Starting phenix.real_space_refine
on Sat Jan 18 14:09:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v25_42898/01_2025/8v25_42898_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v25_42898/01_2025/8v25_42898.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v25_42898/01_2025/8v25_42898.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v25_42898/01_2025/8v25_42898.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v25_42898/01_2025/8v25_42898_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v25_42898/01_2025/8v25_42898_neut.cif"
  }
  resolution = 3.32
  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 17 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: 2
    residue:
      pdb=" N   ARG K  74 " occ=0.95
      ... (9 atoms not shown)
      pdb=" NH2 ARG K  74 " occ=0.95
    residue:
      pdb=" N   GLY K  75 " occ=0.65
      ... (2 atoms not shown)
      pdb=" O   GLY K  75 " occ=0.65
  Time building chain proxies: 7.82, per 1000 atoms: 0.62
  Number of scatterers: 12689
  At special positions: 0
  Unit cell: (101.85, 122.22, 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=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.87
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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:
      37 helices and 9 sheets defined
      66.9% alpha, 4.2% beta
      138 base pairs and 255 stacking pairs defined.
    Time for finding SS restraints: 5.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.520A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.803A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.860A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.622A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLY A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.099A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.656A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.649A  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
    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: 3.588A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 121
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.558A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.599A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.607A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.533A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 77
      removed outlier: 4.190A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 93
      removed outlier: 3.543A  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: 3.506A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (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: 3.611A  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
    Processing helix  chain 'K' and resid 22 through 34
    Processing helix  chain 'K' and resid 37 through 39
      No H-bonds generated for 'chain 'K' and resid 37 through 39'
    Processing helix  chain 'K' and resid 55 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.109A  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: 7.324A  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: 6.895A  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
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.346A  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

    421 hydrogen bonds defined for protein.
    1245 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      354 hydrogen bonds
      708 hydrogen bond angles
      0 basepair planarities
      138 basepair parallelities
      255 stacking parallelities
  Total time for adding SS restraints: 4.63

  Time building geometry restraints manager: 3.41 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: 2639
        1.33 -     1.45: 4191
        1.45 -     1.57: 6065
        1.57 -     1.69: 576
        1.69 -     1.81: 27
  Bond restraints: 13498
  Sorted by residual:
  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=" C1'  DG I -70 "
       pdb=" N9   DG I -70 "
    ideal  model  delta    sigma   weight residual
    1.460  1.391  0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" N   THR K  55 "
       pdb=" CA  THR K  55 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.25e-02 6.40e+03 6.36e+00
  bond pdb=" N   ARG K  72 "
       pdb=" CA  ARG K  72 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.24e-02 6.50e+03 5.94e+00
  bond pdb=" N   LEU K  56 "
       pdb=" CA  LEU K  56 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.27e-02 6.20e+03 4.41e+00
  ... (remaining 13493 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 19259
        2.27 -     4.53: 176
        4.53 -     6.80: 27
        6.80 -     9.06: 3
        9.06 -    11.33: 1
  Bond angle restraints: 19466
  Sorted by residual:
  angle pdb=" C3'  DG J  71 "
        pdb=" O3'  DG J  71 "
        pdb=" P    DA J  72 "
      ideal   model   delta    sigma   weight residual
     120.20  108.87   11.33 1.50e+00 4.44e-01 5.71e+01
  angle pdb=" C3'  DG I  71 "
        pdb=" O3'  DG I  71 "
        pdb=" P    DA I  72 "
      ideal   model   delta    sigma   weight residual
     120.20  112.34    7.86 1.50e+00 4.44e-01 2.74e+01
  angle pdb=" C3'  DC J  70 "
        pdb=" O3'  DC J  70 "
        pdb=" P    DG J  71 "
      ideal   model   delta    sigma   weight residual
     120.20  113.10    7.10 1.50e+00 4.44e-01 2.24e+01
  angle pdb=" C3'  DT J  69 "
        pdb=" O3'  DT J  69 "
        pdb=" P    DC J  70 "
      ideal   model   delta    sigma   weight residual
     120.20  114.19    6.01 1.50e+00 4.44e-01 1.60e+01
  angle pdb=" C   ASP F  24 "
        pdb=" CA  ASP F  24 "
        pdb=" CB  ASP F  24 "
      ideal   model   delta    sigma   weight residual
     111.40  116.33   -4.93 1.29e+00 6.01e-01 1.46e+01
  ... (remaining 19461 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.81: 6017
       35.81 -    71.62: 1378
       71.62 -   107.44: 8
      107.44 -   143.25: 4
      143.25 -   179.06: 1
  Dihedral angle restraints: 7408
    sinusoidal: 4945
      harmonic: 2463
  Sorted by residual:
  dihedral pdb=" CA  MET K   1 "
           pdb=" C   MET K   1 "
           pdb=" N   GLN K   2 "
           pdb=" CA  GLN K   2 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.83  -28.17     0      5.00e+00 4.00e-02 3.17e+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
    -140.00   39.06 -179.06     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   94.61  125.39     1      3.50e+01 8.16e-04 1.24e+01
  ... (remaining 7405 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 2165
       0.098 -    0.196: 48
       0.196 -    0.294: 0
       0.294 -    0.392: 0
       0.392 -    0.490: 6
  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   -2.84   -0.49 2.00e-01 2.50e+01 6.00e+00
  chirality pdb=" P    DT J  69 "
            pdb=" OP1  DT J  69 "
            pdb=" OP2  DT J  69 "
            pdb=" O5'  DT J  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.80   -0.46 2.00e-01 2.50e+01 5.27e+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   -2.79   -0.45 2.00e-01 2.50e+01 5.04e+00
  ... (remaining 2216 not shown)

  Planarity restraints: 1463
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP F  24 "    0.013 2.00e-02 2.50e+03   2.52e-02 6.33e+00
        pdb=" C   ASP F  24 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ASP F  24 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ASN F  25 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "    0.025 2.00e-02 2.50e+03   1.03e-02 3.15e+00
        pdb=" N9   DG I  47 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  37 "    0.026 5.00e-02 4.00e+02   3.85e-02 2.37e+00
        pdb=" N   PRO A  38 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A  38 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  38 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1460 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2675
        2.81 -     3.33: 10636
        3.33 -     3.85: 22521
        3.85 -     4.38: 26626
        4.38 -     4.90: 38325
  Nonbonded interactions: 100783
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU K  51 "
            pdb=" OH  TYR K  59 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OH  TYR B  98 "
            pdb=" OD2 ASP H  65 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   ASP F  24 "
            pdb=" OD1 ASP F  24 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OE1 GLU A  73 "
            pdb=" ND2 ASN B  25 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" O   THR E  58 "
            pdb=" OG1 THR E  58 "
     model   vdw
     2.315 3.040
  ... (remaining 100778 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=0.62 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:             0.960
  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:         0.080
  Set scattering table:                    0.110
  Process input model:                     33.500
  Find NCS groups from input model:        0.270
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
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   0.071  13498  Z= 0.212
  Angle     :  0.600  11.331  19466  Z= 0.360
  Chirality :  0.042   0.490   2219
  Planarity :  0.004   0.038   1463
  Dihedral  : 27.354 179.059   5816
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 20.34 %
    Favored  : 79.24 %
  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:  2.59 (0.30), residues: 831
  helix:  3.13 (0.22), residues: 523
  sheet:  1.31 (0.88), residues: 26
  loop : -1.14 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS K  68 
 PHE   0.008   0.001   PHE F  61 
 TYR   0.008   0.001   TYR H  37 
 ARG   0.006   0.000   ARG D  83 

*********************** 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
  134 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 131
  time to evaluate  : 1.058 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 133
  average time/residue: 0.3856
  time to fit residues: 66.2163
Evaluate side-chains
  129 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain F residue   85 ASP
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:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 84 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0070
   chunk 63 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    1.6004

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.091832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.061904 restraints weight = 28593.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 1.88
r_work: 0.2647 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2648
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2648 r_free = 0.2648    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8816
moved from start:          0.0682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13498  Z= 0.229
  Angle     :  0.546   5.972  19466  Z= 0.332
  Chirality :  0.034   0.138   2219
  Planarity :  0.004   0.038   1463
  Dihedral  : 29.429 179.076   4118
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 19.50 %
    Favored  : 78.40 %
  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:  3.05 (0.22), residues: 547
  sheet:  1.46 (0.89), residues: 26
  loop : -1.17 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.007   0.001   TYR H  37 
 ARG   0.005   0.000   ARG D  83 

*********************** 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: 15
    poor density    : 129
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 ASP cc_start: 0.7912 (t0) cc_final: 0.7610 (t0)
REVERT: B   27 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8579 (mp10)
REVERT: E  118 THR cc_start: 0.9362 (m) cc_final: 0.9153 (p)
REVERT: F   24 ASP cc_start: 0.7597 (p0) cc_final: 0.7282 (p0)
REVERT: H   31 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8393 (mmmt)
REVERT: K    1 MET cc_start: 0.7176 (ppp) cc_final: 0.6797 (ppp)
  outliers start: 15
  outliers final: 12
  residues processed: 136
  average time/residue: 0.3914
  time to fit residues: 69.8430
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  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain K residue   70 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 98 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 37 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 96 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 60 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.091926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.061827 restraints weight = 28851.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 1.99
r_work: 0.2640 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2643
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2643 r_free = 0.2643    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2643 r_free = 0.2643    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2643
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.0891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13498  Z= 0.218
  Angle     :  0.534   6.286  19466  Z= 0.325
  Chirality :  0.034   0.133   2219
  Planarity :  0.004   0.046   1463
  Dihedral  : 29.374 178.662   4114
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.78 %
    Favored  : 77.98 %
  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:  3.14 (0.22), residues: 550
  sheet:  1.30 (0.87), residues: 26
  loop : -1.20 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.008   0.001   PHE F  61 
 TYR   0.008   0.001   TYR K  59 
 ARG   0.007   0.000   ARG D  83 

*********************** 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
  150 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 ASP cc_start: 0.8026 (t0) cc_final: 0.7767 (t0)
REVERT: B   27 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8591 (mp10)
REVERT: E  118 THR cc_start: 0.9392 (m) cc_final: 0.9163 (p)
REVERT: F   92 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8471 (mtp85)
REVERT: H   31 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8237 (mmmt)
REVERT: K    1 MET cc_start: 0.7275 (ppp) cc_final: 0.6797 (ppp)
  outliers start: 16
  outliers final: 9
  residues processed: 144
  average time/residue: 0.3853
  time to fit residues: 71.4941
Evaluate side-chains
  140 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain H residue   98 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 95 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 84 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.089185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.058827 restraints weight = 28784.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.2750 rms_B_bonded: 1.90
r_work: 0.2577 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2577
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2576 r_free = 0.2576    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2576 r_free = 0.2576    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.1173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035  13498  Z= 0.336
  Angle     :  0.591   6.935  19466  Z= 0.356
  Chirality :  0.037   0.143   2219
  Planarity :  0.005   0.042   1463
  Dihedral  : 29.489 179.170   4114
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.21 %
    Favored  : 77.00 %
  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:  2.45 (0.30), residues: 831
  helix:  2.95 (0.22), residues: 544
  sheet:  0.96 (0.87), residues: 26
  loop : -1.35 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.011   0.002   PHE H  67 
 TYR   0.009   0.001   TYR H  39 
 ARG   0.005   0.000   ARG D  83 

*********************** 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
  150 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 123
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7806 (pm20)
REVERT: B   27 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8591 (mp10)
REVERT: F   92 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8429 (mtp85)
REVERT: H   31 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8420 (mmmt)
REVERT: K    1 MET cc_start: 0.7538 (ppp) cc_final: 0.6855 (ppp)
  outliers start: 27
  outliers final: 19
  residues processed: 139
  average time/residue: 0.3856
  time to fit residues: 69.0090
Evaluate side-chains
  142 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain K residue   70 VAL
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:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 63 optimal weight:    0.4980
   chunk 17 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 28 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 25 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 = 0.3444 r_free = 0.3444 target = 0.093834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.064046 restraints weight = 28796.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 1.98
r_work: 0.2698 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8763
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13498  Z= 0.170
  Angle     :  0.519   6.044  19466  Z= 0.316
  Chirality :  0.033   0.153   2219
  Planarity :  0.004   0.041   1463
  Dihedral  : 29.313 178.149   4114
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  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:  2.91 (0.30), residues: 831
  helix:  3.31 (0.22), residues: 549
  sheet:  0.64 (0.84), residues: 26
  loop : -1.24 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.007   0.001   PHE F  61 
 TYR   0.007   0.001   TYR H  37 
 ARG   0.006   0.000   ARG D  83 

*********************** 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
  159 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 1.044 
Fit side-chains
REVERT: B   24 ASP cc_start: 0.7994 (t0) cc_final: 0.7719 (t0)
REVERT: B   25 ASN cc_start: 0.8865 (m-40) cc_final: 0.8334 (m110)
REVERT: B   27 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8610 (mp10)
REVERT: F   92 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8390 (mtp85)
REVERT: G   42 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8036 (mtm180)
REVERT: H   65 ASP cc_start: 0.9113 (t0) cc_final: 0.8725 (t0)
REVERT: K    1 MET cc_start: 0.7669 (ppp) cc_final: 0.6826 (ppp)
  outliers start: 19
  outliers final: 9
  residues processed: 151
  average time/residue: 0.3690
  time to fit residues: 72.4519
Evaluate side-chains
  141 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain K residue   70 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 71 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 105 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.088647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.058076 restraints weight = 28977.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.2736 rms_B_bonded: 1.97
r_work: 0.2557 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2557
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2555
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2555 r_free = 0.2555    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2555 r_free = 0.2555    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2555
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041  13498  Z= 0.396
  Angle     :  0.611   6.138  19466  Z= 0.366
  Chirality :  0.039   0.151   2219
  Planarity :  0.005   0.038   1463
  Dihedral  : 29.485 179.251   4114
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 20.62 %
    Favored  : 75.88 %
  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:  2.42 (0.30), residues: 831
  helix:  2.90 (0.22), residues: 550
  sheet:  0.89 (1.01), residues: 20
  loop : -1.37 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 113 
 PHE   0.013   0.002   PHE H  67 
 TYR   0.009   0.002   TYR H  39 
 ARG   0.006   0.000   ARG D  83 

*********************** 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: 25
    poor density    : 122
  time to evaluate  : 1.097 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7839 (pm20)
REVERT: B   27 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8613 (mp10)
REVERT: C   15 LYS cc_start: 0.8943 (mtpp) cc_final: 0.8706 (ttmm)
REVERT: E  109 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9074 (mp)
REVERT: F   92 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8397 (mtp85)
REVERT: G   42 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8150 (mtm180)
REVERT: H   31 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8320 (mmtm)
REVERT: K    1 MET cc_start: 0.7793 (ppp) cc_final: 0.6895 (ppp)
  outliers start: 25
  outliers final: 16
  residues processed: 140
  average time/residue: 0.3937
  time to fit residues: 70.9680
Evaluate side-chains
  140 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue   72 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 89 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 82 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0060
   chunk 95 optimal weight:    6.9990
   chunk 85 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.0000

-------------------------------------------------------------------------------
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 = 0.3397 r_free = 0.3397 target = 0.091010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.060942 restraints weight = 28572.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 1.88
r_work: 0.2632 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2633 r_free = 0.2633    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2633 r_free = 0.2633    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2633
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8836
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13498  Z= 0.197
  Angle     :  0.549   5.991  19466  Z= 0.332
  Chirality :  0.034   0.157   2219
  Planarity :  0.004   0.039   1463
  Dihedral  : 29.403 178.494   4114
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 21.60 %
    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:  2.68 (0.30), residues: 831
  helix:  3.10 (0.22), residues: 552
  sheet:  0.65 (0.96), residues: 20
  loop : -1.28 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.008   0.001   TYR H  37 
 ARG   0.005   0.000   ARG D  83 

*********************** 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
  148 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 1.043 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7624 (pm20)
REVERT: B   27 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8563 (mp10)
REVERT: F   92 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8400 (mtp85)
REVERT: G   42 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8119 (mtm180)
REVERT: H   31 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8356 (mmtm)
REVERT: H   65 ASP cc_start: 0.9161 (t0) cc_final: 0.8802 (t0)
REVERT: K    1 MET cc_start: 0.7923 (ppp) cc_final: 0.7196 (ppp)
  outliers start: 19
  outliers final: 13
  residues processed: 140
  average time/residue: 0.3762
  time to fit residues: 68.2485
Evaluate side-chains
  141 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain H residue   98 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 89 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0370
   chunk 92 optimal weight:    6.9990
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:    0.2980
   overall best weight:    0.6260

-------------------------------------------------------------------------------
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 = 0.3455 r_free = 0.3455 target = 0.094516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.064838 restraints weight = 29224.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 1.99
r_work: 0.2720 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.1513

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= 0.164
  Angle     :  0.520   7.134  19466  Z= 0.314
  Chirality :  0.032   0.169   2219
  Planarity :  0.004   0.040   1463
  Dihedral  : 29.317 178.417   4114
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 22.44 %
    Favored  : 75.46 %
  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:  3.30 (0.22), residues: 553
  sheet:  0.73 (0.96), residues: 20
  loop : -1.20 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.007   0.001   PHE F  61 
 TYR   0.006   0.001   TYR H  37 
 ARG   0.006   0.000   ARG D  83 

*********************** 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
  146 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.960 
Fit side-chains
REVERT: B   24 ASP cc_start: 0.7967 (t0) cc_final: 0.7749 (t0)
REVERT: B   27 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8611 (mp10)
REVERT: C   15 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8671 (ttmm)
REVERT: F   92 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8407 (mtp85)
REVERT: G   42 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7979 (mtm180)
REVERT: H   65 ASP cc_start: 0.9131 (t0) cc_final: 0.8715 (t0)
REVERT: K    1 MET cc_start: 0.7898 (ppp) cc_final: 0.7216 (ppp)
  outliers start: 15
  outliers final: 11
  residues processed: 143
  average time/residue: 0.3443
  time to fit residues: 64.3477
Evaluate side-chains
  141 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
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:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 105 optimal weight:   20.0000
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** K   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.092424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.062597 restraints weight = 28832.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 1.88
r_work: 0.2666 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2668
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2668
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8801
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13498  Z= 0.222
  Angle     :  0.541   6.977  19466  Z= 0.325
  Chirality :  0.034   0.161   2219
  Planarity :  0.004   0.039   1463
  Dihedral  : 29.349 178.293   4114
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 22.30 %
    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:  2.91 (0.30), residues: 831
  helix:  3.31 (0.22), residues: 553
  sheet:  0.78 (0.99), residues: 20
  loop : -1.27 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.008   0.001   TYR H  37 
 ARG   0.006   0.000   ARG D  83 

*********************** 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
  144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7521 (pm20)
REVERT: B   27 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8580 (mp10)
REVERT: C   15 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8693 (ttmm)
REVERT: F   92 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8369 (mtp85)
REVERT: G   42 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8118 (mtm180)
REVERT: H   65 ASP cc_start: 0.9124 (t0) cc_final: 0.8750 (t0)
  outliers start: 18
  outliers final: 14
  residues processed: 136
  average time/residue: 0.3568
  time to fit residues: 63.5758
Evaluate side-chains
  143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue   98 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 102 optimal weight:   30.0000
   chunk 30 optimal weight:    0.8980
   chunk 79 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 84 optimal weight:    7.9990
   chunk 95 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** K   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.092054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.062226 restraints weight = 28593.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 1.87
r_work: 0.2658 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13498  Z= 0.223
  Angle     :  0.543   6.710  19466  Z= 0.326
  Chirality :  0.034   0.163   2219
  Planarity :  0.004   0.039   1463
  Dihedral  : 29.335 178.281   4114
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 22.44 %
    Favored  : 75.04 %
  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:  2.86 (0.30), residues: 831
  helix:  3.29 (0.22), residues: 551
  sheet:  0.90 (1.04), residues: 20
  loop : -1.33 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.011   0.001   PHE K   4 
 TYR   0.008   0.001   TYR H  37 
 ARG   0.006   0.000   ARG D  83 

********************** 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
  143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7569 (pm20)
REVERT: B   27 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8562 (mp10)
REVERT: C   15 LYS cc_start: 0.8907 (mtpp) cc_final: 0.8683 (ttmm)
REVERT: F   92 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8384 (mtp85)
REVERT: G   42 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8101 (mtm180)
REVERT: H   31 LYS cc_start: 0.8831 (mmmt) cc_final: 0.8535 (mmmt)
REVERT: H   65 ASP cc_start: 0.9131 (t0) cc_final: 0.8750 (t0)
REVERT: K    1 MET cc_start: 0.8280 (ttt) cc_final: 0.6530 (tpp)
  outliers start: 18
  outliers final: 13
  residues processed: 136
  average time/residue: 0.3575
  time to fit residues: 63.6495
Evaluate side-chains
  142 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue   98 LEU
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:    4.9990
   chunk 23 optimal weight:    0.3980
   chunk 69 optimal weight:    0.0470
   chunk 34 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 85 optimal weight:    7.9990
   chunk 59 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.8080

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

Flipped N/Q/H residues before XYZ refinement:
** K   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.092473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.062571 restraints weight = 28776.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 1.88
r_work: 0.2667 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8800
moved from start:          0.1477

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= 0.181
  Angle     :  0.539   6.968  19466  Z= 0.324
  Chirality :  0.033   0.165   2219
  Planarity :  0.004   0.039   1463
  Dihedral  : 29.343 178.361   4114
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 22.58 %
    Favored  : 74.89 %
  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:  2.89 (0.30), residues: 831
  helix:  3.32 (0.22), residues: 551
  sheet:  0.86 (1.04), residues: 20
  loop : -1.30 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.008   0.001   PHE F  61 
 TYR   0.008   0.001   TYR H  37 
 ARG   0.007   0.000   ARG D  83 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4966.24 seconds
wall clock time: 89 minutes 11.17 seconds (5351.17 seconds total)