Starting phenix.real_space_refine
on Wed Jul 30 12:57:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v26_42899/07_2025/8v26_42899_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v26_42899/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v26_42899/07_2025/8v26_42899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v26_42899/07_2025/8v26_42899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v26_42899/07_2025/8v26_42899_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v26_42899/07_2025/8v26_42899_neut.cif"
  }
  resolution = 3.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.98, per 1000 atoms: 0.63
  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: 3.21
  Conformation dependent library (CDL) restraints added in 947.0 milliseconds
  

  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: 5.54
  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: 4.42

  Time building geometry restraints manager: 3.85 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:             1.090
  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:          0.540
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     34.720
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.640
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (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
 HIS   0.003   0.001   HIS B  75 
 PHE   0.008   0.001   PHE H  67 
 TYR   0.013   0.001   TYR H  39 
 ARG   0.007   0.000   ARG D  96 

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

*********************** 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  : 0.918 
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: 0.3484
  time to fit residues: 57.3214
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  : 0.906 
-------------------------------------------------------------------------------
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 91 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   chunk 45 optimal weight:    0.4980
   chunk 27 optimal weight:    0.1980
   chunk 55 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 84 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3470 r_free = 0.3470 target = 0.094628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.063272 restraints weight = 28536.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 2.18
r_work: 0.2699 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2699
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2698 r_free = 0.2698    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.0934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13499  Z= 0.158
  Angle     :  0.523   4.969  19468  Z= 0.320
  Chirality :  0.033   0.257   2219
  Planarity :  0.004   0.036   1463
  Dihedral  : 29.190 179.127   4116
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.06 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.78 (0.30), residues: 831
  helix:  3.26 (0.22), residues: 541
  sheet: -0.46 (0.98), residues: 26
  loop : -1.13 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS K  68 
 PHE   0.009   0.001   PHE H  67 
 TYR   0.007   0.001   TYR H  37 
 ARG   0.006   0.000   ARG K  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05095 (  772)
  hydrogen bonds       : angle       2.93256 ( 1947)
  SS BOND              : bond        0.01040 (    1)
  SS BOND              : angle       2.97186 (    2)
  covalent geometry    : bond        0.00330 (13498)
  covalent geometry    : angle       0.52214 (19466)

*********************** 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
  144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.907 
Fit side-chains
REVERT: F   24 ASP cc_start: 0.7978 (p0) cc_final: 0.7764 (p0)
REVERT: K    1 MET cc_start: 0.6704 (pmm) cc_final: 0.6251 (pmm)
  outliers start: 13
  outliers final: 8
  residues processed: 136
  average time/residue: 0.3213
  time to fit residues: 58.0900
Evaluate side-chains
  132 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
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  112 ILE
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 69 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 37 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 96 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 = 0.3424 r_free = 0.3424 target = 0.091703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.059474 restraints weight = 28886.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 2.14
r_work: 0.2610 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2612 r_free = 0.2612    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2612 r_free = 0.2612    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8821
moved from start:          0.0921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  13499  Z= 0.209
  Angle     :  0.561   7.116  19468  Z= 0.340
  Chirality :  0.035   0.145   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.377 179.952   4116
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 20.90 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.64 (0.30), residues: 831
  helix:  3.18 (0.22), residues: 541
  sheet: -0.57 (0.93), residues: 26
  loop : -1.26 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  31 
 PHE   0.011   0.002   PHE F  61 
 TYR   0.012   0.001   TYR E  54 
 ARG   0.006   0.000   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06802 (  772)
  hydrogen bonds       : angle       3.10081 ( 1947)
  SS BOND              : bond        0.01054 (    1)
  SS BOND              : angle       2.42351 (    2)
  covalent geometry    : bond        0.00471 (13498)
  covalent geometry    : angle       0.56032 (19466)

*********************** 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
  139 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 1.150 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8539 (pm20)
REVERT: F   24 ASP cc_start: 0.7932 (p0) cc_final: 0.7711 (p0)
REVERT: H   31 LYS cc_start: 0.8933 (mmtp) cc_final: 0.8403 (mtpt)
REVERT: K   42 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7785 (ttp80)
  outliers start: 17
  outliers final: 11
  residues processed: 133
  average time/residue: 0.4094
  time to fit residues: 70.9022
Evaluate side-chains
  133 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain K residue   68 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 53 optimal weight:    0.4980
   chunk 95 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 100 optimal weight:    8.9990
   chunk 84 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3445 r_free = 0.3445 target = 0.092954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.061065 restraints weight = 28922.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 2.14
r_work: 0.2642 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8773
moved from start:          0.0987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13499  Z= 0.160
  Angle     :  0.537   7.959  19468  Z= 0.326
  Chirality :  0.034   0.206   2219
  Planarity :  0.004   0.034   1463
  Dihedral  : 29.352 179.335   4114
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 20.90 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.72 (0.30), residues: 831
  helix:  3.26 (0.22), residues: 542
  sheet: -1.24 (0.87), residues: 26
  loop : -1.19 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.019   0.001   HIS K  68 
 PHE   0.009   0.001   PHE H  67 
 TYR   0.007   0.001   TYR H  39 
 ARG   0.005   0.000   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05955 (  772)
  hydrogen bonds       : angle       2.95676 ( 1947)
  SS BOND              : bond        0.00585 (    1)
  SS BOND              : angle       1.19797 (    2)
  covalent geometry    : bond        0.00333 (13498)
  covalent geometry    : angle       0.53732 (19466)

*********************** 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
  147 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8471 (pm20)
REVERT: A   63 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8077 (mmp80)
REVERT: B   79 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8906 (mtmt)
REVERT: F   24 ASP cc_start: 0.7931 (p0) cc_final: 0.7712 (p0)
REVERT: H   31 LYS cc_start: 0.8922 (mmtp) cc_final: 0.8380 (mtpt)
REVERT: K    1 MET cc_start: 0.6617 (pmm) cc_final: 0.6304 (pmm)
REVERT: K   42 ARG cc_start: 0.8280 (ttp80) cc_final: 0.7965 (ptm-80)
  outliers start: 21
  outliers final: 16
  residues processed: 136
  average time/residue: 0.3568
  time to fit residues: 63.0919
Evaluate side-chains
  145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
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   90 MET
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 C residue  101 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   28 LYS
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 102 optimal weight:   20.0000
   chunk 48 optimal weight:    0.6980
   chunk 81 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 17 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0000
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
G  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.096882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.065972 restraints weight = 28996.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.2921 rms_B_bonded: 2.13
r_work: 0.2761 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2761
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2761
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13499  Z= 0.142
  Angle     :  0.497   5.095  19468  Z= 0.303
  Chirality :  0.032   0.130   2219
  Planarity :  0.003   0.035   1463
  Dihedral  : 29.309 178.370   4114
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 21.18 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.03 (0.30), residues: 831
  helix:  3.51 (0.22), residues: 541
  sheet: -1.02 (0.89), residues: 26
  loop : -1.10 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS K  68 
 PHE   0.009   0.001   PHE H  67 
 TYR   0.006   0.001   TYR G  50 
 ARG   0.005   0.000   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04160 (  772)
  hydrogen bonds       : angle       2.68052 ( 1947)
  SS BOND              : bond        0.00318 (    1)
  SS BOND              : angle       0.76522 (    2)
  covalent geometry    : bond        0.00295 (13498)
  covalent geometry    : angle       0.49650 (19466)

*********************** 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
  148 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 1.157 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8431 (pm20)
REVERT: A   63 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7954 (mmp80)
REVERT: D   31 LYS cc_start: 0.9155 (mtmm) cc_final: 0.8907 (mtmm)
REVERT: F   24 ASP cc_start: 0.7849 (p0) cc_final: 0.7640 (p0)
REVERT: H   56 MET cc_start: 0.8503 (tpp) cc_final: 0.8128 (mmm)
  outliers start: 18
  outliers final: 11
  residues processed: 138
  average time/residue: 0.3664
  time to fit residues: 66.9398
Evaluate side-chains
  137 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
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 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   76 GLN
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   98 LEU
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 103 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    1.7986

-------------------------------------------------------------------------------
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 = 0.093259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.061265 restraints weight = 29326.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 2.16
r_work: 0.2650 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2650
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2650 r_free = 0.2650    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2650 r_free = 0.2650    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2650
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8793
moved from start:          0.1330

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= 0.186
  Angle     :  0.535   5.594  19468  Z= 0.324
  Chirality :  0.034   0.173   2219
  Planarity :  0.004   0.034   1463
  Dihedral  : 29.412 179.192   4114
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.72
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.93 (0.30), residues: 831
  helix:  3.43 (0.22), residues: 540
  sheet: -0.58 (0.98), residues: 26
  loop : -1.16 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS K  68 
 PHE   0.010   0.002   PHE F  61 
 TYR   0.008   0.001   TYR A  54 
 ARG   0.006   0.000   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06066 (  772)
  hydrogen bonds       : angle       2.96500 ( 1947)
  SS BOND              : bond        0.00689 (    1)
  SS BOND              : angle       1.37902 (    2)
  covalent geometry    : bond        0.00411 (13498)
  covalent geometry    : angle       0.53437 (19466)

*********************** 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
  147 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8489 (pm20)
REVERT: A   63 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8086 (mmp80)
REVERT: F   24 ASP cc_start: 0.7928 (p0) cc_final: 0.7720 (p0)
REVERT: H   31 LYS cc_start: 0.8968 (mmtp) cc_final: 0.8421 (mtpt)
  outliers start: 23
  outliers final: 15
  residues processed: 139
  average time/residue: 0.3562
  time to fit residues: 64.3241
Evaluate side-chains
  140 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
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 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   73 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   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 16 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 89 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 82 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 95 optimal weight:    7.9990
   chunk 85 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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 = 0.3407 r_free = 0.3407 target = 0.090597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.058327 restraints weight = 28663.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.2753 rms_B_bonded: 2.11
r_work: 0.2576 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2579
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2579 r_free = 0.2579    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2579 r_free = 0.2579    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2579
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.1336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036  13499  Z= 0.243
  Angle     :  0.589   5.615  19468  Z= 0.355
  Chirality :  0.037   0.147   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.485 179.136   4114
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 21.88 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.61 (0.29), residues: 831
  helix:  3.16 (0.22), residues: 539
  sheet: -0.55 (0.98), residues: 26
  loop : -1.25 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C  31 
 PHE   0.012   0.002   PHE D  67 
 TYR   0.012   0.001   TYR A  54 
 ARG   0.008   0.000   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07558 (  772)
  hydrogen bonds       : angle       3.21528 ( 1947)
  SS BOND              : bond        0.00813 (    1)
  SS BOND              : angle       1.71878 (    2)
  covalent geometry    : bond        0.00558 (13498)
  covalent geometry    : angle       0.58899 (19466)

*********************** 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
  145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8524 (pm20)
REVERT: A   63 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8198 (mmp80)
REVERT: F   24 ASP cc_start: 0.7956 (p0) cc_final: 0.7754 (p0)
REVERT: H   31 LYS cc_start: 0.9017 (mmtp) cc_final: 0.8497 (mtpt)
REVERT: H   56 MET cc_start: 0.8990 (tpp) cc_final: 0.8666 (mmm)
  outliers start: 21
  outliers final: 17
  residues processed: 137
  average time/residue: 0.3624
  time to fit residues: 64.8388
Evaluate side-chains
  142 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
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  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   73 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   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 24 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 89 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9990
   chunk 92 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.093117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.061249 restraints weight = 29102.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 2.14
r_work: 0.2649 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2649
-------------------------------------------------------------------------------
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 = 0.18   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 = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2652
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8772
moved from start:          0.1362

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= 0.162
  Angle     :  0.539   5.501  19468  Z= 0.326
  Chirality :  0.033   0.170   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.413 179.318   4114
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 22.58 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.83 (0.30), residues: 831
  helix:  3.37 (0.22), residues: 539
  sheet: -1.13 (0.93), residues: 26
  loop : -1.16 (0.35), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS K  68 
 PHE   0.008   0.001   PHE F  61 
 TYR   0.006   0.001   TYR H  37 
 ARG   0.009   0.000   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05801 (  772)
  hydrogen bonds       : angle       2.91157 ( 1947)
  SS BOND              : bond        0.00436 (    1)
  SS BOND              : angle       0.92472 (    2)
  covalent geometry    : bond        0.00337 (13498)
  covalent geometry    : angle       0.53885 (19466)

*********************** 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
  145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8456 (pm20)
REVERT: A   63 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8068 (mmp80)
REVERT: D   31 LYS cc_start: 0.9258 (mtmm) cc_final: 0.9043 (mtmm)
REVERT: H   31 LYS cc_start: 0.9000 (mmtp) cc_final: 0.8455 (mtpt)
REVERT: H   56 MET cc_start: 0.8819 (tpp) cc_final: 0.8521 (mmm)
  outliers start: 21
  outliers final: 17
  residues processed: 136
  average time/residue: 0.3604
  time to fit residues: 63.7609
Evaluate side-chains
  142 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
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 D residue   85 THR
Chi-restraints excluded: chain D residue   87 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 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   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 83 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 81 optimal weight:    6.9990
   chunk 105 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 106 optimal weight:    7.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3491 r_free = 0.3491 target = 0.095615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.064437 restraints weight = 29196.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 2.14
r_work: 0.2725 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2723
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2723
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8711
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13499  Z= 0.148
  Angle     :  0.512   6.777  19468  Z= 0.310
  Chirality :  0.032   0.138   2219
  Planarity :  0.004   0.036   1463
  Dihedral  : 29.446 179.016   4114
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 23.28 %
    Favored  : 74.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.03 (0.30), residues: 831
  helix:  3.52 (0.22), residues: 542
  sheet: -0.87 (0.95), residues: 26
  loop : -1.15 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS K  68 
 PHE   0.008   0.001   PHE H  67 
 TYR   0.006   0.001   TYR A  54 
 ARG   0.007   0.000   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04598 (  772)
  hydrogen bonds       : angle       2.72701 ( 1947)
  SS BOND              : bond        0.00208 (    1)
  SS BOND              : angle       0.46509 (    2)
  covalent geometry    : bond        0.00309 (13498)
  covalent geometry    : angle       0.51239 (19466)

*********************** 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
  143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8408 (pm20)
REVERT: A   63 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8020 (mmp80)
REVERT: H   31 LYS cc_start: 0.8976 (mmtp) cc_final: 0.8419 (mtpt)
  outliers start: 17
  outliers final: 13
  residues processed: 137
  average time/residue: 0.3308
  time to fit residues: 59.7929
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  : 0.899 
-------------------------------------------------------------------------------
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 D residue   85 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   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 55 optimal weight:    0.4980
   chunk 102 optimal weight:   40.0000
   chunk 30 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 84 optimal weight:    6.9990
   chunk 95 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0270
   chunk 22 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    1.5042

-------------------------------------------------------------------------------
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 = 0.093773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.062120 restraints weight = 28645.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 2.10
r_work: 0.2672 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2672
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.1594

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= 0.173
  Angle     :  0.534   6.264  19468  Z= 0.322
  Chirality :  0.033   0.143   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.473 179.019   4114
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 23.42 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.93 (0.30), residues: 831
  helix:  3.44 (0.22), residues: 541
  sheet: -0.69 (0.99), residues: 26
  loop : -1.18 (0.34), residues: 264

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05640 (  772)
  hydrogen bonds       : angle       2.85330 ( 1947)
  SS BOND              : bond        0.00483 (    1)
  SS BOND              : angle       0.98622 (    2)
  covalent geometry    : bond        0.00378 (13498)
  covalent geometry    : angle       0.53383 (19466)

********************** 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
  140 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8454 (pm20)
REVERT: A   63 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8060 (mmp80)
REVERT: H   31 LYS cc_start: 0.8978 (mmtp) cc_final: 0.8428 (mtpt)
  outliers start: 17
  outliers final: 14
  residues processed: 133
  average time/residue: 0.3473
  time to fit residues: 60.6115
Evaluate side-chains
  137 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
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 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   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 81 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 41 optimal weight:    0.4980
   chunk 91 optimal weight:    6.9990
   chunk 85 optimal weight:    7.9990
   chunk 59 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    2.0386

-------------------------------------------------------------------------------
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 = 0.3433 r_free = 0.3433 target = 0.092222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.060008 restraints weight = 28792.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.2792 rms_B_bonded: 2.12
r_work: 0.2620 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2622
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2622 r_free = 0.2622    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2622 r_free = 0.2622    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2622
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8815
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  13499  Z= 0.202
  Angle     :  0.562   6.437  19468  Z= 0.338
  Chirality :  0.035   0.151   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.511 179.918   4114
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 23.70 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.76 (0.30), residues: 831
  helix:  3.32 (0.22), residues: 539
  sheet: -0.47 (0.99), residues: 26
  loop : -1.27 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  31 
 PHE   0.011   0.002   PHE B  61 
 TYR   0.010   0.001   TYR A  54 
 ARG   0.008   0.000   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06556 (  772)
  hydrogen bonds       : angle       3.00260 ( 1947)
  SS BOND              : bond        0.00574 (    1)
  SS BOND              : angle       1.24426 (    2)
  covalent geometry    : bond        0.00453 (13498)
  covalent geometry    : angle       0.56192 (19466)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5388.64 seconds
wall clock time: 93 minutes 39.99 seconds (5619.99 seconds total)