Starting phenix.real_space_refine
on Wed Feb  4 16:10:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d3r_46545/02_2026/9d3r_46545.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d3r_46545/02_2026/9d3r_46545.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d3r_46545/02_2026/9d3r_46545.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d3r_46545/02_2026/9d3r_46545.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d3r_46545/02_2026/9d3r_46545.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d3r_46545/02_2026/9d3r_46545.cif"
  }
  resolution = 3.3
  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=   0.033
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      14      5.16       5
     C    6540      2.51       5
     N    2227      2.21       5
     O    2787      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11858
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 792
          Classifications: {'peptide': 97}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 636
          Classifications: {'peptide': 81}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 749
          Classifications: {'peptide': 96}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "E"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 730
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 730
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 734
    Chain: "I"
      Number of atoms: 2978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2978
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2967
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "C"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 791
          Classifications: {'peptide': 104}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "G"
      Number of atoms: 777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 777
          Classifications: {'peptide': 102}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 2.69, per 1000 atoms: 0.23
  Number of scatterers: 11858
  At special positions: 0
  Unit cell: (116.875, 82.28, 118.745, 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      14     16.00
     P     290     15.00
     O    2787      8.00
     N    2227      7.00
     C    6540      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: 1.10
  Conformation dependent library (CDL) restraints added in 383.0 milliseconds
  

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1398

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      72.5% alpha, 2.9% beta
      140 base pairs and 239 stacking pairs defined.
    Time for finding SS restraints: 1.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 56
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 4.183A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.879A  pdb=" N   ALA A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.517A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 56 through 85
      removed outlier: 3.884A  pdb=" N   MET D  62 " --> pdb=" O   ALA D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 124
    Processing helix  chain 'E' and resid 44 through 56
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.749A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.966A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 50 through 76
      removed outlier: 3.705A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.570A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.538A  pdb=" N   LYS H  43 " --> pdb=" O   VAL H  39 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 67
    Processing helix  chain 'H' and resid 68 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.500A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.782A  pdb=" N   SER H 112 " --> pdb=" O   LYS H 108 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   GLU H 113 " --> pdb=" O   HIS H 109 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   THR H 122 " --> pdb=" O   VAL H 118 " (cutoff:3.500A)
    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: 4.434A  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 'G' and resid 17 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.523A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.967A  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 97
      removed outlier: 6.601A  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 'D' and resid 53 through 54
      removed outlier: 6.807A  pdb=" N   GLY D  53 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.773A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98
      removed outlier: 6.370A  pdb=" N   THR F  96 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54
      removed outlier: 7.180A  pdb=" N   GLY H  53 " --> pdb=" O   ILE G  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89

    394 hydrogen bonds defined for protein.
    1172 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      366 hydrogen bonds
      732 hydrogen bond angles
      0 basepair planarities
      140 basepair parallelities
      239 stacking parallelities
  Total time for adding SS restraints: 2.31

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        0.94 -     1.12: 1
        1.12 -     1.29: 1228
        1.29 -     1.47: 6187
        1.47 -     1.64: 5217
        1.64 -     1.82: 27
  Bond restraints: 12660
  Sorted by residual:
  bond pdb=" CB  PRO G  26 "
       pdb=" CG  PRO G  26 "
    ideal  model  delta    sigma   weight residual
    1.492  0.942  0.550 5.00e-02 4.00e+02 1.21e+02
  bond pdb=" CG  PRO C  48 "
       pdb=" CD  PRO C  48 "
    ideal  model  delta    sigma   weight residual
    1.503  1.189  0.314 3.40e-02 8.65e+02 8.52e+01
  bond pdb=" CG  PRO G  26 "
       pdb=" CD  PRO G  26 "
    ideal  model  delta    sigma   weight residual
    1.503  1.211  0.292 3.40e-02 8.65e+02 7.35e+01
  bond pdb=" CG  PRO A  66 "
       pdb=" CD  PRO A  66 "
    ideal  model  delta    sigma   weight residual
    1.503  1.232  0.271 3.40e-02 8.65e+02 6.37e+01
  bond pdb=" N   PRO C  48 "
       pdb=" CD  PRO C  48 "
    ideal  model  delta    sigma   weight residual
    1.473  1.557 -0.084 1.40e-02 5.10e+03 3.64e+01
  ... (remaining 12655 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    11.72: 18337
       11.72 -    23.43: 5
       23.43 -    35.15: 2
       35.15 -    46.87: 0
       46.87 -    58.58: 1
  Bond angle restraints: 18345
  Sorted by residual:
  angle pdb=" CB  PRO G  26 "
        pdb=" CG  PRO G  26 "
        pdb=" CD  PRO G  26 "
      ideal   model   delta    sigma   weight residual
     106.10  164.68  -58.58 3.20e+00 9.77e-02 3.35e+02
  angle pdb=" N   PRO G  26 "
        pdb=" CD  PRO G  26 "
        pdb=" CG  PRO G  26 "
      ideal   model   delta    sigma   weight residual
     103.20   76.33   26.87 1.50e+00 4.44e-01 3.21e+02
  angle pdb=" CA  PRO G  26 "
        pdb=" CB  PRO G  26 "
        pdb=" CG  PRO G  26 "
      ideal   model   delta    sigma   weight residual
     104.50   74.47   30.03 1.90e+00 2.77e-01 2.50e+02
  angle pdb=" CA  PRO C  48 "
        pdb=" N   PRO C  48 "
        pdb=" CD  PRO C  48 "
      ideal   model   delta    sigma   weight residual
     112.00   94.11   17.89 1.40e+00 5.10e-01 1.63e+02
  angle pdb=" CA  PRO A  66 "
        pdb=" N   PRO A  66 "
        pdb=" CD  PRO A  66 "
      ideal   model   delta    sigma   weight residual
     112.00   96.36   15.64 1.40e+00 5.10e-01 1.25e+02
  ... (remaining 18340 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.75: 5307
       34.75 -    69.50: 1488
       69.50 -   104.24: 34
      104.24 -   138.99: 0
      138.99 -   173.74: 2
  Dihedral angle restraints: 6831
    sinusoidal: 4659
      harmonic: 2172
  Sorted by residual:
  dihedral pdb=" N   PRO G  26 "
           pdb=" CG  PRO G  26 "
           pdb=" CD  PRO G  26 "
           pdb=" CB  PRO G  26 "
      ideal   model   delta sinusoidal    sigma   weight residual
      30.00  111.03  -81.03     1      1.50e+01 4.44e-03 3.60e+01
  dihedral pdb=" CA  PRO D 103 "
           pdb=" C   PRO D 103 "
           pdb=" N   GLY D 104 "
           pdb=" CA  GLY D 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.63  -20.37     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" C4'  DA J -17 "
           pdb=" C3'  DA J -17 "
           pdb=" O3'  DA J -17 "
           pdb=" P    DG J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   33.74 -173.74     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 6828 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1991
       0.074 -    0.148: 95
       0.148 -    0.222: 0
       0.222 -    0.296: 1
       0.296 -    0.369: 2
  Chirality restraints: 2089
  Sorted by residual:
  chirality pdb=" CA  PRO C  48 "
            pdb=" N   PRO C  48 "
            pdb=" C   PRO C  48 "
            pdb=" CB  PRO C  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.35    0.37 2.00e-01 2.50e+01 3.41e+00
  chirality pdb=" CA  PRO A  66 "
            pdb=" N   PRO A  66 "
            pdb=" C   PRO A  66 "
            pdb=" CB  PRO A  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.42    0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CB  VAL H 111 "
            pdb=" CA  VAL H 111 "
            pdb=" CG1 VAL H 111 "
            pdb=" CG2 VAL H 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 2086 not shown)

  Planarity restraints: 1318
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  65 "    0.086 5.00e-02 4.00e+02   1.17e-01 2.17e+01
        pdb=" N   PRO A  66 "   -0.201 5.00e-02 4.00e+02
        pdb=" CA  PRO A  66 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A  66 "    0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C  47 "    0.071 5.00e-02 4.00e+02   9.44e-02 1.43e+01
        pdb=" N   PRO C  48 "   -0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO C  48 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO C  48 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA G  47 "   -0.062 5.00e-02 4.00e+02   8.82e-02 1.24e+01
        pdb=" N   PRO G  48 "    0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO G  48 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO G  48 "   -0.050 5.00e-02 4.00e+02
  ... (remaining 1315 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1792
        2.76 -     3.30: 10668
        3.30 -     3.83: 23767
        3.83 -     4.37: 27473
        4.37 -     4.90: 39166
  Nonbonded interactions: 102866
  Sorted by model distance:
  nonbonded pdb=" OG  SER D  64 "
            pdb=" O   GLY F 101 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH2 ARG E 131 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OP1  DA I  58 "
            pdb=" OG1 THR G  76 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   SER H 123 "
            pdb=" OG  SER H 123 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   THR A  58 "
            pdb=" OG1 THR A  58 "
     model   vdw
     2.270 3.040
  ... (remaining 102861 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 39 through 78 or (resid 79 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 80 through 133))
  selection = (chain 'E' and (resid 39 through 80 or (resid 81 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 82 through 93 or (resid 94 through 95 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 96 through 133))
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and ((resid 22 through 23 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 24 through 101 or (resid 102 and (name N or name CA or na \ 
me C or name O ))))
}
ncs_group {
  reference = (chain 'C' and (resid 16 or (resid 17 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 18 through 117))
  selection = (chain 'G' and (resid 16 through 19 or (resid 20 through 21 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 22 through 117))
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123))
  selection = (chain 'H' and ((resid 31 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 32 through 107 or resid 109 through 123))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     13.520
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6881
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      :  0.008   0.550  12660  Z= 0.250
  Angle     :  0.890  58.583  18345  Z= 0.488
  Chirality :  0.036   0.369   2089
  Planarity :  0.007   0.117   1318
  Dihedral  : 29.305 173.740   5433
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 30.84 %
    Favored  : 68.67 %
  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 are not related in a simple way.
  whole:  0.29 (0.30), residues: 735
  helix:  0.97 (0.22), residues: 537
  sheet:  None (None), residues: 0
  loop : -1.92 (0.37), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  86 
 TYR   0.041   0.002   TYR E  54 
 PHE   0.021   0.002   PHE C  25 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00788 (12660)
  covalent geometry    : angle       0.88955 (18345)
  hydrogen bonds       : bond        0.08191 (  760)
  hydrogen bonds       : angle       3.94698 ( 1904)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 103
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.7275 (mmt-90) cc_final: 0.6833 (mmt90)
REVERT: D   62 MET cc_start: 0.7634 (tpp) cc_final: 0.7412 (mmt)
  outliers start: 3
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1558
  time to fit residues: 21.3083
Evaluate side-chains
  98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.203189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.158479 restraints weight = 39934.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.4053 rms_B_bonded: 2.70
r_work: 0.3865 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3867
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3867 r_free = 0.3867    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3867 r_free = 0.3867    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3867
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6842
moved from start:          0.0684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12660  Z= 0.152
  Angle     :  0.579  11.851  18345  Z= 0.341
  Chirality :  0.034   0.171   2089
  Planarity :  0.005   0.060   1318
  Dihedral  : 31.214 173.945   3977
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 28.08 %
    Favored  : 68.51 %
  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 are not related in a simple way.
  whole:  0.72 (0.30), residues: 735
  helix:  1.25 (0.22), residues: 539
  sheet:  None (None), residues: 0
  loop : -1.66 (0.38), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  86 
 TYR   0.028   0.002   TYR E  54 
 PHE   0.015   0.002   PHE E  67 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (12660)
  covalent geometry    : angle       0.57919 (18345)
  hydrogen bonds       : bond        0.04193 (  760)
  hydrogen bonds       : angle       3.23411 ( 1904)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  129 ARG cc_start: 0.7428 (mmt-90) cc_final: 0.7013 (mmt90)
REVERT: F   58 LEU cc_start: 0.8508 (tp) cc_final: 0.8284 (tp)
  outliers start: 21
  outliers final: 8
  residues processed: 132
  average time/residue: 0.1375
  time to fit residues: 24.1956
Evaluate side-chains
  111 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain H residue   40 TYR
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   90 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 67 optimal weight:   20.0000
   chunk 71 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9990
   chunk 92 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 88 optimal weight:    9.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.198889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.152201 restraints weight = 45435.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 3.04
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3970
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3970 r_free = 0.3970    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3970 r_free = 0.3970    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3970
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6822
moved from start:          0.1208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12660  Z= 0.204
  Angle     :  0.632   7.313  18345  Z= 0.365
  Chirality :  0.037   0.179   2089
  Planarity :  0.005   0.061   1318
  Dihedral  : 31.552 172.680   3977
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  : 26.46 %
    Favored  : 67.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.36 (0.30), residues: 735
  helix:  0.95 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.76 (0.39), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  86 
 TYR   0.027   0.002   TYR E  54 
 PHE   0.014   0.002   PHE E  67 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 (12660)
  covalent geometry    : angle       0.63247 (18345)
  hydrogen bonds       : bond        0.05296 (  760)
  hydrogen bonds       : angle       3.49423 ( 1904)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 112
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.7914 (tt0) cc_final: 0.7678 (tt0)
REVERT: A  129 ARG cc_start: 0.7011 (mmt-90) cc_final: 0.6676 (mmt90)
REVERT: D   40 TYR cc_start: 0.5668 (OUTLIER) cc_final: 0.5001 (m-80)
REVERT: D   80 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7510 (mp)
REVERT: E   84 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.7279 (t80)
REVERT: F   53 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6220 (mp0)
REVERT: H   84 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.7125 (t0)
REVERT: C   41 GLU cc_start: 0.6854 (tm-30) cc_final: 0.6642 (tm-30)
REVERT: C   83 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7666 (mp)
REVERT: C   91 GLU cc_start: 0.6672 (pm20) cc_final: 0.5591 (tp30)
REVERT: G  101 THR cc_start: 0.8324 (p) cc_final: 0.7998 (p)
  outliers start: 40
  outliers final: 21
  residues processed: 143
  average time/residue: 0.1259
  time to fit residues: 24.0531
Evaluate side-chains
  129 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   53 GLU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   84 ASN
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain H residue   98 VAL
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain G residue   97 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 65 optimal weight:   20.0000
   chunk 12 optimal weight:    4.9990
   chunk 22 optimal weight:    8.9990
   chunk 66 optimal weight:   20.0000
   chunk 21 optimal weight:    0.0770
   chunk 70 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 2 optimal weight:    7.9990
   chunk 44 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    3.6146

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.197660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.152089 restraints weight = 36499.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3976 rms_B_bonded: 2.48
r_work: 0.3802 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3805
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3805 r_free = 0.3805    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3805 r_free = 0.3805    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3805
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6979
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12660  Z= 0.218
  Angle     :  0.639   8.048  18345  Z= 0.368
  Chirality :  0.038   0.196   2089
  Planarity :  0.005   0.061   1318
  Dihedral  : 31.735 171.370   3977
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 28.08 %
    Favored  : 65.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.13 (0.30), residues: 735
  helix:  0.78 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.83 (0.39), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  79 
 TYR   0.023   0.002   TYR E  54 
 PHE   0.015   0.002   PHE B 100 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 (12660)
  covalent geometry    : angle       0.63903 (18345)
  hydrogen bonds       : bond        0.05410 (  760)
  hydrogen bonds       : angle       3.52132 ( 1904)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 107
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7276 (pm20)
REVERT: A  129 ARG cc_start: 0.7350 (mmt-90) cc_final: 0.6903 (mmt90)
REVERT: B   92 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7504 (ptm-80)
REVERT: D   40 TYR cc_start: 0.5901 (OUTLIER) cc_final: 0.5300 (m-80)
REVERT: D   80 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7911 (mp)
REVERT: E   65 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7537 (mm)
REVERT: E  131 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7776 (ptp-170)
REVERT: F   53 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6409 (mp0)
REVERT: F   93 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.5970 (mp10)
REVERT: H   40 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6717 (m-80)
REVERT: H   84 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.7283 (t0)
REVERT: C   39 TYR cc_start: 0.4834 (m-10) cc_final: 0.4585 (m-80)
  outliers start: 37
  outliers final: 20
  residues processed: 138
  average time/residue: 0.1350
  time to fit residues: 24.6177
Evaluate side-chains
  127 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 97
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   53 GLU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   40 TYR
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   84 ASN
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   97 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   chunk 32 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 94 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 93 optimal weight:    0.7980
   chunk 74 optimal weight:   10.0000
   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  85 GLN
B  25 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.202162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.157556 restraints weight = 26954.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.4043 rms_B_bonded: 2.20
r_work: 0.3898 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3907
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3907 r_free = 0.3907    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3907 r_free = 0.3907    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3907
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6819
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12660  Z= 0.147
  Angle     :  0.563   6.851  18345  Z= 0.334
  Chirality :  0.034   0.193   2089
  Planarity :  0.004   0.054   1318
  Dihedral  : 31.372 173.208   3977
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 28.57 %
    Favored  : 66.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.91 (0.30), residues: 735
  helix:  1.37 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -1.68 (0.40), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  36 
 TYR   0.012   0.001   TYR G  57 
 PHE   0.014   0.002   PHE E  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (12660)
  covalent geometry    : angle       0.56296 (18345)
  hydrogen bonds       : bond        0.04169 (  760)
  hydrogen bonds       : angle       3.14373 ( 1904)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7175 (pm20)
REVERT: A   87 SER cc_start: 0.7955 (t) cc_final: 0.7682 (t)
REVERT: A  129 ARG cc_start: 0.7382 (mmt-90) cc_final: 0.7089 (mmt90)
REVERT: E   65 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7433 (mm)
REVERT: E   84 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7376 (t80)
REVERT: E  104 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.6383 (m-80)
REVERT: C   41 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6946 (tm-30)
  outliers start: 31
  outliers final: 13
  residues processed: 134
  average time/residue: 0.1221
  time to fit residues: 22.0788
Evaluate side-chains
  120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain G residue   97 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 84 optimal weight:    6.9990
   chunk 89 optimal weight:    8.9990
   chunk 56 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9980
   chunk 51 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9980
   chunk 82 optimal weight:    9.9990
   chunk 30 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   overall best weight:    2.1182

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  24 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 = 0.4576 r_free = 0.4576 target = 0.200403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.154431 restraints weight = 42504.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 2.89
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4015 r_free = 0.4015    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4015 r_free = 0.4015    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6781
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12660  Z= 0.170
  Angle     :  0.588   7.122  18345  Z= 0.343
  Chirality :  0.035   0.197   2089
  Planarity :  0.004   0.061   1318
  Dihedral  : 31.417 172.257   3977
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 29.06 %
    Favored  : 66.07 %
  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 are not related in a simple way.
  whole:  0.81 (0.30), residues: 735
  helix:  1.27 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.60 (0.40), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 116 
 TYR   0.018   0.001   TYR E  54 
 PHE   0.012   0.002   PHE E  67 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (12660)
  covalent geometry    : angle       0.58770 (18345)
  hydrogen bonds       : bond        0.04648 (  760)
  hydrogen bonds       : angle       3.21772 ( 1904)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7165 (pm20)
REVERT: B   92 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7152 (ptm-80)
REVERT: E   65 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7140 (mm)
REVERT: E   84 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.7176 (t80)
REVERT: E  131 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7870 (ptp-170)
REVERT: F   50 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6764 (pt)
REVERT: F   53 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.6001 (mp0)
REVERT: C   41 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6755 (tm-30)
  outliers start: 30
  outliers final: 19
  residues processed: 130
  average time/residue: 0.1301
  time to fit residues: 22.5607
Evaluate side-chains
  124 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   69 ILE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   53 GLU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   97 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    0.0170
   chunk 12 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 83 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 72 optimal weight:    8.9990
   chunk 70 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.9422

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.203316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.159352 restraints weight = 38831.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 2.71
r_work: 0.3869 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3879 r_free = 0.3879    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3879 r_free = 0.3879    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6829
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12660  Z= 0.144
  Angle     :  0.551   6.982  18345  Z= 0.327
  Chirality :  0.034   0.209   2089
  Planarity :  0.004   0.058   1318
  Dihedral  : 31.244 172.906   3977
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 30.52 %
    Favored  : 65.58 %
  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 are not related in a simple way.
  whole:  1.18 (0.31), residues: 735
  helix:  1.57 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.57 (0.40), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  86 
 TYR   0.009   0.001   TYR G  57 
 PHE   0.012   0.001   PHE E  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (12660)
  covalent geometry    : angle       0.55123 (18345)
  hydrogen bonds       : bond        0.04079 (  760)
  hydrogen bonds       : angle       3.05923 ( 1904)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7318 (pm20)
REVERT: E   65 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7403 (mm)
REVERT: E   84 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7245 (t80)
REVERT: E  131 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7639 (ptp-170)
REVERT: F   50 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7366 (pt)
REVERT: H   47 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7406 (tm-30)
REVERT: C   41 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6792 (tm-30)
REVERT: C   91 GLU cc_start: 0.6804 (pm20) cc_final: 0.5248 (tp30)
  outliers start: 24
  outliers final: 15
  residues processed: 126
  average time/residue: 0.1273
  time to fit residues: 21.4839
Evaluate side-chains
  118 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   69 ILE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain C residue   85 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 65 optimal weight:   20.0000
   chunk 30 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 52 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 83 optimal weight:    0.7980
   chunk 86 optimal weight:    4.9990
   chunk 97 optimal weight:    9.9990
   chunk 41 optimal weight:    0.6980
   chunk 47 optimal weight:    7.9990
   overall best weight:    2.2784

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

Flipped N/Q/H residues before XYZ refinement:
D  49 HIS
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.200664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.154701 restraints weight = 41469.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.4019 rms_B_bonded: 2.79
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4017 r_free = 0.4017    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4017 r_free = 0.4017    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6778
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  12660  Z= 0.175
  Angle     :  0.598  10.950  18345  Z= 0.347
  Chirality :  0.035   0.216   2089
  Planarity :  0.005   0.062   1318
  Dihedral  : 31.362 172.081   3977
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 30.36 %
    Favored  : 65.26 %
  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 are not related in a simple way.
  whole:  0.90 (0.30), residues: 735
  helix:  1.36 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -1.68 (0.40), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  83 
 TYR   0.018   0.002   TYR E  54 
 PHE   0.013   0.002   PHE E  67 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (12660)
  covalent geometry    : angle       0.59801 (18345)
  hydrogen bonds       : bond        0.04690 (  760)
  hydrogen bonds       : angle       3.18061 ( 1904)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7225 (pm20)
REVERT: E   65 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7157 (mm)
REVERT: E   84 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.7200 (t80)
REVERT: E  131 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7765 (ptp-170)
REVERT: F   50 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7415 (pt)
REVERT: F   53 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5737 (mp0)
REVERT: C   39 TYR cc_start: 0.4654 (m-10) cc_final: 0.4444 (m-80)
REVERT: C   91 GLU cc_start: 0.6812 (pm20) cc_final: 0.5331 (tp30)
  outliers start: 27
  outliers final: 19
  residues processed: 123
  average time/residue: 0.1343
  time to fit residues: 22.0633
Evaluate side-chains
  120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   69 ILE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   53 GLU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   61 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain G residue  104 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 97 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9980
   chunk 78 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** G  24 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 = 0.4585 r_free = 0.4585 target = 0.201145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.156497 restraints weight = 36766.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.4039 rms_B_bonded: 2.53
r_work: 0.3860 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3863
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3863 r_free = 0.3863    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3863 r_free = 0.3863    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3863
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12660  Z= 0.166
  Angle     :  0.595  11.883  18345  Z= 0.345
  Chirality :  0.035   0.213   2089
  Planarity :  0.004   0.060   1318
  Dihedral  : 31.336 171.920   3977
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 29.71 %
    Favored  : 65.26 %
  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 are not related in a simple way.
  whole:  0.87 (0.30), residues: 735
  helix:  1.33 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -1.66 (0.40), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG E  83 
 TYR   0.011   0.001   TYR C  57 
 PHE   0.024   0.002   PHE B 100 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (12660)
  covalent geometry    : angle       0.59459 (18345)
  hydrogen bonds       : bond        0.04570 (  760)
  hydrogen bonds       : angle       3.15887 ( 1904)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 98
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7336 (pm20)
REVERT: E   65 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7382 (mm)
REVERT: E   84 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7363 (t80)
REVERT: E  131 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7685 (ptp-170)
REVERT: F   50 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7486 (pt)
REVERT: F   53 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5870 (mp0)
REVERT: F   93 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.5971 (mp10)
REVERT: C   39 TYR cc_start: 0.4931 (m-10) cc_final: 0.4599 (m-80)
REVERT: C   41 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6748 (tm-30)
  outliers start: 31
  outliers final: 21
  residues processed: 125
  average time/residue: 0.1349
  time to fit residues: 22.6011
Evaluate side-chains
  121 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   69 ILE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   53 GLU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain G residue   59 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 76 optimal weight:   10.0000
   chunk 99 optimal weight:    0.7980
   chunk 46 optimal weight:    0.3980
   chunk 29 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9990
   chunk 57 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** G  24 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 = 0.4595 r_free = 0.4595 target = 0.202105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.157277 restraints weight = 44807.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 3.03
r_work (final): 0.4050
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4047 r_free = 0.4047    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4047 r_free = 0.4047    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6723
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  12660  Z= 0.152
  Angle     :  0.586  10.425  18345  Z= 0.341
  Chirality :  0.034   0.211   2089
  Planarity :  0.004   0.061   1318
  Dihedral  : 31.311 172.026   3977
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 29.87 %
    Favored  : 65.58 %
  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 are not related in a simple way.
  whole:  1.02 (0.30), residues: 735
  helix:  1.45 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.61 (0.40), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  79 
 TYR   0.020   0.001   TYR E  54 
 PHE   0.013   0.002   PHE E  67 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (12660)
  covalent geometry    : angle       0.58623 (18345)
  hydrogen bonds       : bond        0.04377 (  760)
  hydrogen bonds       : angle       3.10473 ( 1904)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7228 (pm20)
REVERT: E   65 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7121 (mm)
REVERT: E  131 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7854 (ptp-170)
REVERT: C   39 TYR cc_start: 0.4628 (m-10) cc_final: 0.4422 (m-80)
REVERT: C   41 GLU cc_start: 0.6808 (tm-30) cc_final: 0.6533 (tm-30)
  outliers start: 28
  outliers final: 22
  residues processed: 124
  average time/residue: 0.1452
  time to fit residues: 24.1590
Evaluate side-chains
  120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   69 ILE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain C residue   31 HIS
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   97 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 16 optimal weight:    9.9990
   chunk 59 optimal weight:   10.0000
   chunk 54 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 82 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 63 optimal weight:   10.0000
   chunk 84 optimal weight:    6.9990
   overall best weight:    3.5786

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

Flipped N/Q/H residues before XYZ refinement:
D  84 ASN
E 113 HIS
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.198625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.152784 restraints weight = 28683.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 2.29
r_work: 0.3845 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3855 r_free = 0.3855    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3855 r_free = 0.3855    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  12660  Z= 0.217
  Angle     :  0.656  10.864  18345  Z= 0.373
  Chirality :  0.038   0.227   2089
  Planarity :  0.005   0.059   1318
  Dihedral  : 31.522 171.148   3977
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 29.87 %
    Favored  : 65.42 %
  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 are not related in a simple way.
  whole:  0.39 (0.30), residues: 735
  helix:  0.97 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.76 (0.39), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  79 
 TYR   0.014   0.002   TYR H  83 
 PHE   0.015   0.002   PHE B 100 
 HIS   0.008   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 (12660)
  covalent geometry    : angle       0.65578 (18345)
  hydrogen bonds       : bond        0.05398 (  760)
  hydrogen bonds       : angle       3.40207 ( 1904)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2505.77 seconds
wall clock time: 43 minutes 31.62 seconds (2611.62 seconds total)