Starting phenix.real_space_refine
on Sat Oct 11 06:57:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pc5_17594/10_2025/8pc5_17594.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pc5_17594/10_2025/8pc5_17594.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pc5_17594/10_2025/8pc5_17594.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pc5_17594/10_2025/8pc5_17594.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pc5_17594/10_2025/8pc5_17594.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pc5_17594/10_2025/8pc5_17594.map"
  }
  resolution = 3.02
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.014
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     294      5.49       5
     S      13      5.16       5
     C    7172      2.51       5
     N    2399      2.21       5
     O    2958      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12836
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "A"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 829
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'ML3:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 694
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
    Chain: "G"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "K"
      Number of atoms: 710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 710
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 11, 'TRANS': 74}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Time building chain proxies: 3.24, per 1000 atoms: 0.25
  Number of scatterers: 12836
  At special positions: 0
  Unit cell: (102.533, 125.04, 123.373, 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      13     16.00
     P     294     15.00
     O    2958      8.00
     N    2399      7.00
     C    7172      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: 0.94
  Conformation dependent library (CDL) restraints added in 351.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1598

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 11 sheets defined
      64.4% alpha, 5.0% beta
      146 base pairs and 271 stacking pairs defined.
    Time for finding SS restraints: 2.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 75
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.595A  pdb=" N   ALA A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.605A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.817A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.702A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.528A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.599A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 121
      removed outlier: 3.523A  pdb=" N   HIS D 106 " --> pdb=" O   GLU D 102 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.783A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.548A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.520A  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 45 through 72
      removed outlier: 4.399A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 101 through 121
      removed outlier: 4.113A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   HIS H 106 " --> pdb=" O   GLU H 102 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 76 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.607A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.578A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.345A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.577A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.363A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 53
      removed outlier: 3.850A  pdb=" N   GLU K  49 " --> pdb=" O   PHE K  44 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA K  51 " --> pdb=" O   ILE K  42 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ILE K  42 " --> pdb=" O   ALA K  51 " (cutoff:3.500A)

    407 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      374 hydrogen bonds
      748 hydrogen bond angles
      0 basepair planarities
      146 basepair parallelities
      271 stacking parallelities
  Total time for adding SS restraints: 2.64

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2069
        1.33 -     1.45: 4662
        1.45 -     1.57: 6333
        1.57 -     1.69: 586
        1.69 -     1.81: 26
  Bond restraints: 13676
  Sorted by residual:
  bond pdb=" SG  ML3 A  36 "
       pdb=" CD  ML3 A  36 "
    ideal  model  delta    sigma   weight residual
    1.815  1.758  0.057 2.00e-02 2.50e+03 8.17e+00
  bond pdb=" CB  ML3 A  36 "
       pdb=" SG  ML3 A  36 "
    ideal  model  delta    sigma   weight residual
    1.817  1.766  0.051 2.00e-02 2.50e+03 6.49e+00
  bond pdb=" P    DT J -72 "
       pdb=" OP1  DT J -72 "
    ideal  model  delta    sigma   weight residual
    1.480  1.522 -0.042 2.00e-02 2.50e+03 4.43e+00
  bond pdb=" P    DC I  69 "
       pdb=" OP2  DC I  69 "
    ideal  model  delta    sigma   weight residual
    1.480  1.518 -0.038 2.00e-02 2.50e+03 3.65e+00
  bond pdb=" P    DG J  62 "
       pdb=" OP1  DG J  62 "
    ideal  model  delta    sigma   weight residual
    1.480  1.517 -0.037 2.00e-02 2.50e+03 3.51e+00
  ... (remaining 13671 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 18671
        1.67 -     3.33: 963
        3.33 -     5.00: 68
        5.00 -     6.66: 17
        6.66 -     8.33: 11
  Bond angle restraints: 19730
  Sorted by residual:
  angle pdb=" O3'  DC I  49 "
        pdb=" P    DA I  50 "
        pdb=" O5'  DA I  50 "
      ideal   model   delta    sigma   weight residual
     104.00   95.83    8.17 1.50e+00 4.44e-01 2.97e+01
  angle pdb=" C4'  DC I  49 "
        pdb=" C3'  DC I  49 "
        pdb=" O3'  DC I  49 "
      ideal   model   delta    sigma   weight residual
     110.00  102.83    7.17 1.50e+00 4.44e-01 2.29e+01
  angle pdb=" O3'  DA J -73 "
        pdb=" P    DT J -72 "
        pdb=" O5'  DT J -72 "
      ideal   model   delta    sigma   weight residual
     104.00  109.54   -5.54 1.50e+00 4.44e-01 1.36e+01
  angle pdb=" C3'  DA J -73 "
        pdb=" O3'  DA J -73 "
        pdb=" P    DT J -72 "
      ideal   model   delta    sigma   weight residual
     120.20  125.37   -5.17 1.50e+00 4.44e-01 1.19e+01
  angle pdb=" C3'  DC J  68 "
        pdb=" O3'  DC J  68 "
        pdb=" P    DT J  69 "
      ideal   model   delta    sigma   weight residual
     120.20  125.25   -5.05 1.50e+00 4.44e-01 1.13e+01
  ... (remaining 19725 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.94: 5857
       35.94 -    71.87: 1586
       71.87 -   107.81: 28
      107.81 -   143.75: 3
      143.75 -   179.69: 3
  Dihedral angle restraints: 7477
    sinusoidal: 5003
      harmonic: 2474
  Sorted by residual:
  dihedral pdb=" C4'  DT J  69 "
           pdb=" C3'  DT J  69 "
           pdb=" O3'  DT J  69 "
           pdb=" P    DC J  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.69 -179.69     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC J  68 "
           pdb=" C3'  DC J  68 "
           pdb=" O3'  DC J  68 "
           pdb=" P    DT J  69 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   25.29 -165.29     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DA J -73 "
           pdb=" C3'  DA J -73 "
           pdb=" O3'  DA J -73 "
           pdb=" P    DT J -72 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   18.69 -158.69     1      3.50e+01 8.16e-04 1.51e+01
  ... (remaining 7474 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 2146
       0.113 -    0.226: 73
       0.226 -    0.340: 0
       0.340 -    0.453: 1
       0.453 -    0.566: 9
  Chirality restraints: 2229
  Sorted by residual:
  chirality pdb=" P    DA J  65 "
            pdb=" OP1  DA J  65 "
            pdb=" OP2  DA J  65 "
            pdb=" O5'  DA J  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.91   -0.57 2.00e-01 2.50e+01 8.01e+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   -2.90   -0.56 2.00e-01 2.50e+01 7.77e+00
  chirality pdb=" P    DG J  64 "
            pdb=" OP1  DG J  64 "
            pdb=" OP2  DG J  64 "
            pdb=" O5'  DG J  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.90   -0.55 2.00e-01 2.50e+01 7.56e+00
  ... (remaining 2226 not shown)

  Planarity restraints: 1479
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ML3 A  36 "    0.014 2.00e-02 2.50e+03   2.86e-02 8.17e+00
        pdb=" C   ML3 A  36 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   ML3 A  36 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LYS A  37 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  49 "   -0.029 2.00e-02 2.50e+03   1.85e-02 7.74e+00
        pdb=" N1   DC I  49 "    0.043 2.00e-02 2.50e+03
        pdb=" C2   DC I  49 "   -0.017 2.00e-02 2.50e+03
        pdb=" O2   DC I  49 "    0.009 2.00e-02 2.50e+03
        pdb=" N3   DC I  49 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DC I  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" N4   DC I  49 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5   DC I  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DC I  49 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "   -0.032 2.00e-02 2.50e+03   1.56e-02 7.29e+00
        pdb=" N9   DG I  47 "    0.042 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "    0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1476 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1385
        2.74 -     3.28: 10741
        3.28 -     3.82: 25026
        3.82 -     4.36: 30240
        4.36 -     4.90: 43301
  Nonbonded interactions: 110693
  Sorted by model distance:
  nonbonded pdb=" O   HIS B  75 "
            pdb=" NH2 ARG D  89 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OG1 THR B  73 "
            pdb=" OD2 ASP B  85 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" NH2 ARG B  35 "
            pdb=" OH  TYR B  51 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" NE2 GLN C 104 "
            pdb=" OE2 GLU E  94 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" O   PRO K  60 "
            pdb=" ND2 ASN K  64 "
     model   vdw
     2.277 3.120
  ... (remaining 110688 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 20 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  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=0.00 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:             6.240
  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:             0.020
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.530
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  13676  Z= 0.267
  Angle     :  0.786   8.330  19730  Z= 0.459
  Chirality :  0.060   0.566   2229
  Planarity :  0.006   0.048   1479
  Dihedral  : 29.262 179.686   5879
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 11.08 %
    Favored  : 88.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.29), residues: 831
  helix:  1.76 (0.22), residues: 541
  sheet: -3.81 (0.82), residues: 12
  loop : -1.27 (0.32), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  52 
 TYR   0.010   0.002   TYR H  34 
 PHE   0.014   0.002   PHE A  78 
 TRP   0.004   0.001   TRP K  21 
 HIS   0.006   0.002   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00607 (13676)
  covalent geometry    : angle       0.78649 (19730)
  hydrogen bonds       : bond        0.12744 (  781)
  hydrogen bonds       : angle       4.25811 ( 1951)

*********************** 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
  154 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 151
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: H   84 SER cc_start: 0.8922 (m) cc_final: 0.8721 (t)
  outliers start: 3
  outliers final: 2
  residues processed: 153
  average time/residue: 0.1813
  time to fit residues: 35.8814
Evaluate side-chains
  103 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain K residue   58 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0050
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.3980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    6.9990
   chunk 106 optimal weight:    4.9990
   overall best weight:    1.4598

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C  73 ASN
D  46 HIS
E  76 GLN
G 110 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.082949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.054518 restraints weight = 37620.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 1.72
r_work: 0.2766 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2644 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8932
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  13676  Z= 0.225
  Angle     :  0.611  10.125  19730  Z= 0.365
  Chirality :  0.038   0.154   2229
  Planarity :  0.005   0.037   1479
  Dihedral  : 31.156 164.450   4168
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.62 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.29), residues: 831
  helix:  2.05 (0.22), residues: 559
  sheet: -2.37 (0.85), residues: 24
  loop : -0.99 (0.35), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  96 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.009   0.002   PHE H  62 
 TRP   0.007   0.002   TRP K  21 
 HIS   0.003   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 (13676)
  covalent geometry    : angle       0.61052 (19730)
  hydrogen bonds       : bond        0.04608 (  781)
  hydrogen bonds       : angle       2.99847 ( 1951)

*********************** 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
  118 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   52 PHE cc_start: 0.7846 (m-80) cc_final: 0.7538 (m-80)
  outliers start: 13
  outliers final: 5
  residues processed: 112
  average time/residue: 0.1544
  time to fit residues: 23.0902
Evaluate side-chains
  101 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain K residue   58 ILE
Chi-restraints excluded: chain K residue   62 SER
Chi-restraints excluded: chain K residue   90 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 105 optimal weight:    3.9990
   chunk 108 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0670
   chunk 67 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    1.3722

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
E 108 ASN
F  27 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.082173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.052894 restraints weight = 38140.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 1.78
r_work: 0.2688 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2570 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8939
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  13676  Z= 0.211
  Angle     :  0.584   9.366  19730  Z= 0.351
  Chirality :  0.036   0.134   2229
  Planarity :  0.004   0.040   1479
  Dihedral  : 30.742 165.955   4167
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 13.74 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.29), residues: 831
  helix:  2.25 (0.22), residues: 559
  sheet: -2.26 (0.92), residues: 24
  loop : -0.98 (0.35), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 129 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.008   0.001   PHE E 104 
 TRP   0.019   0.003   TRP K  82 
 HIS   0.004   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 (13676)
  covalent geometry    : angle       0.58409 (19730)
  hydrogen bonds       : bond        0.04519 (  781)
  hydrogen bonds       : angle       2.88490 ( 1951)

*********************** 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
  115 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   72 ASP cc_start: 0.9005 (t0) cc_final: 0.8736 (t0)
REVERT: E   79 LYS cc_start: 0.9053 (tttt) cc_final: 0.8824 (tttt)
REVERT: H   90 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8308 (mp0)
  outliers start: 9
  outliers final: 4
  residues processed: 110
  average time/residue: 0.1663
  time to fit residues: 24.5614
Evaluate side-chains
  101 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain K residue   38 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 71 optimal weight:    0.2980
   chunk 21 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0970
   chunk 80 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 107 optimal weight:    6.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
F  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.082638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.053444 restraints weight = 38499.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.2862 rms_B_bonded: 1.79
r_work: 0.2707 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.2589 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8923
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  13676  Z= 0.185
  Angle     :  0.561   9.211  19730  Z= 0.339
  Chirality :  0.035   0.127   2229
  Planarity :  0.004   0.038   1479
  Dihedral  : 30.529 162.816   4165
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.88 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.29), residues: 831
  helix:  2.44 (0.22), residues: 560
  sheet: -1.85 (0.95), residues: 24
  loop : -0.92 (0.35), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  42 
 TYR   0.010   0.001   TYR K  68 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.012   0.002   TRP K  82 
 HIS   0.003   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (13676)
  covalent geometry    : angle       0.56129 (19730)
  hydrogen bonds       : bond        0.04065 (  781)
  hydrogen bonds       : angle       2.79057 ( 1951)

*********************** 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
  110 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: C   72 ASP cc_start: 0.9009 (t0) cc_final: 0.8768 (t0)
REVERT: E   79 LYS cc_start: 0.9059 (tttt) cc_final: 0.8837 (tttt)
REVERT: H   90 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8321 (mp0)
  outliers start: 12
  outliers final: 5
  residues processed: 107
  average time/residue: 0.1536
  time to fit residues: 22.3981
Evaluate side-chains
  100 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain K residue   47 THR
Chi-restraints excluded: chain K residue   62 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0370
   chunk 53 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 84 optimal weight:    0.5980
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
C  73 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.083228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.054142 restraints weight = 38241.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 1.79
r_work: 0.2729 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2612 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8900
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13676  Z= 0.154
  Angle     :  0.555   9.099  19730  Z= 0.335
  Chirality :  0.034   0.128   2229
  Planarity :  0.004   0.038   1479
  Dihedral  : 30.488 164.527   4165
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.01 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.29), residues: 831
  helix:  2.58 (0.22), residues: 560
  sheet: -1.85 (0.88), residues: 29
  loop : -0.92 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.008   0.001   TYR B  51 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.011   0.001   TRP K  82 
 HIS   0.004   0.001   HIS F  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (13676)
  covalent geometry    : angle       0.55486 (19730)
  hydrogen bonds       : bond        0.03802 (  781)
  hydrogen bonds       : angle       2.73624 ( 1951)

*********************** 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
  109 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: C   72 ASP cc_start: 0.8961 (t0) cc_final: 0.8746 (t0)
  outliers start: 12
  outliers final: 6
  residues processed: 105
  average time/residue: 0.1468
  time to fit residues: 20.7210
Evaluate side-chains
  100 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain K residue   38 ASN
Chi-restraints excluded: chain K residue   47 THR
Chi-restraints excluded: chain K residue   58 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 107 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 45 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 93 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C  73 ASN
F  25 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.081201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.051899 restraints weight = 37891.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.2823 rms_B_bonded: 1.77
r_work: 0.2668 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2550 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8955
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  13676  Z= 0.248
  Angle     :  0.603   9.711  19730  Z= 0.359
  Chirality :  0.037   0.128   2229
  Planarity :  0.004   0.037   1479
  Dihedral  : 30.598 167.487   4165
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.73 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.29), residues: 831
  helix:  2.43 (0.22), residues: 560
  sheet: -1.79 (0.87), residues: 29
  loop : -0.96 (0.35), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 129 
 TYR   0.011   0.001   TYR B  51 
 PHE   0.009   0.002   PHE H  62 
 TRP   0.009   0.002   TRP K  82 
 HIS   0.004   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 (13676)
  covalent geometry    : angle       0.60331 (19730)
  hydrogen bonds       : bond        0.04749 (  781)
  hydrogen bonds       : angle       2.88139 ( 1951)

*********************** 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
  106 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: C   72 ASP cc_start: 0.9038 (t0) cc_final: 0.8808 (t0)
REVERT: F   95 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8985 (mtt-85)
  outliers start: 13
  outliers final: 9
  residues processed: 100
  average time/residue: 0.1496
  time to fit residues: 19.9569
Evaluate side-chains
  102 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain K residue   38 ASN
Chi-restraints excluded: chain K residue   47 THR
Chi-restraints excluded: chain K residue   58 ILE
Chi-restraints excluded: chain K residue   62 SER
Chi-restraints excluded: chain K residue   82 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 75 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 85 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C  73 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.082008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.052810 restraints weight = 37851.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.2847 rms_B_bonded: 1.80
r_work: 0.2687 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2568 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8930
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  13676  Z= 0.167
  Angle     :  0.572   9.539  19730  Z= 0.344
  Chirality :  0.035   0.126   2229
  Planarity :  0.004   0.038   1479
  Dihedral  : 30.544 168.230   4165
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.45 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.29), residues: 831
  helix:  2.52 (0.22), residues: 559
  sheet: -1.71 (0.88), residues: 29
  loop : -0.90 (0.36), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  29 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.009   0.001   PHE A  67 
 TRP   0.010   0.001   TRP K  82 
 HIS   0.003   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (13676)
  covalent geometry    : angle       0.57209 (19730)
  hydrogen bonds       : bond        0.04223 (  781)
  hydrogen bonds       : angle       2.80264 ( 1951)

*********************** 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
  106 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: C   72 ASP cc_start: 0.9021 (t0) cc_final: 0.8806 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 99
  average time/residue: 0.1583
  time to fit residues: 21.0458
Evaluate side-chains
  99 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain K residue   38 ASN
Chi-restraints excluded: chain K residue   47 THR
Chi-restraints excluded: chain K residue   58 ILE
Chi-restraints excluded: chain K residue   62 SER
Chi-restraints excluded: chain K residue   82 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 79 optimal weight:    0.2980
   chunk 105 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.082727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.053741 restraints weight = 37903.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.2872 rms_B_bonded: 1.76
r_work: 0.2716 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2598 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8913
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  13676  Z= 0.164
  Angle     :  0.557   9.192  19730  Z= 0.336
  Chirality :  0.034   0.124   2229
  Planarity :  0.004   0.039   1479
  Dihedral  : 30.342 170.096   4165
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 15.01 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.29), residues: 831
  helix:  2.66 (0.22), residues: 560
  sheet: -1.18 (1.00), residues: 24
  loop : -0.68 (0.36), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  32 
 TYR   0.007   0.001   TYR B  51 
 PHE   0.009   0.001   PHE A  67 
 TRP   0.010   0.001   TRP K  82 
 HIS   0.003   0.001   HIS F  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (13676)
  covalent geometry    : angle       0.55741 (19730)
  hydrogen bonds       : bond        0.03884 (  781)
  hydrogen bonds       : angle       2.71512 ( 1951)

*********************** 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
  103 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: C   72 ASP cc_start: 0.8981 (t0) cc_final: 0.8747 (t0)
REVERT: H   84 SER cc_start: 0.9287 (m) cc_final: 0.8762 (t)
  outliers start: 8
  outliers final: 6
  residues processed: 99
  average time/residue: 0.1448
  time to fit residues: 19.4450
Evaluate side-chains
  100 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain K residue   38 ASN
Chi-restraints excluded: chain K residue   47 THR
Chi-restraints excluded: chain K residue   62 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 84 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 47 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9990
   chunk 101 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.0386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.082406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.053327 restraints weight = 38071.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 1.77
r_work: 0.2705 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2588 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8924
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13676  Z= 0.184
  Angle     :  0.573   9.227  19730  Z= 0.343
  Chirality :  0.035   0.125   2229
  Planarity :  0.004   0.037   1479
  Dihedral  : 30.356 171.570   4165
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 15.29 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.29), residues: 831
  helix:  2.63 (0.22), residues: 561
  sheet: -0.96 (1.02), residues: 24
  loop : -0.66 (0.36), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  29 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.008   0.001   PHE H  62 
 TRP   0.009   0.001   TRP K  82 
 HIS   0.003   0.001   HIS F  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (13676)
  covalent geometry    : angle       0.57329 (19730)
  hydrogen bonds       : bond        0.04106 (  781)
  hydrogen bonds       : angle       2.73373 ( 1951)

*********************** 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
  100 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: C   72 ASP cc_start: 0.8995 (t0) cc_final: 0.8786 (t0)
REVERT: G   41 GLU cc_start: 0.8477 (mp0) cc_final: 0.8174 (mp0)
REVERT: H   84 SER cc_start: 0.9375 (m) cc_final: 0.8420 (t)
  outliers start: 8
  outliers final: 6
  residues processed: 96
  average time/residue: 0.1483
  time to fit residues: 19.5216
Evaluate side-chains
  97 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain K residue   38 ASN
Chi-restraints excluded: chain K residue   62 SER
Chi-restraints excluded: chain K residue   82 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 108 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 92 optimal weight:    0.2980
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.082625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.053568 restraints weight = 37997.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 1.77
r_work: 0.2712 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2595 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8918
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13676  Z= 0.167
  Angle     :  0.572  10.138  19730  Z= 0.341
  Chirality :  0.034   0.125   2229
  Planarity :  0.004   0.038   1479
  Dihedral  : 30.352 171.738   4165
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 15.43 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.46 (0.29), residues: 831
  helix:  2.67 (0.22), residues: 561
  sheet: -0.95 (1.02), residues: 24
  loop : -0.63 (0.36), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  29 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.029   0.001   PHE K  44 
 TRP   0.009   0.001   TRP K  82 
 HIS   0.003   0.001   HIS F  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (13676)
  covalent geometry    : angle       0.57176 (19730)
  hydrogen bonds       : bond        0.04005 (  781)
  hydrogen bonds       : angle       2.71666 ( 1951)

********************** 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
  99 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: C   72 ASP cc_start: 0.8987 (t0) cc_final: 0.8753 (t0)
REVERT: G   41 GLU cc_start: 0.8499 (mp0) cc_final: 0.8198 (mp0)
REVERT: H   84 SER cc_start: 0.9367 (m) cc_final: 0.8402 (t)
  outliers start: 7
  outliers final: 6
  residues processed: 94
  average time/residue: 0.1466
  time to fit residues: 18.8172
Evaluate side-chains
  98 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain K residue   38 ASN
Chi-restraints excluded: chain K residue   62 SER
Chi-restraints excluded: chain K residue   82 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   chunk 55 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 108 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    0.9182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.082685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.053637 restraints weight = 37731.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 1.76
r_work: 0.2713 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2596 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8915
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13676  Z= 0.175
  Angle     :  0.568  10.056  19730  Z= 0.339
  Chirality :  0.034   0.124   2229
  Planarity :  0.004   0.038   1479
  Dihedral  : 30.317 172.009   4165
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 15.29 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.49 (0.29), residues: 831
  helix:  2.69 (0.22), residues: 561
  sheet: -0.91 (1.02), residues: 24
  loop : -0.61 (0.36), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 129 
 TYR   0.008   0.001   TYR B  51 
 PHE   0.017   0.001   PHE K  44 
 TRP   0.009   0.001   TRP K  82 
 HIS   0.003   0.001   HIS F  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (13676)
  covalent geometry    : angle       0.56839 (19730)
  hydrogen bonds       : bond        0.03979 (  781)
  hydrogen bonds       : angle       2.71035 ( 1951)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4300.99 seconds
wall clock time: 73 minutes 46.21 seconds (4426.21 seconds total)