Starting phenix.real_space_refine
on Wed Mar  4 14:34:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xpx_33385/03_2026/7xpx_33385.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xpx_33385/03_2026/7xpx_33385.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xpx_33385/03_2026/7xpx_33385.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xpx_33385/03_2026/7xpx_33385.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xpx_33385/03_2026/7xpx_33385.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xpx_33385/03_2026/7xpx_33385.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1341 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     288      5.49       5
     S      20      5.16       5
     C    7508      2.51       5
     N    2521      2.21       5
     O    3071      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13408
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 820
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 693
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'ECX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 756
          Classifications: {'peptide': 96}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "E"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 808
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "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: 757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 757
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "I"
      Number of atoms: 2970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2970
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2969
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 1338
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 167, 1337
          Classifications: {'peptide': 167}
          Link IDs: {'PTRANS': 3, 'TRANS': 163}
      Conformer: "B"
        Number of residues, atoms: 167, 1337
          Classifications: {'peptide': 167}
          Link IDs: {'PTRANS': 3, 'TRANS': 163}
          bond proxies already assigned to first conformer: 1359
    Chain: "K"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Classifications: {'peptide': 1}
  Time building chain proxies: 3.04, per 1000 atoms: 0.23
  Number of scatterers: 13408
  At special positions: 0
  Unit cell: (94, 120, 121, 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     288     15.00
     O    3071      8.00
     N    2521      7.00
     C    7508      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.15
  Conformation dependent library (CDL) restraints added in 388.7 milliseconds
  

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1748

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 14 sheets defined
      62.1% alpha, 7.0% beta
      137 base pairs and 257 stacking pairs defined.
    Time for finding SS restraints: 1.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.556A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.265A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (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
    Processing helix  chain 'D' and resid 100 through 120
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.798A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (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 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.567A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.289A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    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
    Processing helix  chain 'H' and resid 101 through 121
    Processing helix  chain 'K' and resid 199 through 208
      removed outlier: 3.720A  pdb=" N   ARG K 205 " --> pdb=" O   GLU K 201 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 251 through 265
      removed outlier: 3.982A  pdb=" N   LYS K 257 " --> pdb=" O   THR K 253 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 340 through 347
      removed outlier: 3.577A  pdb=" N   GLU K 345 " --> pdb=" O   LYS K 341 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA K 346 " --> pdb=" O   ALA K 342 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.741A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.559A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.134A  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 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.881A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.477A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 218 through 223
    Processing sheet with id=AB3, first strand: chain 'K' and resid 241 through 245
      removed outlier: 6.934A  pdb=" N   PHE K 241 " --> pdb=" O   ALA K 322 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   ALA K 322 " --> pdb=" O   PHE K 241 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   LEU K 318 " --> pdb=" O   TYR K 245 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'K' and resid 248 through 250
    Processing sheet with id=AB5, first strand: chain 'K' and resid 298 through 299
      removed outlier: 6.611A  pdb=" N   ASN K 298 " --> pdb=" O   TYR K 334 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5

    454 hydrogen bonds defined for protein.
    1329 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      354 hydrogen bonds
      708 hydrogen bond angles
      0 basepair planarities
      137 basepair parallelities
      257 stacking parallelities
  Total time for adding SS restraints: 2.21

  Time building geometry restraints manager: 1.48 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: 3023
        1.34 -     1.46: 4248
        1.46 -     1.58: 6355
        1.58 -     1.70: 576
        1.70 -     1.82: 35
  Bond restraints: 14237
  Sorted by residual:
  bond pdb=" C2  SAM K 401 "
       pdb=" N3  SAM K 401 "
    ideal  model  delta    sigma   weight residual
    1.322  1.380 -0.058 2.00e-02 2.50e+03 8.47e+00
  bond pdb=" C8  SAM K 401 "
       pdb=" N7  SAM K 401 "
    ideal  model  delta    sigma   weight residual
    1.298  1.351 -0.053 2.00e-02 2.50e+03 6.92e+00
  bond pdb=" CB  ECX B  20 "
       pdb=" SC  ECX B  20 "
    ideal  model  delta    sigma   weight residual
    1.819  1.767  0.052 2.00e-02 2.50e+03 6.67e+00
  bond pdb=" C2  SAM K 401 "
       pdb=" N1  SAM K 401 "
    ideal  model  delta    sigma   weight residual
    1.329  1.380 -0.051 2.00e-02 2.50e+03 6.51e+00
  bond pdb=" CD  ECX B  20 "
       pdb=" SC  ECX B  20 "
    ideal  model  delta    sigma   weight residual
    1.817  1.770  0.047 2.00e-02 2.50e+03 5.51e+00
  ... (remaining 14232 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 19986
        1.82 -     3.63: 436
        3.63 -     5.45: 27
        5.45 -     7.26: 3
        7.26 -     9.08: 5
  Bond angle restraints: 20457
  Sorted by residual:
  angle pdb=" C   LYS D  28 "
        pdb=" CA  LYS D  28 "
        pdb=" CB  LYS D  28 "
      ideal   model   delta    sigma   weight residual
     116.54  111.52    5.02 1.15e+00 7.56e-01 1.91e+01
  angle pdb=" N   LYS K 195 "
        pdb=" CA  LYS K 195 "
        pdb=" C   LYS K 195 "
      ideal   model   delta    sigma   weight residual
     111.81  107.04    4.77 1.44e+00 4.82e-01 1.10e+01
  angle pdb=" CB  MET K 272 "
        pdb=" CG  MET K 272 "
        pdb=" SD  MET K 272 "
      ideal   model   delta    sigma   weight residual
     112.70  103.62    9.08 3.00e+00 1.11e-01 9.15e+00
  angle pdb=" O   SAM K 401 "
        pdb=" C   SAM K 401 "
        pdb=" OXT SAM K 401 "
      ideal   model   delta    sigma   weight residual
     126.77  118.08    8.69 3.00e+00 1.11e-01 8.39e+00
  angle pdb=" CA  LYS D  28 "
        pdb=" C   LYS D  28 "
        pdb=" N   THR D  29 "
      ideal   model   delta    sigma   weight residual
     119.52  117.25    2.27 7.90e-01 1.60e+00 8.27e+00
  ... (remaining 20452 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.48: 6410
       35.48 -    70.96: 1429
       70.96 -   106.44: 12
      106.44 -   141.92: 2
      141.92 -   177.40: 3
  Dihedral angle restraints: 7856
    sinusoidal: 5144
      harmonic: 2712
  Sorted by residual:
  dihedral pdb=" C4'  DT J  54 "
           pdb=" C3'  DT J  54 "
           pdb=" O3'  DT J  54 "
           pdb=" P    DC J  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   42.60  177.40     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DT I  54 "
           pdb=" C3'  DT I  54 "
           pdb=" O3'  DT I  54 "
           pdb=" P    DC I  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   36.82 -176.82     1      3.50e+01 8.16e-04 1.57e+01
  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   44.40  175.60     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 7853 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1725
       0.037 -    0.073: 476
       0.073 -    0.110: 83
       0.110 -    0.147: 25
       0.147 -    0.183: 4
  Chirality restraints: 2313
  Sorted by residual:
  chirality pdb=" CA  GLU D  90 "
            pdb=" N   GLU D  90 "
            pdb=" C   GLU D  90 "
            pdb=" CB  GLU D  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.39e-01
  chirality pdb=" C2' SAM K 401 "
            pdb=" C1' SAM K 401 "
            pdb=" C3' SAM K 401 "
            pdb=" O2' SAM K 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.76   -2.57   -0.18 2.00e-01 2.50e+01 8.32e-01
  chirality pdb=" C1' SAM K 401 "
            pdb=" C2' SAM K 401 "
            pdb=" N9  SAM K 401 "
            pdb=" O4' SAM K 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.30    2.47   -0.17 2.00e-01 2.50e+01 7.01e-01
  ... (remaining 2310 not shown)

  Planarity restraints: 1588
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  55 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.15e+00
        pdb=" C   ARG B  55 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ARG B  55 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLY B  56 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  47 "    0.027 2.00e-02 2.50e+03   1.19e-02 3.88e+00
        pdb=" N9   DA I  47 "   -0.025 2.00e-02 2.50e+03
        pdb=" C8   DA I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DA I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DA I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  47 "    0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DA I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I  47 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL K 315 "   -0.029 5.00e-02 4.00e+02   4.40e-02 3.09e+00
        pdb=" N   PRO K 316 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO K 316 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO K 316 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1585 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 922
        2.73 -     3.27: 12385
        3.27 -     3.81: 27071
        3.81 -     4.36: 31892
        4.36 -     4.90: 45811
  Nonbonded interactions: 118081
  Sorted by model distance:
  nonbonded pdb=" O   LYS C  15 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   GLU K 208 "
            pdb=" OG  SER K 212 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH1 ARG A 131 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OE2 GLU D  68 "
            pdb=" NH2 ARG H  76 "
     model   vdw
     2.270 3.120
  ... (remaining 118076 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 38 through 134)
  selection = (chain 'E' and resid 38 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 24 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 14 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 27 through 121)
  selection = (chain 'H' and resid 27 through 121)
}
ncs_group {
  reference = (chain 'I' and (resid -72 through -1 or resid 1 through 72))
  selection = (chain 'J' and (resid -72 through -1 or resid 1 through 72))
}

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=0.50 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:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     13.560
  Find NCS groups from input model:        0.160
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
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      :  0.004   0.058  14237  Z= 0.174
  Angle     :  0.612   9.076  20457  Z= 0.359
  Chirality :  0.036   0.183   2313
  Planarity :  0.005   0.052   1588
  Dihedral  : 27.533 177.402   6108
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.27), residues: 913
  helix:  1.35 (0.21), residues: 572
  sheet: -0.78 (0.81), residues: 38
  loop : -0.77 (0.32), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG K 189 
 TYR   0.019   0.002   TYR K 262 
 PHE   0.013   0.002   PHE G  25 
 TRP   0.003   0.001   TRP K 349 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (14237)
  covalent geometry    : angle       0.61184 (20457)
  hydrogen bonds       : bond        0.10664 (  808)
  hydrogen bonds       : angle       4.14572 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   56 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7311 (tm-30)
REVERT: C   95 LYS cc_start: 0.7621 (tttm) cc_final: 0.7351 (ttmt)
REVERT: D   56 MET cc_start: 0.8281 (tpp) cc_final: 0.8077 (tpp)
REVERT: G   75 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8094 (mttm)
REVERT: K  195 LYS cc_start: 0.7410 (tmmt) cc_final: 0.7209 (tttt)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1658
  time to fit residues: 25.6906
Evaluate side-chains
  114 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    0.3980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
D  44 GLN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  92 GLN
E 108 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.211819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.125315 restraints weight = 14036.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 1.97
r_work: 0.2962 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.1122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14237  Z= 0.170
  Angle     :  0.566   6.095  20457  Z= 0.336
  Chirality :  0.035   0.154   2313
  Planarity :  0.004   0.040   1588
  Dihedral  : 30.425 178.110   4244
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  6.27 %
    Favored  : 93.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.27), residues: 913
  helix:  1.81 (0.21), residues: 587
  sheet: -0.72 (0.84), residues: 38
  loop : -0.58 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  35 
 TYR   0.015   0.001   TYR K 262 
 PHE   0.009   0.001   PHE G  25 
 TRP   0.002   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (14237)
  covalent geometry    : angle       0.56647 (20457)
  hydrogen bonds       : bond        0.03718 (  808)
  hydrogen bonds       : angle       3.17302 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 118
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.7658 (tttm) cc_final: 0.7072 (ttmt)
REVERT: D   56 MET cc_start: 0.8726 (tpp) cc_final: 0.8492 (tpp)
REVERT: G   73 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8488 (t0)
REVERT: K  197 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6567 (mt-10)
  outliers start: 4
  outliers final: 3
  residues processed: 118
  average time/residue: 0.1825
  time to fit residues: 27.8944
Evaluate side-chains
  116 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 112
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain K residue  204 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0370
   chunk 97 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.8860

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.212894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.123735 restraints weight = 14119.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.03
r_work: 0.2919 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14237  Z= 0.180
  Angle     :  0.547   5.777  20457  Z= 0.326
  Chirality :  0.034   0.143   2313
  Planarity :  0.004   0.037   1588
  Dihedral  : 30.289 179.554   4244
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  8.31 %
    Favored  : 90.41 %
  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:  1.64 (0.27), residues: 913
  helix:  1.99 (0.21), residues: 587
  sheet: -0.75 (0.82), residues: 38
  loop : -0.52 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  96 
 TYR   0.013   0.001   TYR K 262 
 PHE   0.008   0.001   PHE G  25 
 TRP   0.000   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (14237)
  covalent geometry    : angle       0.54724 (20457)
  hydrogen bonds       : bond        0.03485 (  808)
  hydrogen bonds       : angle       3.08843 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7731 (mtm-85)
REVERT: C   56 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8318 (tm-30)
REVERT: C   95 LYS cc_start: 0.7693 (tttm) cc_final: 0.7186 (ttmt)
REVERT: D   34 TYR cc_start: 0.9291 (m-80) cc_final: 0.8874 (m-80)
REVERT: D   56 MET cc_start: 0.8729 (tpp) cc_final: 0.8472 (tpp)
REVERT: G   73 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8508 (t0)
  outliers start: 10
  outliers final: 8
  residues processed: 120
  average time/residue: 0.1839
  time to fit residues: 28.6156
Evaluate side-chains
  123 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  209 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 110 optimal weight:    5.9990
   chunk 98 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  18 HIS
B  27 GLN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.212362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.122732 restraints weight = 14165.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.03
r_work: 0.2941 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14237  Z= 0.179
  Angle     :  0.538   5.737  20457  Z= 0.322
  Chirality :  0.034   0.143   2313
  Planarity :  0.004   0.037   1588
  Dihedral  : 30.111 178.791   4244
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  8.70 %
    Favored  : 89.39 %
  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:  1.77 (0.28), residues: 913
  helix:  2.09 (0.21), residues: 583
  sheet: -0.74 (0.83), residues: 38
  loop : -0.43 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  96 
 TYR   0.010   0.001   TYR G  57 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.001   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (14237)
  covalent geometry    : angle       0.53789 (20457)
  hydrogen bonds       : bond        0.03413 (  808)
  hydrogen bonds       : angle       3.00881 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: C   56 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8266 (tm-30)
REVERT: C   95 LYS cc_start: 0.7680 (tttm) cc_final: 0.7160 (ttmt)
REVERT: D   34 TYR cc_start: 0.9277 (m-80) cc_final: 0.8781 (m-80)
REVERT: D   56 MET cc_start: 0.8729 (tpp) cc_final: 0.8480 (tpp)
REVERT: F   90 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7813 (mt)
REVERT: G   73 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8453 (t0)
  outliers start: 14
  outliers final: 9
  residues processed: 119
  average time/residue: 0.1808
  time to fit residues: 27.8758
Evaluate side-chains
  123 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  209 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 48 optimal weight:    0.4980
   chunk 42 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 95 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 96 optimal weight:    4.9990
   chunk 85 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0670
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
D  60 ASN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.220759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.133977 restraints weight = 14244.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.97
r_work: 0.2959 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2944
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2944
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.1972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14237  Z= 0.148
  Angle     :  0.530  10.744  20457  Z= 0.315
  Chirality :  0.033   0.192   2313
  Planarity :  0.004   0.037   1588
  Dihedral  : 30.057 178.944   4244
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  9.59 %
    Favored  : 88.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.28), residues: 913
  helix:  2.24 (0.21), residues: 583
  sheet: -0.82 (0.82), residues: 38
  loop : -0.35 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  96 
 TYR   0.017   0.001   TYR K 262 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.001   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (14237)
  covalent geometry    : angle       0.53022 (20457)
  hydrogen bonds       : bond        0.03259 (  808)
  hydrogen bonds       : angle       2.94665 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.7686 (tttm) cc_final: 0.7142 (ttmt)
REVERT: D   34 TYR cc_start: 0.9274 (m-80) cc_final: 0.8818 (m-80)
REVERT: D   56 MET cc_start: 0.8736 (tpp) cc_final: 0.8503 (tpp)
REVERT: F   90 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7796 (mt)
REVERT: G   73 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8480 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 115
  average time/residue: 0.1784
  time to fit residues: 26.4367
Evaluate side-chains
  117 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain K residue  198 LEU
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 104 optimal weight:   10.0000
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0050
   chunk 36 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0980
   chunk 47 optimal weight:    0.6980
   chunk 55 optimal weight:    0.2980
   chunk 16 optimal weight:    0.3980
   chunk 75 optimal weight:    6.9990
   overall best weight:    0.2994

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.225018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.139096 restraints weight = 14116.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.90
r_work: 0.3011 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2992
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2992
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14237  Z= 0.137
  Angle     :  0.515   5.921  20457  Z= 0.309
  Chirality :  0.033   0.150   2313
  Planarity :  0.004   0.037   1588
  Dihedral  : 29.994 178.650   4244
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 10.23 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.28), residues: 913
  helix:  2.37 (0.21), residues: 583
  sheet: -0.70 (0.83), residues: 38
  loop : -0.26 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  96 
 TYR   0.009   0.001   TYR K 262 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.001   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (14237)
  covalent geometry    : angle       0.51493 (20457)
  hydrogen bonds       : bond        0.03178 (  808)
  hydrogen bonds       : angle       2.87174 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.7658 (tttm) cc_final: 0.7102 (ttmt)
REVERT: D   34 TYR cc_start: 0.9272 (m-80) cc_final: 0.8845 (m-80)
REVERT: D   56 MET cc_start: 0.8675 (tpp) cc_final: 0.8447 (tpp)
REVERT: F   90 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7682 (mt)
REVERT: G   73 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8471 (t0)
REVERT: K  188 ARG cc_start: 0.7563 (tmt170) cc_final: 0.7110 (tmt170)
REVERT: K  214 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.5847 (ttpt)
  outliers start: 10
  outliers final: 6
  residues processed: 111
  average time/residue: 0.1777
  time to fit residues: 25.5649
Evaluate side-chains
  113 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 114 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 75 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 112 optimal weight:    0.0060
   chunk 50 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
K 310 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.220212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.132541 restraints weight = 14077.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 1.97
r_work: 0.2974 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14237  Z= 0.153
  Angle     :  0.528  12.418  20457  Z= 0.312
  Chirality :  0.033   0.188   2313
  Planarity :  0.004   0.036   1588
  Dihedral  : 30.002 178.191   4244
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.36 %
    Favored  : 87.60 %
  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:  2.11 (0.28), residues: 913
  helix:  2.33 (0.21), residues: 584
  sheet: -0.68 (0.82), residues: 38
  loop : -0.20 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 129 
 TYR   0.014   0.001   TYR K 262 
 PHE   0.007   0.001   PHE A  67 
 TRP   0.001   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (14237)
  covalent geometry    : angle       0.52809 (20457)
  hydrogen bonds       : bond        0.03269 (  808)
  hydrogen bonds       : angle       2.91988 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8280 (tm-30)
REVERT: C   95 LYS cc_start: 0.7693 (tttm) cc_final: 0.7150 (ttmt)
REVERT: D   34 TYR cc_start: 0.9300 (m-80) cc_final: 0.8878 (m-80)
REVERT: D   56 MET cc_start: 0.8742 (tpp) cc_final: 0.8510 (tpp)
REVERT: F   90 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7814 (mt)
REVERT: G   73 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8503 (t0)
REVERT: K  214 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.5785 (tttt)
  outliers start: 15
  outliers final: 11
  residues processed: 127
  average time/residue: 0.1855
  time to fit residues: 30.4390
Evaluate side-chains
  133 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  209 LEU
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 0 optimal weight:    9.9990
   chunk 76 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 49 optimal weight:    0.4980
   chunk 30 optimal weight:    0.5980
   chunk 62 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9990
   chunk 108 optimal weight:   20.0000
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.5580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.220468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.133955 restraints weight = 13994.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.91
r_work: 0.2981 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2969
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2969
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14237  Z= 0.148
  Angle     :  0.520   7.649  20457  Z= 0.310
  Chirality :  0.033   0.148   2313
  Planarity :  0.004   0.040   1588
  Dihedral  : 29.990 178.199   4244
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.74 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.28), residues: 913
  helix:  2.32 (0.21), residues: 584
  sheet: -0.57 (0.84), residues: 38
  loop : -0.18 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 129 
 TYR   0.012   0.001   TYR K 262 
 PHE   0.007   0.001   PHE E  67 
 TRP   0.002   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (14237)
  covalent geometry    : angle       0.52033 (20457)
  hydrogen bonds       : bond        0.03263 (  808)
  hydrogen bonds       : angle       2.89589 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8214 (tm-30)
REVERT: C   95 LYS cc_start: 0.7693 (tttm) cc_final: 0.7147 (ttmt)
REVERT: D   34 TYR cc_start: 0.9295 (m-80) cc_final: 0.8793 (m-80)
REVERT: D   56 MET cc_start: 0.8735 (tpp) cc_final: 0.8501 (tpp)
REVERT: F   90 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7788 (mt)
REVERT: G   73 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8498 (t0)
REVERT: K  214 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.5791 (tttt)
  outliers start: 15
  outliers final: 11
  residues processed: 120
  average time/residue: 0.1757
  time to fit residues: 27.4735
Evaluate side-chains
  124 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  209 LEU
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 84 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0020
   chunk 64 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   overall best weight:    0.6388

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.213815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.125754 restraints weight = 14003.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 1.92
r_work: 0.2976 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2963
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2963
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.2390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14237  Z= 0.154
  Angle     :  0.521  10.320  20457  Z= 0.309
  Chirality :  0.033   0.143   2313
  Planarity :  0.004   0.037   1588
  Dihedral  : 29.979 178.032   4244
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 10.74 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.28), residues: 913
  helix:  2.34 (0.21), residues: 584
  sheet: -0.54 (0.84), residues: 38
  loop : -0.16 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 129 
 TYR   0.010   0.001   TYR G  57 
 PHE   0.007   0.001   PHE A  67 
 TRP   0.001   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (14237)
  covalent geometry    : angle       0.52055 (20457)
  hydrogen bonds       : bond        0.03271 (  808)
  hydrogen bonds       : angle       2.88551 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8198 (tm-30)
REVERT: C   95 LYS cc_start: 0.7694 (tttm) cc_final: 0.7145 (ttmt)
REVERT: D   34 TYR cc_start: 0.9296 (m-80) cc_final: 0.8801 (m-80)
REVERT: D   56 MET cc_start: 0.8741 (tpp) cc_final: 0.8506 (tpp)
REVERT: F   90 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7867 (mt)
REVERT: G   73 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8505 (t0)
REVERT: K  214 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.5793 (ttpt)
  outliers start: 18
  outliers final: 14
  residues processed: 129
  average time/residue: 0.1678
  time to fit residues: 28.3239
Evaluate side-chains
  136 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue  198 LEU
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  209 LEU
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 108 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0970
   chunk 83 optimal weight:    7.9990
   chunk 74 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.7378

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.213563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.125426 restraints weight = 14010.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.92
r_work: 0.2969 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2960
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.2436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14237  Z= 0.161
  Angle     :  0.525  10.544  20457  Z= 0.311
  Chirality :  0.033   0.147   2313
  Planarity :  0.004   0.044   1588
  Dihedral  : 29.983 177.904   4244
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 11.13 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.28), residues: 913
  helix:  2.33 (0.21), residues: 584
  sheet: -0.52 (0.85), residues: 38
  loop : -0.13 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 129 
 TYR   0.010   0.001   TYR G  57 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.001   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (14237)
  covalent geometry    : angle       0.52459 (20457)
  hydrogen bonds       : bond        0.03312 (  808)
  hydrogen bonds       : angle       2.90012 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8169 (tm-30)
REVERT: A  129 ARG cc_start: 0.8145 (tpt90) cc_final: 0.7772 (tpt90)
REVERT: C   95 LYS cc_start: 0.7681 (tttm) cc_final: 0.7135 (ttmt)
REVERT: D   34 TYR cc_start: 0.9298 (m-80) cc_final: 0.8799 (m-80)
REVERT: D   56 MET cc_start: 0.8759 (tpp) cc_final: 0.8514 (tpp)
REVERT: F   90 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7847 (mt)
REVERT: G   73 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8503 (t0)
REVERT: K  214 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.5798 (ttpt)
  outliers start: 17
  outliers final: 13
  residues processed: 126
  average time/residue: 0.1570
  time to fit residues: 26.0847
Evaluate side-chains
  129 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  209 LEU
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 61 optimal weight:    0.0270
   chunk 103 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0870
   chunk 53 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0000
   chunk 10 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.2820

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.222244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.135433 restraints weight = 14158.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 1.96
r_work: 0.2979 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14237  Z= 0.135
  Angle     :  0.531  12.373  20457  Z= 0.311
  Chirality :  0.034   0.324   2313
  Planarity :  0.004   0.037   1588
  Dihedral  : 29.984 177.903   4244
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 11.25 %
    Favored  : 86.57 %
  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:  2.20 (0.28), residues: 913
  helix:  2.35 (0.21), residues: 584
  sheet: -0.50 (0.85), residues: 38
  loop : -0.10 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 129 
 TYR   0.009   0.001   TYR G  57 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.001   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (14237)
  covalent geometry    : angle       0.53148 (20457)
  hydrogen bonds       : bond        0.03226 (  808)
  hydrogen bonds       : angle       2.90342 ( 2037)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3867.77 seconds
wall clock time: 66 minutes 26.69 seconds (3986.69 seconds total)