Starting phenix.real_space_refine
on Sat Jan 18 14:25:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v26_42899/01_2025/8v26_42899_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v26_42899/01_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_42899/01_2025/8v26_42899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v26_42899/01_2025/8v26_42899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v26_42899/01_2025/8v26_42899_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v26_42899/01_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-5571/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: 7.48, per 1000 atoms: 0.59
  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: 3.19
  Conformation dependent library (CDL) restraints added in 992.1 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: 6.29
  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: 4.80

  Time building geometry restraints manager: 3.71 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.330
  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:          0.500
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     33.460
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.060
  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:             0.010
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.480
-------------------------------------------------------------------------------
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      :  0.004   0.074  13498  Z= 0.209
  Angle     :  0.604  12.343  19466  Z= 0.364
  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 

*********************** 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  : 1.042 
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: 0.3641
  time to fit residues: 59.7707
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  : 0.940 
-------------------------------------------------------------------------------
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 = 0.094624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.063428 restraints weight = 28500.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 2.18
r_work: 0.2698 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
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 = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
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  13498  Z= 0.180
  Angle     :  0.522   4.969  19466  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 

*********************** 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  : 1.022 
Fit side-chains
REVERT: F   24 ASP cc_start: 0.7980 (p0) cc_final: 0.7765 (p0)
REVERT: K    1 MET cc_start: 0.6686 (pmm) cc_final: 0.6229 (pmm)
  outliers start: 13
  outliers final: 8
  residues processed: 136
  average time/residue: 0.3375
  time to fit residues: 60.9364
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  : 0.964 
-------------------------------------------------------------------------------
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:    1.9990
   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:    2.3988

-------------------------------------------------------------------------------
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 = 0.3411 r_free = 0.3411 target = 0.091081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.058968 restraints weight = 28745.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.2769 rms_B_bonded: 2.17
r_work: 0.2592 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2592
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2592 r_free = 0.2592    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2592 r_free = 0.2592    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2592
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8829
moved from start:          0.0917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  13498  Z= 0.291
  Angle     :  0.568   6.425  19466  Z= 0.344
  Chirality :  0.036   0.144   2219
  Planarity :  0.004   0.035   1463
  Dihedral  : 29.386 179.780   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 :  2.66 %
    Allowed  : 20.62 %
    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:  2.58 (0.30), residues: 831
  helix:  3.14 (0.22), residues: 541
  sheet: -0.60 (0.93), residues: 26
  loop : -1.28 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C  31 
 PHE   0.011   0.002   PHE F  61 
 TYR   0.012   0.001   TYR E  54 
 ARG   0.007   0.000   ARG K  42 

*********************** 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
  142 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 1.017 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8552 (pm20)
REVERT: F   24 ASP cc_start: 0.7976 (p0) cc_final: 0.7756 (p0)
REVERT: H   31 LYS cc_start: 0.8943 (mmtp) cc_final: 0.8409 (mtpt)
REVERT: K   42 ARG cc_start: 0.8313 (ttp80) cc_final: 0.7685 (ttp80)
  outliers start: 19
  outliers final: 12
  residues processed: 135
  average time/residue: 0.3661
  time to fit residues: 64.2263
Evaluate side-chains
  135 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
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   41 GLN
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:    0.5980
   chunk 37 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 100 optimal weight:    8.9990
   chunk 84 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 = 0.3426 r_free = 0.3426 target = 0.091792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.059754 restraints weight = 28892.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 2.13
r_work: 0.2612 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2613
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2613 r_free = 0.2613    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 = 0.2613 r_free = 0.2613    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2613
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
moved from start:          0.1049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  13498  Z= 0.265
  Angle     :  0.551   5.439  19466  Z= 0.335
  Chirality :  0.035   0.163   2219
  Planarity :  0.004   0.036   1463
  Dihedral  : 29.394 179.769   4114
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.48 %
    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 (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:  2.66 (0.30), residues: 831
  helix:  3.19 (0.22), residues: 541
  sheet: -0.41 (0.98), residues: 26
  loop : -1.24 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS K  68 
 PHE   0.010   0.002   PHE H  67 
 TYR   0.010   0.001   TYR A  54 
 ARG   0.007   0.000   ARG D  96 

*********************** 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
  146 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8510 (pm20)
REVERT: A   63 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8153 (mmp80)
REVERT: F   24 ASP cc_start: 0.7939 (p0) cc_final: 0.7723 (p0)
REVERT: H   31 LYS cc_start: 0.8939 (mmtp) cc_final: 0.8431 (mtpt)
REVERT: K    1 MET cc_start: 0.6764 (pmm) cc_final: 0.6375 (pmm)
  outliers start: 22
  outliers final: 16
  residues processed: 139
  average time/residue: 0.3720
  time to fit residues: 67.0222
Evaluate side-chains
  139 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
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   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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 102 optimal weight:   40.0000
   chunk 48 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.3423 r_free = 0.3423 target = 0.091559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.059506 restraints weight = 28722.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.2780 rms_B_bonded: 2.12
r_work: 0.2606 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2607
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2607 r_free = 0.2607    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2607 r_free = 0.2607    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2607
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8839
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  13498  Z= 0.272
  Angle     :  0.553   5.425  19466  Z= 0.336
  Chirality :  0.035   0.151   2219
  Planarity :  0.004   0.036   1463
  Dihedral  : 29.454 179.753   4114
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.04 %
    Favored  : 75.74 %
  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:  2.62 (0.30), residues: 831
  helix:  3.16 (0.22), residues: 541
  sheet: -0.59 (0.93), residues: 26
  loop : -1.25 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  46 
 PHE   0.010   0.002   PHE H  67 
 TYR   0.010   0.001   TYR A  54 
 ARG   0.007   0.000   ARG D  96 

*********************** 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: 23
    poor density    : 125
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8528 (pm20)
REVERT: A   63 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8170 (mmp80)
REVERT: H   31 LYS cc_start: 0.8990 (mmtp) cc_final: 0.8485 (mtpt)
  outliers start: 23
  outliers final: 18
  residues processed: 140
  average time/residue: 0.3533
  time to fit residues: 65.1023
Evaluate side-chains
  144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 105 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.3395 r_free = 0.3395 target = 0.090197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.057963 restraints weight = 28978.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.2751 rms_B_bonded: 2.17
r_work: 0.2574 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2574
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2573
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2573 r_free = 0.2573    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2573 r_free = 0.2573    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2573
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8849
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  13498  Z= 0.311
  Angle     :  0.577   5.597  19466  Z= 0.349
  Chirality :  0.036   0.168   2219
  Planarity :  0.004   0.037   1463
  Dihedral  : 29.504 179.098   4114
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 21.88 %
    Favored  : 74.61 %
  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:  2.50 (0.30), residues: 831
  helix:  3.10 (0.22), residues: 538
  sheet: -0.67 (0.94), residues: 26
  loop : -1.31 (0.34), residues: 267

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   0.010   0.001   TYR A  54 
 ARG   0.008   0.000   ARG D  96 

*********************** 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
  150 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8553 (pm20)
REVERT: A   63 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8186 (mmp80)
REVERT: D   31 LYS cc_start: 0.9271 (mtmm) cc_final: 0.9066 (mtmm)
REVERT: H   31 LYS cc_start: 0.9032 (mmtp) cc_final: 0.8501 (mtpt)
  outliers start: 25
  outliers final: 20
  residues processed: 141
  average time/residue: 0.3521
  time to fit residues: 64.6533
Evaluate side-chains
  146 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
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  101 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  116 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   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   63 LYS
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:    0.6980
   chunk 7 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 89 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 85 optimal weight:    6.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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 = 0.3409 r_free = 0.3409 target = 0.091054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.059046 restraints weight = 28531.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.2771 rms_B_bonded: 2.15
r_work: 0.2595 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2595
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2596
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2596 r_free = 0.2596    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2596 r_free = 0.2596    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2596
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13498  Z= 0.232
  Angle     :  0.557   5.678  19466  Z= 0.338
  Chirality :  0.035   0.157   2219
  Planarity :  0.004   0.036   1463
  Dihedral  : 29.495 179.427   4114
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 22.16 %
    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:  2.57 (0.30), residues: 831
  helix:  3.17 (0.22), residues: 537
  sheet: -0.62 (0.92), residues: 26
  loop : -1.29 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.010   0.001   PHE H  67 
 TYR   0.011   0.001   TYR H  39 
 ARG   0.008   0.000   ARG K  42 

*********************** 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
  149 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8558 (pm20)
REVERT: A   63 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8159 (mmp80)
REVERT: B   79 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8891 (mtmt)
REVERT: D   31 LYS cc_start: 0.9259 (mtmm) cc_final: 0.9037 (mtmm)
REVERT: H   31 LYS cc_start: 0.9031 (mmtp) cc_final: 0.8499 (mtpt)
  outliers start: 24
  outliers final: 18
  residues processed: 141
  average time/residue: 0.3753
  time to fit residues: 68.9122
Evaluate side-chains
  146 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
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   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   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  116 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:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 89 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 92 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.3415 r_free = 0.3415 target = 0.091223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.059067 restraints weight = 29111.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 2.11
r_work: 0.2592 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2592
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2595
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2595 r_free = 0.2595    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2595 r_free = 0.2595    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2595
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8820
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  13498  Z= 0.292
  Angle     :  0.569   5.676  19466  Z= 0.344
  Chirality :  0.036   0.158   2219
  Planarity :  0.004   0.036   1463
  Dihedral  : 29.512 179.286   4114
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 21.88 %
    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 (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:  2.52 (0.30), residues: 831
  helix:  3.14 (0.22), residues: 537
  sheet: -0.73 (0.93), residues: 26
  loop : -1.32 (0.34), residues: 268

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

*********************** 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
  149 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8537 (pm20)
REVERT: A   63 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8173 (mmp80)
REVERT: B   79 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8865 (mtmt)
REVERT: C   42 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8626 (ptp-170)
REVERT: D   31 LYS cc_start: 0.9266 (mtmm) cc_final: 0.9043 (mtmm)
REVERT: H   31 LYS cc_start: 0.9022 (mmtp) cc_final: 0.8483 (mtpt)
  outliers start: 24
  outliers final: 18
  residues processed: 140
  average time/residue: 0.3637
  time to fit residues: 66.4044
Evaluate side-chains
  146 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
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   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   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  116 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   63 LYS
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:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 81 optimal weight:    6.9990
   chunk 105 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0050
   chunk 4 optimal weight:    2.9990
   chunk 106 optimal weight:   30.0000
   chunk 70 optimal weight:    0.0010
   overall best weight:    0.8006

-------------------------------------------------------------------------------
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 = 0.3436 r_free = 0.3436 target = 0.092450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.060500 restraints weight = 28734.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.2803 rms_B_bonded: 2.11
r_work: 0.2631 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2631
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2631 r_free = 0.2631    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2631 r_free = 0.2631    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2631
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13498  Z= 0.174
  Angle     :  0.549   9.218  19466  Z= 0.333
  Chirality :  0.034   0.146   2219
  Planarity :  0.004   0.036   1463
  Dihedral  : 29.504 179.856   4114
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.86 %
    Favored  : 74.05 %
  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:  2.65 (0.30), residues: 831
  helix:  3.24 (0.22), residues: 537
  sheet: -0.88 (0.92), residues: 26
  loop : -1.25 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E  39 
 PHE   0.010   0.001   PHE H  67 
 TYR   0.010   0.001   TYR H  39 
 ARG   0.012   0.000   ARG K  42 

*********************** 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
  153 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8487 (pm20)
REVERT: A   63 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8120 (mmp80)
REVERT: B   27 GLN cc_start: 0.9478 (OUTLIER) cc_final: 0.8623 (mp10)
REVERT: B   79 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8898 (mtmt)
REVERT: D   31 LYS cc_start: 0.9255 (mtmm) cc_final: 0.9034 (mtmm)
REVERT: H   31 LYS cc_start: 0.9016 (mmtp) cc_final: 0.8491 (mtpt)
  outliers start: 22
  outliers final: 17
  residues processed: 145
  average time/residue: 0.3832
  time to fit residues: 72.7341
Evaluate side-chains
  148 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
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   27 GLN
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   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  116 THR
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   63 LYS
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:    0.9980
   chunk 102 optimal weight:    0.0570
   chunk 30 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 84 optimal weight:    7.9990
   chunk 95 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    2.0104

-------------------------------------------------------------------------------
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 = 0.091788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.059801 restraints weight = 28597.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 2.10
r_work: 0.2612 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2613
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2613 r_free = 0.2613    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2613 r_free = 0.2613    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2613
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.1425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13498  Z= 0.258
  Angle     :  0.569   7.957  19466  Z= 0.342
  Chirality :  0.035   0.144   2219
  Planarity :  0.004   0.036   1463
  Dihedral  : 29.512 179.713   4114
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 23.84 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.63 (0.30), residues: 831
  helix:  3.22 (0.22), residues: 538
  sheet: -0.85 (0.95), residues: 26
  loop : -1.28 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.002   PHE H  67 
 TYR   0.009   0.001   TYR A  54 
 ARG   0.009   0.000   ARG K  42 

********************** 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
  148 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8529 (pm20)
REVERT: A   63 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8154 (mmp80)
REVERT: B   27 GLN cc_start: 0.9487 (OUTLIER) cc_final: 0.8623 (mp10)
REVERT: B   79 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8897 (mtmt)
REVERT: H   31 LYS cc_start: 0.9023 (mmtp) cc_final: 0.8496 (mtpt)
  outliers start: 20
  outliers final: 15
  residues processed: 142
  average time/residue: 0.3904
  time to fit residues: 71.7346
Evaluate side-chains
  147 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 1.324 
-------------------------------------------------------------------------------
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   27 GLN
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   85 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  116 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   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 81 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0370
   chunk 34 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 85 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    1.1662

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.092604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.060715 restraints weight = 28825.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 2.10
r_work: 0.2630 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2630
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2633 r_free = 0.2633    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2633 r_free = 0.2633    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2633
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8789
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13498  Z= 0.191
  Angle     :  0.552   6.614  19466  Z= 0.333
  Chirality :  0.034   0.153   2219
  Planarity :  0.004   0.036   1463
  Dihedral  : 29.504 179.845   4114
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 23.84 %
    Favored  : 73.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.69 (0.30), residues: 831
  helix:  3.25 (0.22), residues: 538
  sheet: -0.66 (0.98), residues: 26
  loop : -1.24 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS K  68 
 PHE   0.010   0.001   PHE H  67 
 TYR   0.009   0.001   TYR H  39 
 ARG   0.010   0.000   ARG K  42 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5320.30 seconds
wall clock time: 95 minutes 1.53 seconds (5701.53 seconds total)