Starting phenix.real_space_refine
on Wed Mar  4 11:03:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ohb_12899/03_2026/7ohb_12899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ohb_12899/03_2026/7ohb_12899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ohb_12899/03_2026/7ohb_12899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ohb_12899/03_2026/7ohb_12899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ohb_12899/03_2026/7ohb_12899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ohb_12899/03_2026/7ohb_12899.cif"
  }
  resolution = 3.4
  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=   0.000 sd=   0.005
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     290      5.49       5
     S      18      5.16       5
     C    7560      2.51       5
     N    2501      2.21       5
     O    3055      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13424
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, '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: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 756
          Classifications: {'peptide': 96}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "E"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 746
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2990
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 1416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1416
          Classifications: {'peptide': 180}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 171}
  Time building chain proxies: 3.02, per 1000 atoms: 0.22
  Number of scatterers: 13424
  At special positions: 0
  Unit cell: (92.4, 116.55, 133.35, 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      18     16.00
     P     290     15.00
     O    3055      8.00
     N    2501      7.00
     C    7560      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: 1.01
  Conformation dependent library (CDL) restraints added in 497.8 milliseconds
  

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1768

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 10 sheets defined
      64.8% alpha, 7.2% beta
      144 base pairs and 266 stacking pairs defined.
    Time for finding SS restraints: 2.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.991A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.807A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.318A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    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 100 through 121
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 4.144A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.853A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.563A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
      removed outlier: 3.590A  pdb=" N   ARG G  20 " --> pdb=" O   THR G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.377A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 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 100 through 121
    Processing helix  chain 'K' and resid 81 through 88
      removed outlier: 3.649A  pdb=" N   VAL K  85 " --> pdb=" O   ASP K  81 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 128 through 147
    Processing helix  chain 'K' and resid 171 through 179
      removed outlier: 3.599A  pdb=" N   LEU K 175 " --> pdb=" O   ARG K 171 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 219 through 236
      removed outlier: 4.087A  pdb=" N   ILE K 223 " --> pdb=" O   GLN K 219 " (cutoff:3.500A)
      Proline residue:  K 232  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.004A  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: 6.471A  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: 7.132A  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: 6.998A  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: 7.512A  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 'K' and resid 92 through 93
      removed outlier: 3.602A  pdb=" N   VAL K 102 " --> pdb=" O   ILE K 115 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   THR K 124 " --> pdb=" O   THR K 112 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   LYS K 120 " --> pdb=" O   PHE K 116 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLY K 125 " --> pdb=" O   ILE K  70 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   ILE K  70 " --> pdb=" O   GLY K 125 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   VAL K 161 " --> pdb=" O   GLN K  68 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   ILE K  70 " --> pdb=" O   ASN K 159 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ASN K 159 " --> pdb=" O   ILE K  70 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ALA K  72 " --> pdb=" O   ILE K 157 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ILE K 157 " --> pdb=" O   ALA K  72 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   VAL K  74 " --> pdb=" O   PHE K 155 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   PHE K 155 " --> pdb=" O   VAL K  74 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE K 212 " --> pdb=" O   CYS K 164 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   VAL K 213 " --> pdb=" O   LEU K 205 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU K 205 " --> pdb=" O   VAL K 213 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   THR K 215 " --> pdb=" O   VAL K 203 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   VAL K 203 " --> pdb=" O   THR K 215 " (cutoff:3.500A)

    472 hydrogen bonds defined for protein.
    1389 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      368 hydrogen bonds
      736 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      266 stacking parallelities
  Total time for adding SS restraints: 2.33

  Time building geometry restraints manager: 1.36 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: 2665
        1.33 -     1.45: 4528
        1.45 -     1.57: 6451
        1.57 -     1.69: 578
        1.69 -     1.82: 32
  Bond restraints: 14254
  Sorted by residual:
  bond pdb=" C3'  DT I  60 "
       pdb=" O3'  DT I  60 "
    ideal  model  delta    sigma   weight residual
    1.422  1.519 -0.097 3.00e-02 1.11e+03 1.05e+01
  bond pdb=" O5'  DA I  61 "
       pdb=" C5'  DA I  61 "
    ideal  model  delta    sigma   weight residual
    1.423  1.468 -0.045 3.00e-02 1.11e+03 2.30e+00
  bond pdb=" C5'  DA I  61 "
       pdb=" C4'  DA I  61 "
    ideal  model  delta    sigma   weight residual
    1.518  1.548 -0.030 2.00e-02 2.50e+03 2.23e+00
  bond pdb=" CB  VAL A  46 "
       pdb=" CG1 VAL A  46 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.13e+00
  bond pdb=" CB  VAL E  46 "
       pdb=" CG1 VAL E  46 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.02e+00
  ... (remaining 14249 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 19692
        2.06 -     4.11: 711
        4.11 -     6.17: 64
        6.17 -     8.22: 16
        8.22 -    10.28: 3
  Bond angle restraints: 20486
  Sorted by residual:
  angle pdb=" CB  ARG B  40 "
        pdb=" CG  ARG B  40 "
        pdb=" CD  ARG B  40 "
      ideal   model   delta    sigma   weight residual
     111.30  121.58  -10.28 2.30e+00 1.89e-01 2.00e+01
  angle pdb=" C   ASN G  73 "
        pdb=" N   LYS G  74 "
        pdb=" CA  LYS G  74 "
      ideal   model   delta    sigma   weight residual
     122.40  127.54   -5.14 1.45e+00 4.76e-01 1.26e+01
  angle pdb=" O3'  DT I  60 "
        pdb=" C3'  DT I  60 "
        pdb=" C2'  DT I  60 "
      ideal   model   delta    sigma   weight residual
     111.50  116.71   -5.21 1.50e+00 4.44e-01 1.21e+01
  angle pdb=" N   GLY H 101 "
        pdb=" CA  GLY H 101 "
        pdb=" C   GLY H 101 "
      ideal   model   delta    sigma   weight residual
     113.18  121.37   -8.19 2.37e+00 1.78e-01 1.19e+01
  angle pdb=" CB  LYS G  15 "
        pdb=" CG  LYS G  15 "
        pdb=" CD  LYS G  15 "
      ideal   model   delta    sigma   weight residual
     111.30  119.22   -7.92 2.30e+00 1.89e-01 1.19e+01
  ... (remaining 20481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.96: 5269
       20.96 -    41.91: 1340
       41.91 -    62.87: 1178
       62.87 -    83.83: 66
       83.83 -   104.78: 6
  Dihedral angle restraints: 7859
    sinusoidal: 5121
      harmonic: 2738
  Sorted by residual:
  dihedral pdb=" CA  GLU K 108 "
           pdb=" C   GLU K 108 "
           pdb=" N   PRO K 109 "
           pdb=" CA  PRO K 109 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -39.57   39.57     0      5.00e+00 4.00e-02 6.26e+01
  dihedral pdb=" CA  PRO D 100 "
           pdb=" C   PRO D 100 "
           pdb=" N   GLY D 101 "
           pdb=" CA  GLY D 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.58  -21.42     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  LYS K 199 "
           pdb=" C   LYS K 199 "
           pdb=" N   PRO K 200 "
           pdb=" CA  PRO K 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.94   20.06     0      5.00e+00 4.00e-02 1.61e+01
  ... (remaining 7856 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 2073
       0.080 -    0.161: 242
       0.161 -    0.241: 17
       0.241 -    0.321: 3
       0.321 -    0.402: 1
  Chirality restraints: 2336
  Sorted by residual:
  chirality pdb=" C1'  DT I  60 "
            pdb=" O4'  DT I  60 "
            pdb=" C2'  DT I  60 "
            pdb=" N1   DT I  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.07    0.40 2.00e-01 2.50e+01 4.03e+00
  chirality pdb=" CB  ILE K 212 "
            pdb=" CA  ILE K 212 "
            pdb=" CG1 ILE K 212 "
            pdb=" CG2 ILE K 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.14e+00
  chirality pdb=" CB  THR K 111 "
            pdb=" CA  THR K 111 "
            pdb=" OG1 THR K 111 "
            pdb=" CG2 THR K 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.29    0.27 2.00e-01 2.50e+01 1.77e+00
  ... (remaining 2333 not shown)

  Planarity restraints: 1584
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL G  27 "   -0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   VAL G  27 "    0.058 2.00e-02 2.50e+03
        pdb=" O   VAL G  27 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLY G  28 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  60 "    0.006 2.00e-02 2.50e+03   1.84e-02 8.44e+00
        pdb=" N1   DT I  60 "   -0.037 2.00e-02 2.50e+03
        pdb=" C2   DT I  60 "    0.041 2.00e-02 2.50e+03
        pdb=" O2   DT I  60 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3   DT I  60 "   -0.009 2.00e-02 2.50e+03
        pdb=" C4   DT I  60 "    0.004 2.00e-02 2.50e+03
        pdb=" O4   DT I  60 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5   DT I  60 "    0.004 2.00e-02 2.50e+03
        pdb=" C7   DT I  60 "    0.005 2.00e-02 2.50e+03
        pdb=" C6   DT I  60 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.046 5.00e-02 4.00e+02   7.00e-02 7.84e+00
        pdb=" N   PRO G  80 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1581 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2703
        2.78 -     3.31: 11633
        3.31 -     3.84: 27034
        3.84 -     4.37: 31845
        4.37 -     4.90: 45229
  Nonbonded interactions: 118444
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  29 "
            pdb=" OP1  DT I  30 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   GLY K 174 "
            pdb=" OG  SER K 178 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" NE2 GLN G  24 "
            pdb=" OE1 GLN H  44 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.322 3.120
  ... (remaining 118439 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'
}
ncs_group {
  reference = (chain 'B' and resid 24 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 27 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=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.320
  Find NCS groups from input model:        0.120
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
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      :  0.005   0.097  14254  Z= 0.222
  Angle     :  0.856  10.276  20486  Z= 0.496
  Chirality :  0.053   0.402   2336
  Planarity :  0.007   0.070   1584
  Dihedral  : 28.695 104.782   6091
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  4.32 %
    Favored  : 94.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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 are not related in a simple way.
  whole: -2.05 (0.23), residues: 925
  helix: -1.01 (0.18), residues: 588
  sheet: -0.37 (0.82), residues: 41
  loop : -1.97 (0.29), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H  96 
 TYR   0.039   0.002   TYR G  50 
 PHE   0.025   0.002   PHE K  99 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 (14254)
  covalent geometry    : angle       0.85562 (20486)
  hydrogen bonds       : bond        0.12750 (  840)
  hydrogen bonds       : angle       5.17632 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 192
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.7946 (t0) cc_final: 0.7506 (t70)
REVERT: B   25 ASN cc_start: 0.8125 (m-40) cc_final: 0.7878 (m110)
REVERT: C   36 LYS cc_start: 0.8709 (mmtp) cc_final: 0.8461 (mmmm)
REVERT: C   74 LYS cc_start: 0.8764 (mppt) cc_final: 0.8531 (mptt)
REVERT: E  106 ASP cc_start: 0.7443 (m-30) cc_final: 0.7178 (m-30)
REVERT: F   74 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7767 (mt-10)
REVERT: G   91 GLU cc_start: 0.8047 (tt0) cc_final: 0.7818 (tt0)
REVERT: H   33 SER cc_start: 0.8880 (t) cc_final: 0.8493 (p)
REVERT: H   34 TYR cc_start: 0.8858 (m-80) cc_final: 0.8608 (m-80)
REVERT: K   69 ASN cc_start: 0.7863 (t0) cc_final: 0.6762 (m110)
REVERT: K  121 MET cc_start: 0.7527 (tpt) cc_final: 0.7033 (mtm)
  outliers start: 7
  outliers final: 1
  residues processed: 196
  average time/residue: 0.1470
  time to fit residues: 38.5606
Evaluate side-chains
  146 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:   20.0000
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    9.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
C 110 ASN
D  92 GLN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
E 113 HIS
F  93 GLN
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 110 ASN
G 112 GLN
** H  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  95 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.090518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.054582 restraints weight = 38327.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 2.04
r_work: 0.2644 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14254  Z= 0.184
  Angle     :  0.605   6.471  20486  Z= 0.359
  Chirality :  0.037   0.167   2336
  Planarity :  0.005   0.048   1584
  Dihedral  : 30.999  90.082   4227
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 10.80 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  0.24 (0.26), residues: 925
  helix:  1.04 (0.20), residues: 599
  sheet: -0.10 (0.71), residues: 47
  loop : -1.72 (0.31), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  29 
 TYR   0.017   0.002   TYR K 231 
 PHE   0.013   0.001   PHE K  99 
 HIS   0.008   0.001   HIS D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (14254)
  covalent geometry    : angle       0.60542 (20486)
  hydrogen bonds       : bond        0.03919 (  840)
  hydrogen bonds       : angle       3.36802 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 161
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9044 (pm20) cc_final: 0.8668 (pm20)
REVERT: A   81 ASP cc_start: 0.8697 (t0) cc_final: 0.8325 (t70)
REVERT: B   25 ASN cc_start: 0.8264 (m-40) cc_final: 0.7958 (m110)
REVERT: C   74 LYS cc_start: 0.9114 (mppt) cc_final: 0.8873 (mptt)
REVERT: E   76 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8340 (tp-100)
REVERT: F   74 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8438 (mt-10)
REVERT: H   30 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7875 (mtp85)
REVERT: H   33 SER cc_start: 0.8938 (t) cc_final: 0.8708 (p)
REVERT: H   42 LEU cc_start: 0.9459 (tp) cc_final: 0.9238 (tp)
REVERT: K   69 ASN cc_start: 0.7870 (t0) cc_final: 0.6348 (m110)
  outliers start: 11
  outliers final: 7
  residues processed: 165
  average time/residue: 0.1336
  time to fit residues: 30.2243
Evaluate side-chains
  147 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain K residue  164 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0980
   chunk 43 optimal weight:    3.9990
   chunk 104 optimal weight:   50.0000
   chunk 87 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
C 110 ASN
E  76 GLN
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 110 ASN
G 112 GLN
K 159 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.090861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.054686 restraints weight = 38471.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 2.04
r_work: 0.2648 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14254  Z= 0.171
  Angle     :  0.577   7.090  20486  Z= 0.345
  Chirality :  0.036   0.179   2336
  Planarity :  0.004   0.042   1584
  Dihedral  : 30.501  88.661   4226
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.34 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  1.16 (0.27), residues: 925
  helix:  1.82 (0.20), residues: 599
  sheet:  0.03 (0.70), residues: 47
  loop : -1.49 (0.33), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  40 
 TYR   0.012   0.001   TYR K 139 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.002   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (14254)
  covalent geometry    : angle       0.57732 (20486)
  hydrogen bonds       : bond        0.03581 (  840)
  hydrogen bonds       : angle       3.11934 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9118 (pm20) cc_final: 0.8692 (pm20)
REVERT: A   81 ASP cc_start: 0.8695 (t0) cc_final: 0.8371 (t70)
REVERT: B   25 ASN cc_start: 0.8547 (m-40) cc_final: 0.8318 (m110)
REVERT: F   74 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8492 (mt-10)
REVERT: H   28 LYS cc_start: 0.7609 (ptmt) cc_final: 0.7399 (pttp)
REVERT: H   30 ARG cc_start: 0.8308 (mtp85) cc_final: 0.8044 (mtp85)
REVERT: H   33 SER cc_start: 0.8931 (t) cc_final: 0.8719 (p)
REVERT: H   42 LEU cc_start: 0.9396 (tp) cc_final: 0.9170 (tp)
REVERT: H   48 ASP cc_start: 0.8025 (p0) cc_final: 0.7809 (p0)
REVERT: K   69 ASN cc_start: 0.8051 (t0) cc_final: 0.6409 (m110)
REVERT: K  121 MET cc_start: 0.8312 (tpt) cc_final: 0.7534 (mtm)
  outliers start: 17
  outliers final: 9
  residues processed: 164
  average time/residue: 0.1293
  time to fit residues: 29.7763
Evaluate side-chains
  151 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 142
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain H residue   57 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 111 optimal weight:   30.0000
   chunk 34 optimal weight:    0.9990
   chunk 112 optimal weight:    2.9990
   chunk 98 optimal weight:    8.9990
   chunk 18 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 99 optimal weight:   50.0000
   chunk 12 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
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**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.090633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.054334 restraints weight = 38438.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.2840 rms_B_bonded: 2.00
r_work: 0.2629 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14254  Z= 0.184
  Angle     :  0.576   7.729  20486  Z= 0.341
  Chirality :  0.036   0.174   2336
  Planarity :  0.004   0.041   1584
  Dihedral  : 30.372  88.384   4226
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.12 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  1.52 (0.27), residues: 925
  helix:  2.11 (0.21), residues: 599
  sheet:  0.31 (0.72), residues: 47
  loop : -1.39 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  83 
 TYR   0.012   0.001   TYR G  57 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.002   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (14254)
  covalent geometry    : angle       0.57562 (20486)
  hydrogen bonds       : bond        0.03548 (  840)
  hydrogen bonds       : angle       3.05502 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9080 (pm20) cc_final: 0.8686 (pm20)
REVERT: A   81 ASP cc_start: 0.8678 (t0) cc_final: 0.8360 (t70)
REVERT: B   25 ASN cc_start: 0.8611 (m-40) cc_final: 0.8391 (m110)
REVERT: D   30 ARG cc_start: 0.8105 (mtm110) cc_final: 0.7812 (mtm180)
REVERT: F   74 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8468 (mt-10)
REVERT: H   28 LYS cc_start: 0.7528 (ptmt) cc_final: 0.7038 (pttt)
REVERT: H   30 ARG cc_start: 0.8389 (mtp85) cc_final: 0.8031 (mtp85)
REVERT: H   42 LEU cc_start: 0.9423 (tp) cc_final: 0.9198 (tp)
REVERT: H   48 ASP cc_start: 0.8037 (p0) cc_final: 0.7824 (p0)
REVERT: K   69 ASN cc_start: 0.7901 (t0) cc_final: 0.6212 (m110)
REVERT: K  121 MET cc_start: 0.8310 (tpt) cc_final: 0.7460 (mpp)
  outliers start: 16
  outliers final: 11
  residues processed: 161
  average time/residue: 0.1388
  time to fit residues: 30.6218
Evaluate side-chains
  152 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain H residue   57 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 54 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 106 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   chunk 111 optimal weight:   30.0000
   chunk 39 optimal weight:    0.6980
   chunk 91 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.090614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.053903 restraints weight = 38720.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 2.00
r_work: 0.2623 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14254  Z= 0.192
  Angle     :  0.580   7.111  20486  Z= 0.342
  Chirality :  0.037   0.232   2336
  Planarity :  0.004   0.040   1584
  Dihedral  : 30.299  88.034   4226
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.28 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  1.65 (0.28), residues: 925
  helix:  2.16 (0.21), residues: 605
  sheet:  0.41 (0.72), residues: 47
  loop : -1.31 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  83 
 TYR   0.014   0.001   TYR K 139 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.003   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (14254)
  covalent geometry    : angle       0.57961 (20486)
  hydrogen bonds       : bond        0.03550 (  840)
  hydrogen bonds       : angle       3.04228 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9077 (pm20) cc_final: 0.8650 (pm20)
REVERT: A   81 ASP cc_start: 0.8653 (t0) cc_final: 0.8349 (t70)
REVERT: B   25 ASN cc_start: 0.8782 (m-40) cc_final: 0.8506 (m110)
REVERT: D  102 GLU cc_start: 0.7750 (tp30) cc_final: 0.7541 (tp30)
REVERT: F   53 GLU cc_start: 0.7682 (tt0) cc_final: 0.7454 (tt0)
REVERT: F   74 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8468 (mt-10)
REVERT: H   28 LYS cc_start: 0.7625 (ptmt) cc_final: 0.7166 (pttt)
REVERT: H   42 LEU cc_start: 0.9460 (tp) cc_final: 0.9259 (tp)
REVERT: K   64 VAL cc_start: 0.8199 (OUTLIER) cc_final: 0.7697 (p)
REVERT: K   69 ASN cc_start: 0.7642 (t0) cc_final: 0.7114 (t0)
REVERT: K  121 MET cc_start: 0.8428 (tpt) cc_final: 0.7559 (mpp)
REVERT: K  159 ASN cc_start: 0.7790 (t0) cc_final: 0.7396 (m-40)
  outliers start: 19
  outliers final: 12
  residues processed: 160
  average time/residue: 0.1412
  time to fit residues: 31.0447
Evaluate side-chains
  153 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 104 optimal weight:   40.0000
   chunk 31 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 106 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 95 optimal weight:    5.9990
   chunk 59 optimal weight:    0.5980
   chunk 86 optimal weight:    7.9990
   chunk 68 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0770
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.092254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.056092 restraints weight = 38275.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 1.97
r_work: 0.2679 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14254  Z= 0.148
  Angle     :  0.565   7.159  20486  Z= 0.335
  Chirality :  0.035   0.239   2336
  Planarity :  0.004   0.043   1584
  Dihedral  : 30.033  89.122   4226
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 18.55 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  1.92 (0.28), residues: 925
  helix:  2.40 (0.21), residues: 605
  sheet:  0.51 (0.72), residues: 47
  loop : -1.27 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  30 
 TYR   0.019   0.001   TYR K 224 
 PHE   0.011   0.001   PHE E  67 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (14254)
  covalent geometry    : angle       0.56460 (20486)
  hydrogen bonds       : bond        0.03366 (  840)
  hydrogen bonds       : angle       2.87713 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 154
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9064 (pm20) cc_final: 0.8673 (pm20)
REVERT: A   76 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8531 (mm-40)
REVERT: A   81 ASP cc_start: 0.8607 (t0) cc_final: 0.8273 (t0)
REVERT: B   25 ASN cc_start: 0.8780 (m-40) cc_final: 0.8504 (m110)
REVERT: D   73 GLU cc_start: 0.8976 (tp30) cc_final: 0.8748 (tp30)
REVERT: D   86 ILE cc_start: 0.9564 (mt) cc_final: 0.9331 (mt)
REVERT: F   74 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8435 (mt-10)
REVERT: H   28 LYS cc_start: 0.7608 (ptmt) cc_final: 0.7166 (pttt)
REVERT: H   30 ARG cc_start: 0.8278 (mtp85) cc_final: 0.8025 (mtp85)
REVERT: H   42 LEU cc_start: 0.9396 (tp) cc_final: 0.9193 (tp)
REVERT: K   64 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7803 (p)
REVERT: K   69 ASN cc_start: 0.7545 (t0) cc_final: 0.5608 (m110)
REVERT: K  121 MET cc_start: 0.8380 (tpt) cc_final: 0.7588 (mpp)
REVERT: K  159 ASN cc_start: 0.7490 (t0) cc_final: 0.7247 (m110)
  outliers start: 12
  outliers final: 7
  residues processed: 161
  average time/residue: 0.1465
  time to fit residues: 32.3145
Evaluate side-chains
  147 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   71 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 52 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   chunk 8 optimal weight:    4.9990
   chunk 96 optimal weight:    5.9990
   chunk 105 optimal weight:   20.0000
   chunk 74 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 101 optimal weight:   50.0000
   chunk 85 optimal weight:   10.0000
   chunk 33 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   overall best weight:    3.0986

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN
K 225 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.089030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.052026 restraints weight = 38303.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.2777 rms_B_bonded: 1.95
r_work: 0.2569 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8725
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.072  14254  Z= 0.300
  Angle     :  0.646   9.862  20486  Z= 0.372
  Chirality :  0.040   0.238   2336
  Planarity :  0.004   0.039   1584
  Dihedral  : 30.599  89.719   4226
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.70 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  1.47 (0.27), residues: 925
  helix:  2.02 (0.21), residues: 605
  sheet:  0.32 (0.72), residues: 47
  loop : -1.37 (0.34), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K 220 
 TYR   0.028   0.002   TYR K 224 
 PHE   0.010   0.001   PHE E 104 
 HIS   0.004   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00682 (14254)
  covalent geometry    : angle       0.64633 (20486)
  hydrogen bonds       : bond        0.04043 (  840)
  hydrogen bonds       : angle       3.28618 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9083 (pm20) cc_final: 0.8617 (pm20)
REVERT: A   76 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8639 (mm-40)
REVERT: A   81 ASP cc_start: 0.8697 (t0) cc_final: 0.8423 (t70)
REVERT: B   25 ASN cc_start: 0.8859 (m110) cc_final: 0.8641 (m110)
REVERT: H   28 LYS cc_start: 0.7593 (ptmt) cc_final: 0.7198 (pttt)
REVERT: H   30 ARG cc_start: 0.8374 (mtp85) cc_final: 0.8153 (mtp85)
REVERT: K  121 MET cc_start: 0.8534 (tpt) cc_final: 0.7574 (mpp)
  outliers start: 16
  outliers final: 13
  residues processed: 148
  average time/residue: 0.1400
  time to fit residues: 28.2082
Evaluate side-chains
  144 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain K residue   71 VAL
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 102 optimal weight:    6.9990
   chunk 105 optimal weight:   30.0000
   chunk 36 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 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 = 0.3750 r_free = 0.3750 target = 0.091019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.054665 restraints weight = 37999.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 1.96
r_work: 0.2641 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14254  Z= 0.162
  Angle     :  0.589   8.177  20486  Z= 0.346
  Chirality :  0.036   0.209   2336
  Planarity :  0.004   0.039   1584
  Dihedral  : 30.182  87.785   4226
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 20.58 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  1.75 (0.27), residues: 925
  helix:  2.28 (0.21), residues: 605
  sheet:  0.33 (0.70), residues: 47
  loop : -1.34 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 220 
 TYR   0.015   0.001   TYR G  57 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.003   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (14254)
  covalent geometry    : angle       0.58872 (20486)
  hydrogen bonds       : bond        0.03444 (  840)
  hydrogen bonds       : angle       3.01442 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9079 (pm20) cc_final: 0.8651 (pm20)
REVERT: A   81 ASP cc_start: 0.8650 (t0) cc_final: 0.8324 (t0)
REVERT: B   25 ASN cc_start: 0.8902 (m110) cc_final: 0.8622 (m110)
REVERT: F   74 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8468 (mt-10)
REVERT: H   28 LYS cc_start: 0.7614 (ptmt) cc_final: 0.7221 (pttt)
REVERT: H   30 ARG cc_start: 0.8354 (mtp85) cc_final: 0.8146 (mtp85)
REVERT: H   43 LYS cc_start: 0.9198 (mmtm) cc_final: 0.8982 (mptt)
REVERT: K  121 MET cc_start: 0.8467 (tpt) cc_final: 0.7569 (mpp)
REVERT: K  159 ASN cc_start: 0.9147 (t0) cc_final: 0.8909 (t0)
  outliers start: 11
  outliers final: 7
  residues processed: 154
  average time/residue: 0.1358
  time to fit residues: 28.8361
Evaluate side-chains
  142 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 135
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   chunk 107 optimal weight:    7.9990
   chunk 3 optimal weight:    0.4980
   chunk 23 optimal weight:    4.9990
   chunk 75 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 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 = 0.3743 r_free = 0.3743 target = 0.090569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.054124 restraints weight = 38568.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 1.97
r_work: 0.2628 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.3293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14254  Z= 0.189
  Angle     :  0.608   9.972  20486  Z= 0.353
  Chirality :  0.036   0.217   2336
  Planarity :  0.004   0.039   1584
  Dihedral  : 30.200  87.565   4226
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 20.71 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  1.73 (0.27), residues: 925
  helix:  2.26 (0.21), residues: 605
  sheet:  0.26 (0.69), residues: 47
  loop : -1.33 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  83 
 TYR   0.017   0.002   TYR K 195 
 PHE   0.014   0.001   PHE K  99 
 HIS   0.002   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (14254)
  covalent geometry    : angle       0.60803 (20486)
  hydrogen bonds       : bond        0.03569 (  840)
  hydrogen bonds       : angle       3.04562 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9083 (pm20) cc_final: 0.8680 (pm20)
REVERT: A   81 ASP cc_start: 0.8595 (t0) cc_final: 0.8244 (t0)
REVERT: B   25 ASN cc_start: 0.8910 (m110) cc_final: 0.8640 (m110)
REVERT: E   90 MET cc_start: 0.8909 (mmm) cc_final: 0.8570 (mmp)
REVERT: F   74 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8487 (mt-10)
REVERT: F   84 MET cc_start: 0.8906 (mmm) cc_final: 0.8640 (tpt)
REVERT: H   28 LYS cc_start: 0.7644 (ptmt) cc_final: 0.7247 (pttt)
REVERT: H   30 ARG cc_start: 0.8366 (mtp85) cc_final: 0.8156 (mtp85)
REVERT: K  121 MET cc_start: 0.8528 (tpt) cc_final: 0.7642 (mpp)
REVERT: K  159 ASN cc_start: 0.9140 (t0) cc_final: 0.8852 (t0)
  outliers start: 14
  outliers final: 12
  residues processed: 144
  average time/residue: 0.1232
  time to fit residues: 24.5475
Evaluate side-chains
  143 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 79 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 81 optimal weight:    6.9990
   chunk 57 optimal weight:    0.8980
   chunk 9 optimal weight:    8.9990
   chunk 105 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 106 optimal weight:    8.9990
   chunk 110 optimal weight:   20.0000
   chunk 75 optimal weight:    6.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  85 GLN
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.087620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.050614 restraints weight = 38698.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.2740 rms_B_bonded: 2.01
r_work: 0.2530 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.3467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.093  14254  Z= 0.386
  Angle     :  0.713   8.420  20486  Z= 0.405
  Chirality :  0.043   0.208   2336
  Planarity :  0.005   0.039   1584
  Dihedral  : 30.919  88.980   4226
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 21.09 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  1.09 (0.27), residues: 925
  helix:  1.75 (0.21), residues: 606
  sheet: -0.14 (0.71), residues: 49
  loop : -1.52 (0.33), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  30 
 TYR   0.016   0.002   TYR G  39 
 PHE   0.011   0.002   PHE E 104 
 HIS   0.006   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00885 (14254)
  covalent geometry    : angle       0.71341 (20486)
  hydrogen bonds       : bond        0.04595 (  840)
  hydrogen bonds       : angle       3.44180 ( 2125)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9101 (pm20) cc_final: 0.8654 (pm20)
REVERT: A   81 ASP cc_start: 0.8741 (t0) cc_final: 0.8496 (t70)
REVERT: B   25 ASN cc_start: 0.8921 (m110) cc_final: 0.8622 (m110)
REVERT: E  120 MET cc_start: 0.8863 (mmt) cc_final: 0.8604 (mtt)
REVERT: F   84 MET cc_start: 0.8954 (mmm) cc_final: 0.8686 (tpt)
REVERT: G  104 GLN cc_start: 0.9006 (mm110) cc_final: 0.8564 (mm110)
REVERT: H   28 LYS cc_start: 0.7636 (ptmt) cc_final: 0.7296 (pttt)
REVERT: H   39 TYR cc_start: 0.8493 (t80) cc_final: 0.8082 (t80)
REVERT: K  121 MET cc_start: 0.8694 (tpt) cc_final: 0.7703 (mpp)
REVERT: K  159 ASN cc_start: 0.9076 (t0) cc_final: 0.8804 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 145
  average time/residue: 0.1345
  time to fit residues: 26.9666
Evaluate side-chains
  142 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 90 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  85 GLN
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.090169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.053630 restraints weight = 38393.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 1.97
r_work: 0.2621 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.3446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14254  Z= 0.174
  Angle     :  0.613   8.790  20486  Z= 0.355
  Chirality :  0.036   0.207   2336
  Planarity :  0.004   0.049   1584
  Dihedral  : 30.269  88.236   4226
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 22.24 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  1.52 (0.27), residues: 925
  helix:  2.12 (0.21), residues: 605
  sheet: -0.25 (0.74), residues: 44
  loop : -1.36 (0.34), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  83 
 TYR   0.016   0.002   TYR K 139 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.003   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (14254)
  covalent geometry    : angle       0.61296 (20486)
  hydrogen bonds       : bond        0.03555 (  840)
  hydrogen bonds       : angle       3.07698 ( 2125)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3050.31 seconds
wall clock time: 52 minutes 52.06 seconds (3172.06 seconds total)