Starting phenix.real_space_refine
on Thu Jun 12 20:40:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xpx_33385/06_2025/7xpx_33385.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xpx_33385/06_2025/7xpx_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_33385/06_2025/7xpx_33385.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xpx_33385/06_2025/7xpx_33385.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xpx_33385/06_2025/7xpx_33385.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xpx_33385/06_2025/7xpx_33385.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.39, per 1000 atoms: 0.70
  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: 3.68
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 6.37
  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: 5.79

  Time building geometry restraints manager: 4.32 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:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     39.550
  Find NCS groups from input model:        0.440
  Set up NCS constraints:                  0.050
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.830
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.003   0.001   TRP K 349 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.013   0.002   PHE G  25 
 TYR   0.019   0.002   TYR K 262 
 ARG   0.014   0.001   ARG K 189 

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

*********************** 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  : 0.953 
Fit side-chains
   revert: symmetry clash
REVERT: C   56 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7310 (tm-30)
REVERT: C   95 LYS cc_start: 0.7621 (tttm) cc_final: 0.7349 (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: 0.8093 (mttm)
REVERT: K  195 LYS cc_start: 0.7410 (tmmt) cc_final: 0.7204 (tttt)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.3746
  time to fit residues: 58.3654
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  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 87 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0970
   chunk 104 optimal weight:    8.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
D  81 ASN
D  92 GLN
E 108 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.209556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.121991 restraints weight = 13911.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 1.97
r_work: 0.2917 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2900
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2900 r_free = 0.2900    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2900 r_free = 0.2900    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2900
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.0969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  14237  Z= 0.222
  Angle     :  0.590   6.290  20457  Z= 0.347
  Chirality :  0.036   0.159   2313
  Planarity :  0.004   0.037   1588
  Dihedral  : 30.520 178.184   4244
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  6.52 %
    Favored  : 92.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.27), residues: 913
  helix:  1.72 (0.21), residues: 587
  sheet: -0.77 (0.82), residues: 38
  loop : -0.63 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K 349 
 HIS   0.006   0.001   HIS C  31 
 PHE   0.010   0.002   PHE A  78 
 TYR   0.014   0.002   TYR K 262 
 ARG   0.005   0.001   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03787 (  808)
  hydrogen bonds       : angle       3.32026 ( 2037)
  covalent geometry    : bond        0.00509 (14237)
  covalent geometry    : angle       0.59003 (20457)

*********************** 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
  131 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 125
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.7985 (mmm) cc_final: 0.7542 (mmm)
REVERT: B   91 LYS cc_start: 0.8699 (tttm) cc_final: 0.8367 (ttpp)
REVERT: B   92 ARG cc_start: 0.8496 (ttp80) cc_final: 0.8222 (ttp80)
REVERT: C   56 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8261 (tm-30)
REVERT: C   95 LYS cc_start: 0.7695 (tttm) cc_final: 0.7145 (ttmt)
REVERT: D   56 MET cc_start: 0.8761 (tpp) cc_final: 0.8504 (tpp)
REVERT: E   56 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7978 (tttt)
REVERT: G   73 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8461 (t0)
REVERT: G   75 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7759 (mttm)
REVERT: K  197 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6576 (mt-10)
REVERT: K  205 ARG cc_start: 0.7789 (tmm160) cc_final: 0.7575 (tmm-80)
  outliers start: 6
  outliers final: 4
  residues processed: 125
  average time/residue: 0.3916
  time to fit residues: 63.7638
Evaluate side-chains
  127 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 122
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
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 G residue  101 THR
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 72 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 79 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 44 optimal weight:    0.4980
   chunk 9 optimal weight:   10.0000
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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
F  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.207510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.119926 restraints weight = 14012.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.91
r_work: 0.2885 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2872
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2872 r_free = 0.2872    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2872 r_free = 0.2872    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2872
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  14237  Z= 0.265
  Angle     :  0.588   6.154  20457  Z= 0.346
  Chirality :  0.037   0.174   2313
  Planarity :  0.004   0.038   1588
  Dihedral  : 30.415 179.575   4244
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  9.59 %
    Favored  : 88.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.27), residues: 913
  helix:  1.64 (0.21), residues: 587
  sheet: -0.70 (0.82), residues: 38
  loop : -0.67 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP K 349 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.010   0.002   PHE G  25 
 TYR   0.012   0.002   TYR F  51 
 ARG   0.005   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03858 (  808)
  hydrogen bonds       : angle       3.24617 ( 2037)
  covalent geometry    : bond        0.00612 (14237)
  covalent geometry    : angle       0.58803 (20457)

*********************** 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
  140 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
REVERT: B   91 LYS cc_start: 0.8758 (tttm) cc_final: 0.8446 (ttpp)
REVERT: C   35 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7711 (mtm-85)
REVERT: C   56 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8333 (tm-30)
REVERT: C   95 LYS cc_start: 0.7697 (tttm) cc_final: 0.7143 (ttmt)
REVERT: D   56 MET cc_start: 0.8757 (tpp) cc_final: 0.8485 (tpp)
REVERT: E   56 LYS cc_start: 0.8295 (mtmt) cc_final: 0.7960 (tttt)
REVERT: F   90 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7866 (mt)
REVERT: G   73 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8478 (t0)
REVERT: K  197 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6659 (mt-10)
REVERT: K  214 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7864 (mtmm)
  outliers start: 12
  outliers final: 6
  residues processed: 132
  average time/residue: 0.3834
  time to fit residues: 66.4272
Evaluate side-chains
  134 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
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   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 K residue  204 LYS
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 113 optimal weight:   20.0000
   chunk 11 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 14 optimal weight:    0.5980
   chunk 71 optimal weight:   10.0000
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  18 HIS
D  60 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.218521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.129927 restraints weight = 14035.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 1.99
r_work: 0.2922 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2904
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2904
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.1659

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= 0.169
  Angle     :  0.540   6.178  20457  Z= 0.324
  Chirality :  0.034   0.139   2313
  Planarity :  0.004   0.037   1588
  Dihedral  : 30.203 179.859   4244
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.10 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.27), residues: 913
  helix:  1.93 (0.21), residues: 587
  sheet: -0.83 (0.82), residues: 38
  loop : -0.53 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP K 349 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.011   0.001   TYR F  51 
 ARG   0.007   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03388 (  808)
  hydrogen bonds       : angle       3.04744 ( 2037)
  covalent geometry    : bond        0.00379 (14237)
  covalent geometry    : angle       0.54025 (20457)

*********************** 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
  129 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.7689 (tttm) cc_final: 0.7156 (ttmt)
REVERT: D   34 TYR cc_start: 0.9288 (m-80) cc_final: 0.8849 (m-80)
REVERT: D   56 MET cc_start: 0.8724 (tpp) cc_final: 0.8508 (tpp)
REVERT: E   56 LYS cc_start: 0.8351 (mtmt) cc_final: 0.7993 (tttt)
REVERT: G   73 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8440 (t0)
REVERT: K  214 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7783 (mtmm)
  outliers start: 8
  outliers final: 6
  residues processed: 123
  average time/residue: 0.3852
  time to fit residues: 62.1268
Evaluate side-chains
  128 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
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   96 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 114 optimal weight:   40.0000
   chunk 106 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 105 optimal weight:    8.9990
   chunk 1 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
D  44 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.216418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.126671 restraints weight = 14103.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 2.01
r_work: 0.2879 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2860
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2860
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  14237  Z= 0.241
  Angle     :  0.566   5.923  20457  Z= 0.335
  Chirality :  0.036   0.167   2313
  Planarity :  0.004   0.036   1588
  Dihedral  : 30.242 178.852   4244
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 10.74 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.27), residues: 913
  helix:  1.84 (0.21), residues: 586
  sheet: -0.90 (0.80), residues: 38
  loop : -0.52 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.010   0.002   PHE A  67 
 TYR   0.012   0.001   TYR F  51 
 ARG   0.006   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03663 (  808)
  hydrogen bonds       : angle       3.11599 ( 2037)
  covalent geometry    : bond        0.00556 (14237)
  covalent geometry    : angle       0.56553 (20457)

*********************** 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
  147 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
REVERT: B   91 LYS cc_start: 0.8829 (ttpp) cc_final: 0.8553 (ttpp)
REVERT: C   35 ARG cc_start: 0.8238 (mtm-85) cc_final: 0.7760 (mtm-85)
REVERT: C   95 LYS cc_start: 0.7703 (tttm) cc_final: 0.7178 (ttmt)
REVERT: D   34 TYR cc_start: 0.9315 (m-80) cc_final: 0.8951 (m-80)
REVERT: D   56 MET cc_start: 0.8754 (tpp) cc_final: 0.8509 (tpp)
REVERT: E   56 LYS cc_start: 0.8330 (mtmt) cc_final: 0.7996 (tttt)
REVERT: F   90 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7844 (mt)
REVERT: F   93 GLN cc_start: 0.8487 (mt0) cc_final: 0.7766 (mp10)
REVERT: G   73 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8436 (t0)
REVERT: K  214 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7780 (mtmm)
  outliers start: 12
  outliers final: 9
  residues processed: 140
  average time/residue: 0.4039
  time to fit residues: 72.7701
Evaluate side-chains
  144 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
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   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 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 34 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 86 optimal weight:    8.9990
   chunk 102 optimal weight:   20.0000
   chunk 9 optimal weight:    9.9990
   chunk 7 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.218063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.136124 restraints weight = 14214.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.09
r_work: 0.2892 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2874
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2874 r_free = 0.2874    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2874 r_free = 0.2874    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2874
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1922

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= 0.159
  Angle     :  0.539   6.694  20457  Z= 0.323
  Chirality :  0.034   0.153   2313
  Planarity :  0.004   0.053   1588
  Dihedral  : 30.195 179.214   4244
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 11.13 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.27), residues: 913
  helix:  1.97 (0.21), residues: 586
  sheet: -0.93 (0.79), residues: 38
  loop : -0.43 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.012   0.001   TYR F  51 
 ARG   0.008   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03363 (  808)
  hydrogen bonds       : angle       3.02276 ( 2037)
  covalent geometry    : bond        0.00354 (14237)
  covalent geometry    : angle       0.53871 (20457)

*********************** 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
  146 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.7701 (tttm) cc_final: 0.7165 (ttmt)
REVERT: D   34 TYR cc_start: 0.9305 (m-80) cc_final: 0.8945 (m-80)
REVERT: D   56 MET cc_start: 0.8759 (tpp) cc_final: 0.8552 (tpp)
REVERT: E   56 LYS cc_start: 0.8301 (mtmt) cc_final: 0.7976 (tttt)
REVERT: F   90 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7824 (mt)
REVERT: G   73 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8453 (t0)
REVERT: K  214 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7762 (mtmm)
  outliers start: 16
  outliers final: 12
  residues processed: 138
  average time/residue: 0.3541
  time to fit residues: 64.9001
Evaluate side-chains
  143 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain D residue   49 THR
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  214 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 113 optimal weight:    0.2980
   chunk 94 optimal weight:    4.9990
   chunk 104 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.4182 r_free = 0.4182 target = 0.209221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.119011 restraints weight = 14094.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 2.03
r_work: 0.2870 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2857
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2857
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  14237  Z= 0.226
  Angle     :  0.557   6.392  20457  Z= 0.330
  Chirality :  0.035   0.172   2313
  Planarity :  0.004   0.037   1588
  Dihedral  : 30.192 178.628   4244
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 11.38 %
    Favored  : 86.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.28), residues: 913
  helix:  1.95 (0.21), residues: 586
  sheet: -0.63 (0.84), residues: 36
  loop : -0.39 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP K 349 
 HIS   0.006   0.001   HIS B  75 
 PHE   0.010   0.002   PHE A  67 
 TYR   0.011   0.001   TYR G  57 
 ARG   0.008   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03558 (  808)
  hydrogen bonds       : angle       3.06680 ( 2037)
  covalent geometry    : bond        0.00518 (14237)
  covalent geometry    : angle       0.55747 (20457)

*********************** 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
  148 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.7701 (tttm) cc_final: 0.7165 (ttmt)
REVERT: D   34 TYR cc_start: 0.9299 (m-80) cc_final: 0.8857 (m-80)
REVERT: D   56 MET cc_start: 0.8744 (tpp) cc_final: 0.8513 (tpp)
REVERT: E   56 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7967 (tttt)
REVERT: F   90 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7826 (mt)
REVERT: G   73 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8415 (t0)
REVERT: K  214 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7722 (mtmm)
  outliers start: 17
  outliers final: 14
  residues processed: 139
  average time/residue: 0.3598
  time to fit residues: 65.9566
Evaluate side-chains
  147 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain D residue   49 THR
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  214 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 109 optimal weight:   40.0000
   chunk 32 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 75 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 108 optimal weight:    6.9990
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.217970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.128800 restraints weight = 14117.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.98
r_work: 0.2898 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2883
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14237  Z= 0.167
  Angle     :  0.543   7.671  20457  Z= 0.324
  Chirality :  0.034   0.156   2313
  Planarity :  0.004   0.043   1588
  Dihedral  : 30.183 178.765   4244
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.15 %
    Favored  : 85.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.28), residues: 913
  helix:  2.03 (0.21), residues: 586
  sheet: -0.73 (0.82), residues: 38
  loop : -0.42 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.012   0.001   PHE A  78 
 TYR   0.012   0.001   TYR G  57 
 ARG   0.009   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03384 (  808)
  hydrogen bonds       : angle       3.02340 ( 2037)
  covalent geometry    : bond        0.00374 (14237)
  covalent geometry    : angle       0.54286 (20457)

*********************** 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
  144 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7688 (mtm-85)
REVERT: C   95 LYS cc_start: 0.7676 (tttm) cc_final: 0.7144 (ttmt)
REVERT: D   34 TYR cc_start: 0.9296 (m-80) cc_final: 0.8937 (m-80)
REVERT: D   56 MET cc_start: 0.8728 (tpp) cc_final: 0.8511 (tpp)
REVERT: E   56 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7945 (tttt)
REVERT: F   90 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7774 (mt)
REVERT: G   73 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8408 (t0)
REVERT: K  214 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7729 (mtmm)
  outliers start: 15
  outliers final: 12
  residues processed: 136
  average time/residue: 0.3923
  time to fit residues: 70.3408
Evaluate side-chains
  144 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain D residue   49 THR
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  214 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 101 optimal weight:    0.0570
   chunk 107 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0570
   chunk 47 optimal weight:    0.3980
   chunk 4 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 99 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    0.3816

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.220513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.133684 restraints weight = 14091.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.88
r_work: 0.2945 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2133

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= 0.143
  Angle     :  0.539  15.541  20457  Z= 0.320
  Chirality :  0.034   0.147   2313
  Planarity :  0.004   0.041   1588
  Dihedral  : 30.118 178.888   4244
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.66 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.28), residues: 913
  helix:  2.14 (0.21), residues: 586
  sheet: -0.61 (0.83), residues: 38
  loop : -0.37 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.022   0.001   TYR G  39 
 ARG   0.008   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03241 (  808)
  hydrogen bonds       : angle       2.94404 ( 2037)
  covalent geometry    : bond        0.00311 (14237)
  covalent geometry    : angle       0.53909 (20457)

*********************** 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: 14
    poor density    : 123
  time to evaluate  : 1.429 
Fit side-chains
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.7687 (tttm) cc_final: 0.7149 (ttmt)
REVERT: D   34 TYR cc_start: 0.9290 (m-80) cc_final: 0.8875 (m-80)
REVERT: D   56 MET cc_start: 0.8713 (tpp) cc_final: 0.8488 (tpp)
REVERT: E   56 LYS cc_start: 0.8301 (mtmt) cc_final: 0.7963 (tttt)
REVERT: F   90 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7763 (mt)
REVERT: G   73 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8414 (t0)
REVERT: K  214 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7711 (mtmm)
  outliers start: 14
  outliers final: 11
  residues processed: 131
  average time/residue: 0.4183
  time to fit residues: 72.5705
Evaluate side-chains
  136 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
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  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  214 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 96 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 103 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 97 optimal weight:    5.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.220776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.133958 restraints weight = 14022.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.88
r_work: 0.2951 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.2241

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= 0.156
  Angle     :  0.535  10.358  20457  Z= 0.318
  Chirality :  0.033   0.150   2313
  Planarity :  0.004   0.038   1588
  Dihedral  : 30.056 178.603   4244
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.66 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.28), residues: 913
  helix:  2.19 (0.21), residues: 586
  sheet: -0.56 (0.84), residues: 38
  loop : -0.38 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.013   0.001   TYR G  39 
 ARG   0.008   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03300 (  808)
  hydrogen bonds       : angle       2.93311 ( 2037)
  covalent geometry    : bond        0.00349 (14237)
  covalent geometry    : angle       0.53531 (20457)

********************** 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: 14
    poor density    : 116
  time to evaluate  : 1.449 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8116 (tpt90) cc_final: 0.7800 (tpt90)
REVERT: C   35 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7643 (mtm-85)
REVERT: C   95 LYS cc_start: 0.7636 (tttm) cc_final: 0.7095 (ttmt)
REVERT: D   34 TYR cc_start: 0.9261 (m-80) cc_final: 0.8849 (m-80)
REVERT: D   56 MET cc_start: 0.8685 (tpp) cc_final: 0.8447 (tpp)
REVERT: E   56 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7923 (tttt)
REVERT: F   90 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7692 (mt)
REVERT: G   73 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8475 (t0)
REVERT: K  214 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7712 (mtmm)
  outliers start: 14
  outliers final: 11
  residues processed: 125
  average time/residue: 0.4012
  time to fit residues: 67.2551
Evaluate side-chains
  130 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 1.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
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  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  214 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 75 optimal weight:    6.9990
   chunk 30 optimal weight:    0.2980
   chunk 6 optimal weight:    0.6980
   chunk 95 optimal weight:    4.9990
   chunk 101 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9990
   chunk 111 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.4313 r_free = 0.4313 target = 0.220692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.133188 restraints weight = 14119.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.96
r_work: 0.2931 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2918
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2918 r_free = 0.2918    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2918 r_free = 0.2918    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2918
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14237  Z= 0.164
  Angle     :  0.546  13.987  20457  Z= 0.319
  Chirality :  0.034   0.195   2313
  Planarity :  0.004   0.038   1588
  Dihedral  : 30.044 178.434   4244
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.04 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.28), residues: 913
  helix:  2.22 (0.21), residues: 586
  sheet: -0.53 (0.84), residues: 38
  loop : -0.34 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.011   0.001   TYR G  57 
 ARG   0.008   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03300 (  808)
  hydrogen bonds       : angle       2.95796 ( 2037)
  covalent geometry    : bond        0.00367 (14237)
  covalent geometry    : angle       0.54615 (20457)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8273.45 seconds
wall clock time: 143 minutes 33.40 seconds (8613.40 seconds total)