Starting phenix.real_space_refine
on Sat Oct 11 06:27:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v26_42899/10_2025/8v26_42899_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v26_42899/10_2025/8v26_42899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v26_42899/10_2025/8v26_42899_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v26_42899/10_2025/8v26_42899_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v26_42899/10_2025/8v26_42899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v26_42899/10_2025/8v26_42899.map"
  }
  resolution = 3.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     288      5.49       5
     S      16      5.16       5
     C    7063      2.51       5
     N    2387      2.21       5
     O    2935      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12689
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 859
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 5, 'TRANS': 105}
    Chain: "D"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 764
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
    Chain: "E"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 817
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 841
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 754
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "I"
      Number of atoms: 2952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2952
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 604
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N   LEU K  73 " occ=0.95
      ... (6 atoms not shown)
      pdb=" CD2 LEU K  73 " occ=0.95
    residue:
      pdb=" N   ARG K  74 " occ=0.77
      ... (9 atoms not shown)
      pdb=" NH2 ARG K  74 " occ=0.77
    residue:
      pdb=" N   GLY K  75 " occ=0.75
      ... (2 atoms not shown)
      pdb=" O   GLY K  75 " occ=0.75
  Time building chain proxies: 2.81, per 1000 atoms: 0.22
  Number of scatterers: 12689
  At special positions: 0
  Unit cell: (100.88, 123.19, 119.31, 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      16     16.00
     P     288     15.00
     O    2935      8.00
     N    2387      7.00
     C    7063      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 117 " - pdb=" SG  CYS K  76 " distance=2.56

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 353.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1592

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      66.5% alpha, 4.4% beta
      139 base pairs and 249 stacking pairs defined.
    Time for finding SS restraints: 2.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.525A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.834A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.833A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.651A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.557A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.196A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.541A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
      removed outlier: 3.548A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.628A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    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
      removed outlier: 3.665A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.567A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 121
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.517A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.568A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.786A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.572A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.512A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.230A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.918A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.502A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
      removed outlier: 3.520A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    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
      removed outlier: 3.723A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
      removed outlier: 3.591A  pdb=" N   ALA H 121 " --> pdb=" O   CYS H 117 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 22 through 35
    Processing helix  chain 'K' and resid 37 through 39
      No H-bonds generated for 'chain 'K' and resid 37 through 39'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.170A  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 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.389A  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 100 through 102
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.797A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.510A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.357A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'K' and resid 12 through 16
      removed outlier: 4.011A  pdb=" N   SER K  65 " --> pdb=" O   GLN K   2 " (cutoff:3.500A)

    415 hydrogen bonds defined for protein.
    1233 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      357 hydrogen bonds
      714 hydrogen bond angles
      0 basepair planarities
      139 basepair parallelities
      249 stacking parallelities
  Total time for adding SS restraints: 2.57

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2575
        1.33 -     1.45: 4230
        1.45 -     1.57: 6090
        1.57 -     1.69: 576
        1.69 -     1.81: 27
  Bond restraints: 13498
  Sorted by residual:
  bond pdb=" C1'  DG I -70 "
       pdb=" N9   DG I -70 "
    ideal  model  delta    sigma   weight residual
    1.460  1.386  0.074 2.00e-02 2.50e+03 1.36e+01
  bond pdb=" C1'  DG J -70 "
       pdb=" N9   DG J -70 "
    ideal  model  delta    sigma   weight residual
    1.460  1.389  0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" N   ARG K  74 "
       pdb=" CA  ARG K  74 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.27e-02 6.20e+03 6.40e+00
  bond pdb=" C1'  DT J -72 "
       pdb=" N1   DT J -72 "
    ideal  model  delta    sigma   weight residual
    1.490  1.549 -0.059 3.00e-02 1.11e+03 3.86e+00
  bond pdb=" C1'  DT I -72 "
       pdb=" N1   DT I -72 "
    ideal  model  delta    sigma   weight residual
    1.490  1.547 -0.057 3.00e-02 1.11e+03 3.62e+00
  ... (remaining 13493 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 19340
        2.47 -     4.94: 109
        4.94 -     7.41: 13
        7.41 -     9.87: 2
        9.87 -    12.34: 2
  Bond angle restraints: 19466
  Sorted by residual:
  angle pdb=" C3'  DG I  71 "
        pdb=" O3'  DG I  71 "
        pdb=" P    DA I  72 "
      ideal   model   delta    sigma   weight residual
     120.20  108.21   11.99 1.50e+00 4.44e-01 6.39e+01
  angle pdb=" C3'  DC I  70 "
        pdb=" O3'  DC I  70 "
        pdb=" P    DG I  71 "
      ideal   model   delta    sigma   weight residual
     120.20  111.30    8.90 1.50e+00 4.44e-01 3.52e+01
  angle pdb=" CA  GLY K  75 "
        pdb=" C   GLY K  75 "
        pdb=" O   GLY K  75 "
      ideal   model   delta    sigma   weight residual
     120.91  117.90    3.01 6.90e-01 2.10e+00 1.90e+01
  angle pdb=" C3'  DG J  71 "
        pdb=" O3'  DG J  71 "
        pdb=" P    DA J  72 "
      ideal   model   delta    sigma   weight residual
     120.20  113.88    6.32 1.50e+00 4.44e-01 1.78e+01
  angle pdb=" CB  MET H  56 "
        pdb=" CG  MET H  56 "
        pdb=" SD  MET H  56 "
      ideal   model   delta    sigma   weight residual
     112.70  100.36   12.34 3.00e+00 1.11e-01 1.69e+01
  ... (remaining 19461 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.92: 6043
       35.92 -    71.83: 1355
       71.83 -   107.75: 8
      107.75 -   143.67: 4
      143.67 -   179.58: 1
  Dihedral angle restraints: 7411
    sinusoidal: 4948
      harmonic: 2463
  Sorted by residual:
  dihedral pdb=" CB  CYS D 117 "
           pdb=" SG  CYS D 117 "
           pdb=" SG  CYS K  76 "
           pdb=" CB  CYS K  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   20.45   72.55     1      1.00e+01 1.00e-02 6.72e+01
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.42  179.58     1      3.50e+01 8.16e-04 1.57e+01
  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  100.64  119.36     1      3.50e+01 8.16e-04 1.17e+01
  ... (remaining 7408 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 2168
       0.096 -    0.191: 47
       0.191 -    0.287: 0
       0.287 -    0.383: 0
       0.383 -    0.479: 4
  Chirality restraints: 2219
  Sorted by residual:
  chirality pdb=" P    DG J  71 "
            pdb=" OP1  DG J  71 "
            pdb=" OP2  DG J  71 "
            pdb=" O5'  DG J  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.82   -0.48 2.00e-01 2.50e+01 5.72e+00
  chirality pdb=" P    DG I  71 "
            pdb=" OP1  DG I  71 "
            pdb=" OP2  DG I  71 "
            pdb=" O5'  DG I  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.81   -0.46 2.00e-01 2.50e+01 5.34e+00
  chirality pdb=" P    DA J  72 "
            pdb=" OP1  DA J  72 "
            pdb=" OP2  DA J  72 "
            pdb=" O5'  DA J  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.80   -0.46 2.00e-01 2.50e+01 5.23e+00
  ... (remaining 2216 not shown)

  Planarity restraints: 1463
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP F  24 "    0.011 2.00e-02 2.50e+03   2.22e-02 4.94e+00
        pdb=" CG  ASP F  24 "   -0.038 2.00e-02 2.50e+03
        pdb=" OD1 ASP F  24 "    0.014 2.00e-02 2.50e+03
        pdb=" OD2 ASP F  24 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP F  24 "    0.011 2.00e-02 2.50e+03   2.14e-02 4.59e+00
        pdb=" C   ASP F  24 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   ASP F  24 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ASN F  25 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B  24 "   -0.010 2.00e-02 2.50e+03   1.98e-02 3.92e+00
        pdb=" CG  ASP B  24 "    0.034 2.00e-02 2.50e+03
        pdb=" OD1 ASP B  24 "   -0.012 2.00e-02 2.50e+03
        pdb=" OD2 ASP B  24 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1460 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2181
        2.78 -     3.31: 10455
        3.31 -     3.84: 22518
        3.84 -     4.37: 26520
        4.37 -     4.90: 38861
  Nonbonded interactions: 100535
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN K  40 "
            pdb=" NE2 GLN K  41 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" NH1 ARG K  42 "
            pdb=" OE1 GLN K  49 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   THR E  58 "
            pdb=" OG1 THR E  58 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" N   MET K   1 "
            pdb=" O   VAL K  17 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" OE1 GLU E  73 "
            pdb=" ND2 ASN F  25 "
     model   vdw
     2.320 3.120
  ... (remaining 100530 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 37 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 23 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 10 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 26 through 121)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.59 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:             1.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.910
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8765
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      :  0.006   0.527  13499  Z= 0.294
  Angle     :  0.622  15.432  19468  Z= 0.371
  Chirality :  0.039   0.479   2219
  Planarity :  0.004   0.038   1463
  Dihedral  : 27.205 179.584   5816
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 20.76 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.29), residues: 831
  helix:  3.00 (0.22), residues: 525
  sheet: -0.73 (0.98), residues: 26
  loop : -1.31 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  96 
 TYR   0.013   0.001   TYR H  39 
 PHE   0.008   0.001   PHE H  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (13498)
  covalent geometry    : angle       0.60409 (19466)
  SS BOND              : bond        0.52747 (    1)
  SS BOND              : angle      14.42575 (    2)
  hydrogen bonds       : bond        0.11579 (  772)
  hydrogen bonds       : angle       3.63269 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 0.309 
Fit side-chains
REVERT: K    6 LYS cc_start: 0.9172 (pttt) cc_final: 0.8944 (tptp)
REVERT: K   68 HIS cc_start: 0.8962 (m170) cc_final: 0.8598 (m90)
  outliers start: 2
  outliers final: 1
  residues processed: 126
  average time/residue: 0.1769
  time to fit residues: 29.1459
Evaluate side-chains
  125 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   36 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.3184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.093474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.062084 restraints weight = 28690.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 2.17
r_work: 0.2664 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2664
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2664 r_free = 0.2664    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8773
moved from start:          0.0817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.115  13499  Z= 0.173
  Angle     :  0.533   5.520  19468  Z= 0.326
  Chirality :  0.034   0.228   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.220 179.499   4116
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 19.92 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.72 (0.30), residues: 831
  helix:  3.21 (0.22), residues: 541
  sheet: -0.43 (0.98), residues: 26
  loop : -1.17 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  96 
 TYR   0.007   0.001   TYR A  54 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.004   0.001   HIS K  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (13498)
  covalent geometry    : angle       0.53223 (19466)
  SS BOND              : bond        0.01421 (    1)
  SS BOND              : angle       3.04607 (    2)
  hydrogen bonds       : bond        0.05622 (  772)
  hydrogen bonds       : angle       3.01595 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.355 
Fit side-chains
REVERT: F   24 ASP cc_start: 0.8017 (p0) cc_final: 0.7812 (p0)
REVERT: K    1 MET cc_start: 0.6722 (pmm) cc_final: 0.6283 (pmm)
REVERT: K   42 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7616 (ttp80)
  outliers start: 14
  outliers final: 7
  residues processed: 134
  average time/residue: 0.1678
  time to fit residues: 29.7279
Evaluate side-chains
  129 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 122
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 99 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   chunk 78 optimal weight:    7.9990
   chunk 74 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.9588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.092179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.060097 restraints weight = 28957.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.2797 rms_B_bonded: 2.15
r_work: 0.2625 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8789
moved from start:          0.0910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13499  Z= 0.197
  Angle     :  0.548   6.537  19468  Z= 0.333
  Chirality :  0.034   0.161   2219
  Planarity :  0.004   0.036   1463
  Dihedral  : 29.342 179.786   4116
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 20.90 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.67 (0.30), residues: 831
  helix:  3.18 (0.22), residues: 541
  sheet: -0.26 (0.99), residues: 26
  loop : -1.21 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  96 
 TYR   0.009   0.001   TYR A  54 
 PHE   0.010   0.002   PHE H  67 
 HIS   0.003   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (13498)
  covalent geometry    : angle       0.54741 (19466)
  SS BOND              : bond        0.01004 (    1)
  SS BOND              : angle       2.15357 (    2)
  hydrogen bonds       : bond        0.06412 (  772)
  hydrogen bonds       : angle       3.05185 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8510 (pm20)
REVERT: H   31 LYS cc_start: 0.8917 (mmtp) cc_final: 0.8375 (mtpt)
REVERT: K    6 LYS cc_start: 0.9300 (pptt) cc_final: 0.8730 (tptp)
REVERT: K   42 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7837 (ptm-80)
  outliers start: 14
  outliers final: 10
  residues processed: 133
  average time/residue: 0.1739
  time to fit residues: 30.3194
Evaluate side-chains
  134 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0980
   chunk 69 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 88 optimal weight:    8.9990
   chunk 54 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.093038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.061213 restraints weight = 28821.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 2.13
r_work: 0.2647 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2651
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2651 r_free = 0.2651    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2651 r_free = 0.2651    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2651
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8771
moved from start:          0.1085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13499  Z= 0.177
  Angle     :  0.528   5.335  19468  Z= 0.323
  Chirality :  0.034   0.161   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.344 179.516   4114
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 21.18 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.77 (0.30), residues: 831
  helix:  3.26 (0.22), residues: 542
  sheet: -0.29 (1.01), residues: 26
  loop : -1.18 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  96 
 TYR   0.008   0.001   TYR A  54 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.002   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (13498)
  covalent geometry    : angle       0.52798 (19466)
  SS BOND              : bond        0.00698 (    1)
  SS BOND              : angle       1.49436 (    2)
  hydrogen bonds       : bond        0.05828 (  772)
  hydrogen bonds       : angle       2.92720 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8487 (pm20)
REVERT: A   63 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8041 (mmp80)
REVERT: F   24 ASP cc_start: 0.7977 (p0) cc_final: 0.7761 (p0)
REVERT: H   31 LYS cc_start: 0.8926 (mmtp) cc_final: 0.8389 (mtpt)
REVERT: K    6 LYS cc_start: 0.9300 (pptt) cc_final: 0.8757 (tptp)
REVERT: K   42 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7917 (ptm-80)
  outliers start: 17
  outliers final: 13
  residues processed: 136
  average time/residue: 0.1798
  time to fit residues: 31.8093
Evaluate side-chains
  138 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   28 LYS
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Chi-restraints excluded: chain K residue   68 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 78 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 105 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.093406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.061675 restraints weight = 29023.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 2.14
r_work: 0.2659 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2661
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2661 r_free = 0.2661    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2661 r_free = 0.2661    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2661
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.1167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13499  Z= 0.166
  Angle     :  0.520   5.316  19468  Z= 0.318
  Chirality :  0.033   0.144   2219
  Planarity :  0.004   0.040   1463
  Dihedral  : 29.362 179.414   4114
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.48 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.84 (0.30), residues: 831
  helix:  3.31 (0.22), residues: 542
  sheet: -0.19 (1.02), residues: 26
  loop : -1.18 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  96 
 TYR   0.007   0.001   TYR A  54 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (13498)
  covalent geometry    : angle       0.51981 (19466)
  SS BOND              : bond        0.00566 (    1)
  SS BOND              : angle       1.14407 (    2)
  hydrogen bonds       : bond        0.05606 (  772)
  hydrogen bonds       : angle       2.88354 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8459 (pm20)
REVERT: A   63 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8038 (mmp80)
REVERT: F   24 ASP cc_start: 0.7926 (p0) cc_final: 0.7687 (p0)
REVERT: H   31 LYS cc_start: 0.8967 (mmtp) cc_final: 0.8415 (mtpt)
REVERT: H   56 MET cc_start: 0.8789 (tpp) cc_final: 0.8300 (mmm)
REVERT: K    1 MET cc_start: 0.6663 (pmm) cc_final: 0.6208 (pmm)
  outliers start: 23
  outliers final: 17
  residues processed: 141
  average time/residue: 0.1768
  time to fit residues: 32.7220
Evaluate side-chains
  143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   28 LYS
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Chi-restraints excluded: chain K residue   68 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.7988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.092615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.060548 restraints weight = 28701.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 2.12
r_work: 0.2638 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2637
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2637 r_free = 0.2637    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2637 r_free = 0.2637    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2637
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8803
moved from start:          0.1208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13499  Z= 0.187
  Angle     :  0.537   5.416  19468  Z= 0.326
  Chirality :  0.034   0.144   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.423 179.712   4114
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 20.90 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.77 (0.30), residues: 831
  helix:  3.29 (0.22), residues: 540
  sheet: -0.13 (1.03), residues: 26
  loop : -1.24 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  96 
 TYR   0.009   0.001   TYR A  54 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.002   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (13498)
  covalent geometry    : angle       0.53636 (19466)
  SS BOND              : bond        0.00665 (    1)
  SS BOND              : angle       1.34730 (    2)
  hydrogen bonds       : bond        0.06142 (  772)
  hydrogen bonds       : angle       2.95790 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8510 (pm20)
REVERT: A   63 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8117 (mmp80)
REVERT: B   27 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.8666 (mp10)
REVERT: F   24 ASP cc_start: 0.7906 (p0) cc_final: 0.7695 (p0)
REVERT: H   31 LYS cc_start: 0.8992 (mmtp) cc_final: 0.8465 (mtpt)
REVERT: H   56 MET cc_start: 0.8829 (tpp) cc_final: 0.8552 (mmm)
REVERT: K    1 MET cc_start: 0.6345 (pmm) cc_final: 0.5902 (pmm)
REVERT: K    6 LYS cc_start: 0.9311 (pptt) cc_final: 0.8795 (tptp)
  outliers start: 25
  outliers final: 19
  residues processed: 139
  average time/residue: 0.1796
  time to fit residues: 32.5651
Evaluate side-chains
  145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   28 LYS
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Chi-restraints excluded: chain K residue   68 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 101 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 13 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    1.0982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.093159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.061344 restraints weight = 28657.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 2.11
r_work: 0.2651 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2652
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2652 r_free = 0.2652    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2652 r_free = 0.2652    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2652
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13499  Z= 0.160
  Angle     :  0.529   5.552  19468  Z= 0.321
  Chirality :  0.033   0.148   2219
  Planarity :  0.004   0.034   1463
  Dihedral  : 29.421 179.526   4114
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 21.46 %
    Favored  : 75.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.82 (0.30), residues: 831
  helix:  3.33 (0.22), residues: 540
  sheet: -0.14 (1.03), residues: 26
  loop : -1.22 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  96 
 TYR   0.007   0.001   TYR A  54 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (13498)
  covalent geometry    : angle       0.52846 (19466)
  SS BOND              : bond        0.00540 (    1)
  SS BOND              : angle       1.04995 (    2)
  hydrogen bonds       : bond        0.05831 (  772)
  hydrogen bonds       : angle       2.90464 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8483 (pm20)
REVERT: A   63 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8076 (mmp80)
REVERT: D   31 LYS cc_start: 0.9234 (mtmm) cc_final: 0.9029 (mtmm)
REVERT: F   24 ASP cc_start: 0.7904 (p0) cc_final: 0.7682 (p0)
REVERT: H   31 LYS cc_start: 0.8984 (mmtp) cc_final: 0.8455 (mtpt)
REVERT: H   56 MET cc_start: 0.8800 (tpp) cc_final: 0.8530 (mmm)
REVERT: K    6 LYS cc_start: 0.9292 (pptt) cc_final: 0.8710 (tptp)
  outliers start: 24
  outliers final: 20
  residues processed: 138
  average time/residue: 0.1716
  time to fit residues: 31.0443
Evaluate side-chains
  144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   28 LYS
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Chi-restraints excluded: chain K residue   68 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 45 optimal weight:    0.0970
   chunk 9 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 79 optimal weight:    6.9990
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 102 optimal weight:   10.0000
   overall best weight:    1.3580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.093263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.061458 restraints weight = 28652.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 2.12
r_work: 0.2655 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13499  Z= 0.168
  Angle     :  0.526   5.339  19468  Z= 0.320
  Chirality :  0.033   0.148   2219
  Planarity :  0.004   0.034   1463
  Dihedral  : 29.402 179.320   4114
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.60 %
    Favored  : 75.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.84 (0.30), residues: 831
  helix:  3.37 (0.22), residues: 537
  sheet: -0.18 (1.01), residues: 26
  loop : -1.23 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  96 
 TYR   0.007   0.001   TYR A  54 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (13498)
  covalent geometry    : angle       0.52548 (19466)
  SS BOND              : bond        0.00515 (    1)
  SS BOND              : angle       0.99682 (    2)
  hydrogen bonds       : bond        0.05729 (  772)
  hydrogen bonds       : angle       2.88517 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8463 (pm20)
REVERT: A   63 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8067 (mmp80)
REVERT: F   24 ASP cc_start: 0.7917 (p0) cc_final: 0.7699 (p0)
REVERT: H   31 LYS cc_start: 0.8963 (mmtp) cc_final: 0.8416 (mtpt)
REVERT: H   56 MET cc_start: 0.8790 (tpp) cc_final: 0.8522 (mmm)
REVERT: K    6 LYS cc_start: 0.9308 (pptt) cc_final: 0.8740 (tptp)
  outliers start: 23
  outliers final: 19
  residues processed: 139
  average time/residue: 0.1743
  time to fit residues: 31.6252
Evaluate side-chains
  144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Chi-restraints excluded: chain K residue   68 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0470
   chunk 60 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.8086

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.092687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.060833 restraints weight = 28737.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 2.11
r_work: 0.2640 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2641
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2641
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8798
moved from start:          0.1313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13499  Z= 0.188
  Angle     :  0.540   6.305  19468  Z= 0.327
  Chirality :  0.034   0.148   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.439 179.698   4114
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 22.30 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.78 (0.30), residues: 831
  helix:  3.30 (0.22), residues: 540
  sheet: -0.19 (1.02), residues: 26
  loop : -1.24 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  96 
 TYR   0.008   0.001   TYR A  54 
 PHE   0.009   0.001   PHE F  61 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (13498)
  covalent geometry    : angle       0.53958 (19466)
  SS BOND              : bond        0.00611 (    1)
  SS BOND              : angle       1.23409 (    2)
  hydrogen bonds       : bond        0.06093 (  772)
  hydrogen bonds       : angle       2.93834 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8510 (pm20)
REVERT: A   63 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8129 (mmp80)
REVERT: H   28 LYS cc_start: 0.8399 (mtmm) cc_final: 0.7969 (pttm)
REVERT: H   31 LYS cc_start: 0.8963 (mmtp) cc_final: 0.8426 (mtpt)
REVERT: H   56 MET cc_start: 0.8801 (tpp) cc_final: 0.8540 (mmm)
REVERT: K    6 LYS cc_start: 0.9310 (pptt) cc_final: 0.8918 (tptp)
  outliers start: 21
  outliers final: 19
  residues processed: 137
  average time/residue: 0.1620
  time to fit residues: 28.7834
Evaluate side-chains
  144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Chi-restraints excluded: chain K residue   68 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 97 optimal weight:    6.9990
   chunk 75 optimal weight:    6.9990
   chunk 27 optimal weight:    0.4980
   chunk 42 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 85 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0870
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.9160

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.093838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.062103 restraints weight = 29006.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 2.12
r_work: 0.2672 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2671
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13499  Z= 0.155
  Angle     :  0.528   6.641  19468  Z= 0.319
  Chirality :  0.033   0.145   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.422 179.143   4114
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 23.28 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.88 (0.30), residues: 831
  helix:  3.37 (0.22), residues: 540
  sheet: -0.19 (1.02), residues: 26
  loop : -1.19 (0.35), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  96 
 TYR   0.006   0.001   TYR G  50 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (13498)
  covalent geometry    : angle       0.52752 (19466)
  SS BOND              : bond        0.00446 (    1)
  SS BOND              : angle       0.92116 (    2)
  hydrogen bonds       : bond        0.05492 (  772)
  hydrogen bonds       : angle       2.82469 ( 1947)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8439 (pm20)
REVERT: A   63 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8059 (mmp80)
REVERT: B   79 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8907 (mtmt)
REVERT: H   28 LYS cc_start: 0.8420 (mtmm) cc_final: 0.7906 (pttm)
REVERT: H   31 LYS cc_start: 0.8964 (mmtp) cc_final: 0.8427 (mtpt)
REVERT: H   56 MET cc_start: 0.8787 (tpp) cc_final: 0.8524 (mmm)
REVERT: K    6 LYS cc_start: 0.9321 (pptt) cc_final: 0.8938 (tptp)
  outliers start: 18
  outliers final: 15
  residues processed: 137
  average time/residue: 0.1746
  time to fit residues: 31.1291
Evaluate side-chains
  144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue    3 ILE
Chi-restraints excluded: chain K residue   44 ILE
Chi-restraints excluded: chain K residue   68 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 48 optimal weight:    0.5980
   chunk 102 optimal weight:    0.2980
   chunk 42 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 89 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 107 optimal weight:    0.6980
   chunk 9 optimal weight:    0.2980
   overall best weight:    1.1782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.094253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.062594 restraints weight = 28959.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 2.12
r_work: 0.2684 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13499  Z= 0.161
  Angle     :  0.525   6.516  19468  Z= 0.318
  Chirality :  0.033   0.143   2219
  Planarity :  0.004   0.036   1463
  Dihedral  : 29.419 178.978   4114
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 22.72 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.92 (0.30), residues: 831
  helix:  3.42 (0.22), residues: 540
  sheet: -0.15 (1.03), residues: 26
  loop : -1.20 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  96 
 TYR   0.007   0.001   TYR A  54 
 PHE   0.009   0.001   PHE H  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (13498)
  covalent geometry    : angle       0.52487 (19466)
  SS BOND              : bond        0.00425 (    1)
  SS BOND              : angle       0.85965 (    2)
  hydrogen bonds       : bond        0.05284 (  772)
  hydrogen bonds       : angle       2.79872 ( 1947)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2783.86 seconds
wall clock time: 48 minutes 17.56 seconds (2897.56 seconds total)