average time/residue: 0.1173
  time to fit residues: 14.0649
Evaluate side-chains
  95 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   75 ARG
Chi-restraints excluded: chain F residue   94 VAL
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue  102 VAL
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   73 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 66 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 17 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 69 optimal weight:    9.9990
   chunk 24 optimal weight:    0.0670
   chunk 51 optimal weight:    6.9990
   overall best weight:    0.6318

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.148730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.099523 restraints weight = 13297.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.12
r_work: 0.3092 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10511  Z= 0.130
  Angle     :  0.554   8.073  15184  Z= 0.325
  Chirality :  0.036   0.190   1757
  Planarity :  0.003   0.025   1113
  Dihedral  : 30.499 127.989   3230
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.40 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.60 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.76 (0.32), residues: 643
  helix:  2.59 (0.22), residues: 499
  sheet:  None (None), residues: 0
  loop : -1.05 (0.44), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  87 
 TYR   0.020   0.002   TYR B  73 
 PHE   0.013   0.002   PHE H  53 
 TRP   0.005   0.001   TRP H  25 
 HIS   0.002   0.001   HIS C  91 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00228 /  0.13 (10511)
  covalent geometry    : angle       0.55372 /  0.33 (15184)
  hydrogen bonds       : bond        0.03893 /  2.54 (  649)
  hydrogen bonds       : angle       2.60583 /  1.85 ( 1657)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7447 (t0) cc_final: 0.7061 (p0)
REVERT: A   87 MET cc_start: 0.8416 (mmt) cc_final: 0.7381 (mmm)
REVERT: A  128 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7576 (mt0)
REVERT: B   25 ARG cc_start: 0.7822 (ptt90) cc_final: 0.7494 (ptt-90)
REVERT: B   72 GLU cc_start: 0.8400 (tp30) cc_final: 0.7768 (tt0)
REVERT: D   37 ASN cc_start: 0.8473 (t0) cc_final: 0.7894 (t0)
REVERT: D   42 MET cc_start: 0.8223 (ptm) cc_final: 0.7909 (ptm)
REVERT: D   73 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7640 (tpp-160)
REVERT: F   75 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8290 (ttp-170)
REVERT: H   96 LYS cc_start: 0.7997 (tttt) cc_final: 0.7740 (tttm)
  outliers start: 16
  outliers final: 12
  residues processed: 95
  average time/residue: 0.0990
  time to fit residues: 12.4551
Evaluate side-chains
  97 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain F residue   24 VAL
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   75 ARG
Chi-restraints excluded: chain F residue   94 VAL
Chi-restraints excluded: chain G residue  102 VAL
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain H residue   88 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 81 optimal weight:    9.9990
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 62 optimal weight:   20.0000
   chunk 66 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.5988

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.146432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.097119 restraints weight = 13278.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.09
r_work: 0.3056 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10511  Z= 0.191
  Angle     :  0.601   8.602  15184  Z= 0.341
  Chirality :  0.037   0.188   1757
  Planarity :  0.003   0.026   1113
  Dihedral  : 30.626 128.339   3230
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.24 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.25 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.54 (0.32), residues: 643
  helix:  2.41 (0.22), residues: 503
  sheet:  None (None), residues: 0
  loop : -1.11 (0.44), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  87 
 TYR   0.023   0.002   TYR B  73 
 PHE   0.016   0.002   PHE H  53 
 TRP   0.007   0.001   TRP H  25 
 HIS   0.004   0.001   HIS C  91 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.19 (10511)
  covalent geometry    : angle       0.60140 /  0.34 (15184)
  hydrogen bonds       : bond        0.04186 /  2.79 (  649)
  hydrogen bonds       : angle       2.69248 /  1.92 ( 1657)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7432 (t0) cc_final: 0.7043 (p0)
REVERT: A  128 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7566 (mt0)
REVERT: B   25 ARG cc_start: 0.7913 (ptt90) cc_final: 0.7586 (ptt-90)
REVERT: B   72 GLU cc_start: 0.8408 (tp30) cc_final: 0.7770 (tt0)
REVERT: D   37 ASN cc_start: 0.8463 (t0) cc_final: 0.7872 (t0)
REVERT: D   93 ASP cc_start: 0.8301 (t70) cc_final: 0.7922 (t0)
REVERT: E   75 ARG cc_start: 0.7175 (tpp80) cc_final: 0.6494 (mtm-85)
REVERT: F   75 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8336 (ttp-170)
REVERT: H   96 LYS cc_start: 0.7994 (tttt) cc_final: 0.7729 (tttm)
  outliers start: 15
  outliers final: 9
  residues processed: 98
  average time/residue: 0.1200
  time to fit residues: 15.3907
Evaluate side-chains
  99 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain F residue   24 VAL
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   75 ARG
Chi-restraints excluded: chain F residue   94 VAL
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue  102 VAL
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   36 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 20 optimal weight:    0.1980
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 75 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 72 optimal weight:   30.0000
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  66 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.148450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.099224 restraints weight = 13318.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 2.11
r_work: 0.3090 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10511  Z= 0.134
  Angle     :  0.560   8.241  15184  Z= 0.325
  Chirality :  0.036   0.189   1757
  Planarity :  0.003   0.032   1113
  Dihedral  : 30.522 128.038   3230
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.40 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.80 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.85 (0.32), residues: 643
  helix:  2.60 (0.22), residues: 500
  sheet:  None (None), residues: 0
  loop : -0.83 (0.46), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  41 
 TYR   0.018   0.001   TYR B  73 
 PHE   0.013   0.002   PHE H  53 
 TRP   0.005   0.001   TRP H  25 
 HIS   0.003   0.001   HIS C  91 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.13 (10511)
  covalent geometry    : angle       0.55975 /  0.33 (15184)
  hydrogen bonds       : bond        0.03880 /  2.54 (  649)
  hydrogen bonds       : angle       2.59429 /  1.85 ( 1657)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7473 (t0) cc_final: 0.7091 (p0)
REVERT: A  128 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7533 (mt0)
REVERT: B   25 ARG cc_start: 0.7839 (ptt90) cc_final: 0.7501 (ptt-90)
REVERT: B   72 GLU cc_start: 0.8376 (tp30) cc_final: 0.7726 (tt0)
REVERT: D   37 ASN cc_start: 0.8437 (t0) cc_final: 0.7832 (t0)
REVERT: D   73 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7649 (tpp-160)
REVERT: D   93 ASP cc_start: 0.8274 (t70) cc_final: 0.7890 (t0)
REVERT: E   75 ARG cc_start: 0.7103 (tpp80) cc_final: 0.6453 (mtm-85)
REVERT: F   75 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8259 (ttp-170)
REVERT: H   96 LYS cc_start: 0.7965 (tttt) cc_final: 0.7700 (tttm)
  outliers start: 16
  outliers final: 13
  residues processed: 100
  average time/residue: 0.1345
  time to fit residues: 17.5898
Evaluate side-chains
  102 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain E residue   79 SER
Chi-restraints excluded: chain E residue   99 THR
Chi-restraints excluded: chain F residue   24 VAL
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   75 ARG
Chi-restraints excluded: chain F residue   94 VAL
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue  102 VAL
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   88 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 14 optimal weight:    5.9990
   chunk 64 optimal weight:   10.0000
   chunk 61 optimal weight:   30.0000
   chunk 72 optimal weight:   30.0000
   chunk 28 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.1388

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.147587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.098242 restraints weight = 13205.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.13
r_work: 0.3069 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10511  Z= 0.156
  Angle     :  0.582   9.027  15184  Z= 0.332
  Chirality :  0.036   0.189   1757
  Planarity :  0.003   0.026   1113
  Dihedral  : 30.564 128.144   3230
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.27 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.32), residues: 643
  helix:  2.47 (0.22), residues: 503
  sheet:  None (None), residues: 0
  loop : -0.98 (0.45), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  41 
 TYR   0.020   0.002   TYR B  73 
 PHE   0.014   0.002   PHE H  53 
 TRP   0.006   0.001   TRP H  25 
 HIS   0.003   0.001   HIS C  91 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.16 (10511)
  covalent geometry    : angle       0.58178 /  0.33 (15184)
  hydrogen bonds       : bond        0.04033 /  2.67 (  649)
  hydrogen bonds       : angle       2.62612 /  1.87 ( 1657)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7476 (t0) cc_final: 0.7095 (p0)
REVERT: A  128 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7572 (mt0)
REVERT: B   25 ARG cc_start: 0.7920 (ptt90) cc_final: 0.7591 (ptt-90)
REVERT: B   72 GLU cc_start: 0.8407 (tp30) cc_final: 0.7765 (tt0)
REVERT: D   37 ASN cc_start: 0.8452 (t0) cc_final: 0.7864 (t0)
REVERT: D   42 MET cc_start: 0.7814 (ptm) cc_final: 0.7483 (ptm)
REVERT: D   73 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7682 (tpp-160)
REVERT: D   93 ASP cc_start: 0.8297 (t70) cc_final: 0.7906 (t0)
REVERT: E   75 ARG cc_start: 0.7179 (tpp80) cc_final: 0.6502 (mtm-85)
REVERT: F   75 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8283 (ttp-170)
REVERT: H   96 LYS cc_start: 0.7991 (tttt) cc_final: 0.7727 (tttm)
  outliers start: 13
  outliers final: 9
  residues processed: 95
  average time/residue: 0.1288
  time to fit residues: 16.0435
Evaluate side-chains
  98 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain F residue   24 VAL
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   75 ARG
Chi-restraints excluded: chain F residue   94 VAL
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue  102 VAL
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   36 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 61 optimal weight:   30.0000
   chunk 35 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 81 optimal weight:   20.0000
   chunk 40 optimal weight:    0.6980
   chunk 14 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.7580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.148997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.099854 restraints weight = 13403.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.12
r_work: 0.3096 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10511  Z= 0.133
  Angle     :  0.554   8.881  15184  Z= 0.322
  Chirality :  0.035   0.189   1757
  Planarity :  0.003   0.029   1113
  Dihedral  : 30.493 127.846   3230
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 19.08 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.86 (0.32), residues: 643
  helix:  2.60 (0.22), residues: 501
  sheet:  None (None), residues: 0
  loop : -0.81 (0.47), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  41 
 TYR   0.018   0.001   TYR B  73 
 PHE   0.013   0.001   PHE H  53 
 TRP   0.005   0.001   TRP H  25 
 HIS   0.002   0.000   HIS C  91 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.13 (10511)
  covalent geometry    : angle       0.55379 /  0.32 (15184)
  hydrogen bonds       : bond        0.03885 /  2.54 (  649)
  hydrogen bonds       : angle       2.56075 /  1.82 ( 1657)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1803.99 seconds
wall clock time: 31 minutes 33.08 seconds (1893.08 seconds total)