Starting phenix.real_space_refine
on Wed Mar  4 14:53:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e8d_31015/03_2026/7e8d_31015.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e8d_31015/03_2026/7e8d_31015.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e8d_31015/03_2026/7e8d_31015.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e8d_31015/03_2026/7e8d_31015.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e8d_31015/03_2026/7e8d_31015.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e8d_31015/03_2026/7e8d_31015.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     Zn      3      6.06       5
     P     344      5.49       5
     S      36      5.16       5
     C    8248      2.51       5
     N    2766      2.21       5
     O    3455      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14852
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 633
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 833
          Classifications: {'peptide': 109}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 845
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 4, 'TRANS': 99}
    Chain: "F"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 841
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 3504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 3504
          Classifications: {'DNA': 172}
          Link IDs: {'rna3p': 171}
    Chain: "J"
      Number of atoms: 3548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 3548
          Classifications: {'DNA': 172}
          Link IDs: {'rna3p': 171}
    Chain: "K"
      Number of atoms: 1714
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 218, 1709
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 13, 'TRANS': 204}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
      Conformer: "B"
        Number of residues, atoms: 218, 1709
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 13, 'TRANS': 204}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
          bond proxies already assigned to first conformer: 1743
    Chain: "K"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 30
          Unusual residues: {' ZN': 3}
          Classifications: {'peptide': 1, 'undetermined': 3}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  14390  SG  CYS K1144      42.120  51.544  56.429  1.00114.62           S
  ATOM  14749  SG  CYS K1191      42.466  50.214  52.961  1.00118.29           S
  ATOM  14760  SG  CYS K1193      45.111  49.280  55.494  1.00118.84           S
  ATOM  14789  SG  CYS K1198      41.809  47.729  55.847  1.00118.80           S
  ATOM  13361  SG  CYS K1016      58.936  85.318  59.757  1.00 85.99           S
  ATOM  13375  SG  CYS K1018      60.570  83.394  62.687  1.00 92.56           S
  ATOM  13436  SG  CYS K1026      61.418  82.746  59.075  1.00 89.86           S
  ATOM  13480  SG  CYS K1032      58.078  81.605  60.455  1.00 81.97           S
  ATOM  13436  SG  CYS K1026      61.418  82.746  59.075  1.00 89.86           S
  ATOM  13557  SG  CYS K1041      58.478  83.005  56.585  1.00 88.34           S
  ATOM  13596  SG  CYS K1046      61.568  85.205  56.581  1.00 92.31           S
  ATOM  13638  SG  CYS K1052      61.850  81.503  55.483  1.00 93.46           S

  Time building chain proxies: 3.29, per 1000 atoms: 0.22
  Number of scatterers: 14852
  At special positions: 0
  Unit cell: (87.15, 168.49, 142.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      3     29.99
     S      36     16.00
     P     344     15.00
     O    3455      8.00
     N    2766      7.00
     C    8248      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: 1.40
  Conformation dependent library (CDL) restraints added in 371.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K1301 "
        pdb="ZN    ZN K1301 " - pdb=" SG  CYS K1193 "
        pdb="ZN    ZN K1301 " - pdb=" SG  CYS K1191 "
        pdb="ZN    ZN K1301 " - pdb=" SG  CYS K1198 "
        pdb="ZN    ZN K1301 " - pdb=" SG  CYS K1144 "
      pdb="  ZN K1302 "
        pdb="ZN    ZN K1302 " - pdb=" SG  CYS K1026 "
        pdb="ZN    ZN K1302 " - pdb=" SG  CYS K1016 "
        pdb="ZN    ZN K1302 " - pdb=" SG  CYS K1018 "
        pdb="ZN    ZN K1302 " - pdb=" SG  CYS K1032 "
      pdb="  ZN K1303 "
        pdb="ZN    ZN K1303 " - pdb=" SG  CYS K1026 "
        pdb="ZN    ZN K1303 " - pdb=" SG  CYS K1046 "
        pdb="ZN    ZN K1303 " - pdb=" SG  CYS K1041 "
        pdb="ZN    ZN K1303 " - pdb=" SG  CYS K1052 "
      Number of angles added : 18


  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1832

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 14 sheets defined
      58.7% alpha, 6.2% beta
      172 base pairs and 318 stacking pairs defined.
    Time for finding SS restraints: 2.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.730A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    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
      removed outlier: 3.706A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
      removed outlier: 3.842A  pdb=" N   ARG C  20 " --> pdb=" O   THR C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.399A  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 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
      removed outlier: 3.604A  pdb=" N   SER D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.631A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.368A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.688A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'K' and resid 1009 through 1013
      removed outlier: 3.933A  pdb=" N   ILE K1013 " --> pdb=" O   ILE K1010 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1032 through 1037
      removed outlier: 3.803A  pdb=" N   LEU K1037 " --> pdb=" O   LEU K1033 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1098 through 1112
    Processing helix  chain 'K' and resid 1135 through 1140
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.784A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.969A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.661A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.937A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.019A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 992 through 993
    Processing sheet with id=AB3, first strand: chain 'K' and resid 998 through 999
      removed outlier: 7.023A  pdb=" N   LYS K 998 " --> pdb=" O   LEU K1096 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ARG K1126 " --> pdb=" O   ILE K1122 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'K' and resid 1065 through 1069
      removed outlier: 4.770A  pdb=" N   LEU K1077 " --> pdb=" O   LEU K1175 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'K' and resid 1088 through 1092
      removed outlier: 6.726A  pdb=" N   PHE K1088 " --> pdb=" O   ALA K1165 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ALA K1165 " --> pdb=" O   PHE K1088 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   VAL K1161 " --> pdb=" O   TYR K1092 " (cutoff:3.500A)

    447 hydrogen bonds defined for protein.
    1305 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      444 hydrogen bonds
      884 hydrogen bond angles
      0 basepair planarities
      172 basepair parallelities
      318 stacking parallelities
  Total time for adding SS restraints: 3.44

  Time building geometry restraints manager: 1.65 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2521
        1.33 -     1.45: 5349
        1.45 -     1.57: 7222
        1.57 -     1.69: 686
        1.69 -     1.81: 52
  Bond restraints: 15830
  Sorted by residual:
  bond pdb=" C4  SFG K1304 "
       pdb=" C5  SFG K1304 "
    ideal  model  delta    sigma   weight residual
    1.394  1.465 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" C5  SFG K1304 "
       pdb=" C6  SFG K1304 "
    ideal  model  delta    sigma   weight residual
    1.408  1.474 -0.066 2.00e-02 2.50e+03 1.09e+01
  bond pdb=" CA  SFG K1304 "
       pdb=" C   SFG K1304 "
    ideal  model  delta    sigma   weight residual
    1.553  1.496  0.057 2.00e-02 2.50e+03 7.99e+00
  bond pdb=" C4  SFG K1304 "
       pdb=" N9  SFG K1304 "
    ideal  model  delta    sigma   weight residual
    1.377  1.326  0.051 2.00e-02 2.50e+03 6.48e+00
  bond pdb=" C8  SFG K1304 "
       pdb=" N7  SFG K1304 "
    ideal  model  delta    sigma   weight residual
    1.310  1.354 -0.044 2.00e-02 2.50e+03 4.86e+00
  ... (remaining 15825 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 21956
        1.70 -     3.40: 839
        3.40 -     5.10: 53
        5.10 -     6.79: 11
        6.79 -     8.49: 2
  Bond angle restraints: 22861
  Sorted by residual:
  angle pdb=" C2  SFG K1304 "
        pdb=" N3  SFG K1304 "
        pdb=" C4  SFG K1304 "
      ideal   model   delta    sigma   weight residual
     111.90  120.39   -8.49 3.00e+00 1.11e-01 8.01e+00
  angle pdb=" N   GLY H 104 "
        pdb=" CA  GLY H 104 "
        pdb=" C   GLY H 104 "
      ideal   model   delta    sigma   weight residual
     113.18  119.72   -6.54 2.37e+00 1.78e-01 7.61e+00
  angle pdb=" C3'  DG I  21 "
        pdb=" C2'  DG I  21 "
        pdb=" C1'  DG I  21 "
      ideal   model   delta    sigma   weight residual
     101.60   97.54    4.06 1.50e+00 4.44e-01 7.34e+00
  angle pdb=" C4'  DA I  41 "
        pdb=" C3'  DA I  41 "
        pdb=" C2'  DA I  41 "
      ideal   model   delta    sigma   weight residual
     102.40  106.11   -3.71 1.50e+00 4.44e-01 6.10e+00
  angle pdb=" C3'  DC J  49 "
        pdb=" C2'  DC J  49 "
        pdb=" C1'  DC J  49 "
      ideal   model   delta    sigma   weight residual
     101.60   97.94    3.66 1.50e+00 4.44e-01 5.95e+00
  ... (remaining 22856 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.23: 6846
       35.23 -    70.46: 1759
       70.46 -   105.68: 20
      105.68 -   140.91: 1
      140.91 -   176.14: 7
  Dihedral angle restraints: 8633
    sinusoidal: 5787
      harmonic: 2846
  Sorted by residual:
  dihedral pdb=" CA  LYS C  15 "
           pdb=" C   LYS C  15 "
           pdb=" N   THR C  16 "
           pdb=" CA  THR C  16 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.55   31.45     0      5.00e+00 4.00e-02 3.96e+01
  dihedral pdb=" CA  ASN K1186 "
           pdb=" C   ASN K1186 "
           pdb=" N   GLU K1187 "
           pdb=" CA  GLU K1187 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.13  -20.87     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  ASN K1180 "
           pdb=" C   ASN K1180 "
           pdb=" N   LEU K1181 "
           pdb=" CA  LEU K1181 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.51   20.49     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 8630 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1568
       0.039 -    0.078: 776
       0.078 -    0.117: 200
       0.117 -    0.156: 32
       0.156 -    0.194: 4
  Chirality restraints: 2580
  Sorted by residual:
  chirality pdb=" C1' SFG K1304 "
            pdb=" C2' SFG K1304 "
            pdb=" N9  SFG K1304 "
            pdb=" O4' SFG K1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.38    2.57   -0.19 2.00e-01 2.50e+01 9.45e-01
  chirality pdb=" CA  THR C  16 "
            pdb=" N   THR C  16 "
            pdb=" C   THR C  16 "
            pdb=" CB  THR C  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.33    0.19 2.00e-01 2.50e+01 9.33e-01
  chirality pdb=" CA  SFG K1304 "
            pdb=" N   SFG K1304 "
            pdb=" C   SFG K1304 "
            pdb=" CB  SFG K1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.63    2.45    0.18 2.00e-01 2.50e+01 7.80e-01
  ... (remaining 2577 not shown)

  Planarity restraints: 1709
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  20 "   -0.030 2.00e-02 2.50e+03   1.34e-02 4.90e+00
        pdb=" N9   DA I  20 "    0.031 2.00e-02 2.50e+03
        pdb=" C8   DA I  20 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DA I  20 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DA I  20 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DA I  20 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I  20 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I  20 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I  20 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DA I  20 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I  20 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA J 100 "   -0.024 2.00e-02 2.50e+03   1.12e-02 3.47e+00
        pdb=" N9   DA J 100 "    0.027 2.00e-02 2.50e+03
        pdb=" C8   DA J 100 "    0.001 2.00e-02 2.50e+03
        pdb=" N7   DA J 100 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA J 100 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DA J 100 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6   DA J 100 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DA J 100 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2   DA J 100 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DA J 100 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DA J 100 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  48 "    0.024 2.00e-02 2.50e+03   1.15e-02 3.32e+00
        pdb=" N1   DT I  48 "   -0.024 2.00e-02 2.50e+03
        pdb=" C2   DT I  48 "   -0.004 2.00e-02 2.50e+03
        pdb=" O2   DT I  48 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DT I  48 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DT I  48 "    0.007 2.00e-02 2.50e+03
        pdb=" O4   DT I  48 "    0.007 2.00e-02 2.50e+03
        pdb=" C5   DT I  48 "   -0.003 2.00e-02 2.50e+03
        pdb=" C7   DT I  48 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DT I  48 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1706 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 288
        2.64 -     3.20: 12341
        3.20 -     3.77: 27657
        3.77 -     4.33: 38159
        4.33 -     4.90: 53341
  Nonbonded interactions: 131786
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG C  11 "
            pdb=" O2   DT I 117 "
     model   vdw
     2.070 3.120
  nonbonded pdb=" OD2 ASP D  68 "
            pdb=" OH  TYR F  98 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" OH  TYR B  98 "
            pdb=" OD2 ASP H  68 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OH  TYR E  99 "
            pdb=" OE1 GLU E 133 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OE2 GLU K1101 "
            pdb=" NE  ARG K1105 "
     model   vdw
     2.251 3.120
  ... (remaining 131781 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 38 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 24 through 101)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and (resid 11 through 35 or (resid 36 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 37 through 98 or (resid 99 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 100 through 119))
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 31 through 124)
}

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:             1.580
  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:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     18.160
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  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:6.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
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      :  0.010   0.071  15842  Z= 0.450
  Angle     :  0.729  11.195  22879  Z= 0.428
  Chirality :  0.046   0.194   2580
  Planarity :  0.004   0.044   1709
  Dihedral  : 28.802 176.140   6801
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.08 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  6.20 %
    Favored  : 91.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.71 (0.25), residues: 966
  helix:  0.52 (0.21), residues: 561
  sheet: -2.44 (0.68), residues: 38
  loop : -1.79 (0.28), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 134 
 TYR   0.013   0.002   TYR A  54 
 PHE   0.012   0.002   PHE K1088 
 TRP   0.010   0.003   TRP K1075 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.01023 (15830)
  covalent geometry    : angle       0.72078 (22861)
  hydrogen bonds       : bond        0.11535 (  891)
  hydrogen bonds       : angle       4.61703 ( 2189)
  metal coordination   : bond        0.00821 (   12)
  metal coordination   : angle       3.95529 (   18)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 188
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: C   15 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8247 (ttpp)
REVERT: D   71 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7467 (mt-10)
REVERT: D  113 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7785 (tt0)
REVERT: H   34 LYS cc_start: 0.8575 (mptt) cc_final: 0.8279 (mmtm)
REVERT: K 1126 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7658 (mtm110)
  outliers start: 15
  outliers final: 7
  residues processed: 196
  average time/residue: 0.8230
  time to fit residues: 172.4936
Evaluate side-chains
  176 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 168
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain K residue 1093 VAL
Chi-restraints excluded: chain K residue 1115 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    8.9990
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    7.9990
   chunk 123 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
D  95 GLN
K1110 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.140663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.095647 restraints weight = 27113.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 1.38
r_work: 0.3188 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3035
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3035
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8737
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  15842  Z= 0.204
  Angle     :  0.620   9.930  22879  Z= 0.361
  Chirality :  0.038   0.205   2580
  Planarity :  0.005   0.055   1709
  Dihedral  : 31.973 175.774   4873
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.21 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.38 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.41 (0.26), residues: 966
  helix:  1.52 (0.21), residues: 567
  sheet: -2.24 (0.70), residues: 38
  loop : -1.49 (0.30), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K1060 
 TYR   0.011   0.001   TYR E  41 
 PHE   0.017   0.002   PHE K1051 
 TRP   0.009   0.002   TRP K1075 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (15830)
  covalent geometry    : angle       0.61328 (22861)
  hydrogen bonds       : bond        0.04599 (  891)
  hydrogen bonds       : angle       3.27777 ( 2189)
  metal coordination   : bond        0.00563 (   12)
  metal coordination   : angle       3.36137 (   18)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 184
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: D  113 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8032 (tt0)
REVERT: E   79 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.9009 (tttm)
REVERT: G   75 LYS cc_start: 0.8940 (mmtp) cc_final: 0.8634 (mmmt)
REVERT: H   34 LYS cc_start: 0.8792 (mptt) cc_final: 0.8531 (mmtm)
REVERT: K 1126 ARG cc_start: 0.7985 (mtm180) cc_final: 0.7754 (mtm180)
  outliers start: 12
  outliers final: 5
  residues processed: 189
  average time/residue: 0.7969
  time to fit residues: 161.6907
Evaluate side-chains
  181 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 174
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   79 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain K residue  996 VAL
Chi-restraints excluded: chain K residue 1093 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 104 optimal weight:   40.0000
   chunk 9 optimal weight:    6.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
E 108 ASN
G  24 GLN
H  63 ASN
K1044 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.141991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.097447 restraints weight = 27241.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.40
r_work: 0.3216 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3066
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3066
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.1421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15842  Z= 0.187
  Angle     :  0.599   8.937  22879  Z= 0.351
  Chirality :  0.037   0.227   2580
  Planarity :  0.004   0.045   1709
  Dihedral  : 31.615 176.777   4868
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.21 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.99 (0.27), residues: 966
  helix:  2.03 (0.21), residues: 567
  sheet: -2.16 (0.69), residues: 38
  loop : -1.31 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG K1084 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.010   0.001   PHE E  67 
 TRP   0.004   0.001   TRP K1075 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (15830)
  covalent geometry    : angle       0.59355 (22861)
  hydrogen bonds       : bond        0.04278 (  891)
  hydrogen bonds       : angle       3.03481 ( 2189)
  metal coordination   : bond        0.00438 (   12)
  metal coordination   : angle       2.96979 (   18)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 183
  time to evaluate  : 0.458 
Fit side-chains
REVERT: G   75 LYS cc_start: 0.8885 (mmtp) cc_final: 0.8552 (mmmt)
REVERT: G   99 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8772 (mtpt)
REVERT: H   34 LYS cc_start: 0.8812 (mptt) cc_final: 0.8569 (mptt)
REVERT: K 1028 PHE cc_start: 0.8606 (t80) cc_final: 0.8379 (t80)
REVERT: K 1126 ARG cc_start: 0.7976 (mtm180) cc_final: 0.7698 (mtm180)
  outliers start: 12
  outliers final: 6
  residues processed: 186
  average time/residue: 0.8727
  time to fit residues: 173.7613
Evaluate side-chains
  184 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 177
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain G residue   99 LYS
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain K residue  996 VAL
Chi-restraints excluded: chain K residue 1093 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 78 optimal weight:    4.9990
   chunk 120 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 113 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.140039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.094450 restraints weight = 26817.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.37
r_work: 0.3175 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  15842  Z= 0.283
  Angle     :  0.640   9.622  22879  Z= 0.370
  Chirality :  0.040   0.232   2580
  Planarity :  0.005   0.045   1709
  Dihedral  : 31.702 174.317   4864
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.94 %
    Favored  : 81.51 %
  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:  0.94 (0.27), residues: 966
  helix:  2.01 (0.21), residues: 561
  sheet: -2.13 (0.70), residues: 38
  loop : -1.34 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K1060 
 TYR   0.011   0.002   TYR G  57 
 PHE   0.010   0.002   PHE K1088 
 TRP   0.006   0.002   TRP K1075 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00645 (15830)
  covalent geometry    : angle       0.63392 (22861)
  hydrogen bonds       : bond        0.05072 (  891)
  hydrogen bonds       : angle       3.10358 ( 2189)
  metal coordination   : bond        0.00613 (   12)
  metal coordination   : angle       3.28728 (   18)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 179
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7570 (ttp-110)
REVERT: B   77 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8674 (mtpt)
REVERT: D  113 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8134 (tt0)
REVERT: G   99 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8788 (mtpt)
REVERT: G  107 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.9026 (m)
REVERT: H   68 ASP cc_start: 0.9176 (t70) cc_final: 0.8948 (t70)
REVERT: K 1081 ARG cc_start: 0.6913 (pmm-80) cc_final: 0.6689 (pmm-80)
  outliers start: 20
  outliers final: 7
  residues processed: 185
  average time/residue: 0.8245
  time to fit residues: 162.9260
Evaluate side-chains
  186 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 174
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   99 LYS
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain K residue  996 VAL
Chi-restraints excluded: chain K residue 1093 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:    0.4980
   chunk 71 optimal weight:   40.0000
   chunk 42 optimal weight:    0.9990
   chunk 122 optimal weight:    6.9990
   chunk 106 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 118 optimal weight:    9.9990
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
K1044 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.140633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.095108 restraints weight = 33221.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.54
r_work: 0.3168 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  15842  Z= 0.223
  Angle     :  0.628  10.655  22879  Z= 0.363
  Chirality :  0.039   0.238   2580
  Planarity :  0.004   0.053   1709
  Dihedral  : 31.705 174.661   4864
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 17.52 %
    Favored  : 80.78 %
  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:  0.99 (0.27), residues: 966
  helix:  2.07 (0.21), residues: 561
  sheet: -2.18 (0.69), residues: 38
  loop : -1.32 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K1060 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.015   0.002   PHE K1028 
 TRP   0.006   0.001   TRP K1075 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 (15830)
  covalent geometry    : angle       0.62149 (22861)
  hydrogen bonds       : bond        0.04834 (  891)
  hydrogen bonds       : angle       3.07761 ( 2189)
  metal coordination   : bond        0.00507 (   12)
  metal coordination   : angle       3.26940 (   18)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 175
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7575 (ttp-110)
REVERT: B   77 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8707 (mppt)
REVERT: D  113 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8142 (tt0)
REVERT: G   99 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8789 (mtpt)
REVERT: G  107 VAL cc_start: 0.9225 (OUTLIER) cc_final: 0.9016 (m)
REVERT: K 1081 ARG cc_start: 0.6941 (pmm-80) cc_final: 0.6686 (pmm-80)
  outliers start: 13
  outliers final: 6
  residues processed: 180
  average time/residue: 0.8824
  time to fit residues: 169.7031
Evaluate side-chains
  186 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 175
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   99 LYS
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain K residue 1093 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 107 optimal weight:    0.0970
   chunk 25 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 113 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
K1044 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.142044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.097201 restraints weight = 25375.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 1.32
r_work: 0.3223 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3071
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8726
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15842  Z= 0.163
  Angle     :  0.612  11.586  22879  Z= 0.354
  Chirality :  0.037   0.254   2580
  Planarity :  0.005   0.049   1709
  Dihedral  : 31.680 175.472   4864
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 18.25 %
    Favored  : 80.17 %
  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 (0.27), residues: 966
  helix:  2.24 (0.21), residues: 561
  sheet: -2.15 (0.70), residues: 38
  loop : -1.27 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K1084 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.017   0.001   PHE K1139 
 TRP   0.005   0.001   TRP K1075 
 HIS   0.003   0.001   HIS K1142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (15830)
  covalent geometry    : angle       0.60549 (22861)
  hydrogen bonds       : bond        0.04324 (  891)
  hydrogen bonds       : angle       3.02392 ( 2189)
  metal coordination   : bond        0.00467 (   12)
  metal coordination   : angle       3.24056 (   18)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 181
  time to evaluate  : 0.389 
Fit side-chains
REVERT: B   77 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8649 (mppt)
REVERT: C   73 ASN cc_start: 0.8266 (m110) cc_final: 0.7913 (t160)
REVERT: D   93 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7767 (mp0)
REVERT: D  113 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8127 (tt0)
REVERT: H   34 LYS cc_start: 0.8831 (mptt) cc_final: 0.8559 (mmtm)
REVERT: K 1081 ARG cc_start: 0.6902 (pmm-80) cc_final: 0.6646 (pmm-80)
  outliers start: 12
  outliers final: 5
  residues processed: 185
  average time/residue: 0.8346
  time to fit residues: 165.4778
Evaluate side-chains
  184 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 176
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain K residue 1093 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 86 optimal weight:   20.0000
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 53 optimal weight:    0.4980
   chunk 46 optimal weight:    0.6980
   chunk 89 optimal weight:   20.0000
   chunk 16 optimal weight:    0.6980
   chunk 115 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.142913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.098081 restraints weight = 26175.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 1.40
r_work: 0.3239 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8702
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15842  Z= 0.156
  Angle     :  0.596   9.813  22879  Z= 0.347
  Chirality :  0.036   0.258   2580
  Planarity :  0.004   0.046   1709
  Dihedral  : 31.542 175.821   4864
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.52 %
    Favored  : 80.54 %
  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:  1.34 (0.27), residues: 966
  helix:  2.38 (0.21), residues: 560
  sheet: -2.15 (0.71), residues: 38
  loop : -1.19 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K1084 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.016   0.002   PHE K1051 
 TRP   0.004   0.001   TRP K1075 
 HIS   0.003   0.001   HIS K1142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (15830)
  covalent geometry    : angle       0.58992 (22861)
  hydrogen bonds       : bond        0.03989 (  891)
  hydrogen bonds       : angle       2.95699 ( 2189)
  metal coordination   : bond        0.00424 (   12)
  metal coordination   : angle       3.06357 (   18)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 184
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7523 (ttp-110)
REVERT: B   77 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8664 (mppt)
REVERT: C   61 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8011 (tp30)
REVERT: C   73 ASN cc_start: 0.8222 (m110) cc_final: 0.7874 (t160)
REVERT: D   93 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7739 (mp0)
REVERT: D  113 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8134 (tt0)
REVERT: K 1081 ARG cc_start: 0.6911 (pmm-80) cc_final: 0.6627 (pmm-80)
  outliers start: 15
  outliers final: 5
  residues processed: 188
  average time/residue: 0.8517
  time to fit residues: 171.4547
Evaluate side-chains
  190 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 180
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain K residue 1093 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 109 optimal weight:    8.9990
   chunk 68 optimal weight:    0.6980
   chunk 33 optimal weight:    0.1980
   chunk 52 optimal weight:    0.9990
   chunk 122 optimal weight:    5.9990
   chunk 121 optimal weight:    0.9980
   chunk 108 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0020
   chunk 64 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
K1044 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.143468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.098567 restraints weight = 33854.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.58
r_work: 0.3226 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3065
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15842  Z= 0.152
  Angle     :  0.602  12.484  22879  Z= 0.347
  Chirality :  0.037   0.313   2580
  Planarity :  0.004   0.081   1709
  Dihedral  : 31.468 176.471   4864
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 18.73 %
    Favored  : 79.68 %
  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:  1.43 (0.27), residues: 966
  helix:  2.43 (0.21), residues: 560
  sheet: -1.93 (0.77), residues: 36
  loop : -1.15 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG K1084 
 TYR   0.011   0.001   TYR G  57 
 PHE   0.016   0.002   PHE K1139 
 TRP   0.004   0.001   TRP K1075 
 HIS   0.003   0.001   HIS K1142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (15830)
  covalent geometry    : angle       0.59682 (22861)
  hydrogen bonds       : bond        0.03886 (  891)
  hydrogen bonds       : angle       2.92693 ( 2189)
  metal coordination   : bond        0.00404 (   12)
  metal coordination   : angle       2.98022 (   18)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 183
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
REVERT: C   61 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8076 (tp30)
REVERT: C   73 ASN cc_start: 0.8206 (m110) cc_final: 0.7854 (t160)
REVERT: D   93 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7785 (mp0)
REVERT: D  113 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8088 (tt0)
REVERT: G   73 ASN cc_start: 0.8610 (m110) cc_final: 0.7953 (t0)
REVERT: K 1081 ARG cc_start: 0.6931 (pmm-80) cc_final: 0.6647 (pmm-80)
  outliers start: 12
  outliers final: 6
  residues processed: 186
  average time/residue: 0.7935
  time to fit residues: 158.5120
Evaluate side-chains
  183 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 174
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain K residue 1093 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 71 optimal weight:   40.0000
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 116 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 120 optimal weight:    7.9990
   chunk 41 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 72 optimal weight:   20.0000
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
K1044 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.144235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.099765 restraints weight = 26153.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.33
r_work: 0.3268 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3121
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3121
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15842  Z= 0.158
  Angle     :  0.597  11.384  22879  Z= 0.343
  Chirality :  0.036   0.263   2580
  Planarity :  0.004   0.046   1709
  Dihedral  : 31.225 177.255   4864
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 19.10 %
    Favored  : 79.56 %
  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:  1.62 (0.27), residues: 966
  helix:  2.54 (0.21), residues: 563
  sheet: -2.35 (0.68), residues: 38
  loop : -0.94 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG K1084 
 TYR   0.009   0.001   TYR E  41 
 PHE   0.009   0.001   PHE E  67 
 TRP   0.003   0.001   TRP K1075 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (15830)
  covalent geometry    : angle       0.59264 (22861)
  hydrogen bonds       : bond        0.03753 (  891)
  hydrogen bonds       : angle       2.85190 ( 2189)
  metal coordination   : bond        0.00367 (   12)
  metal coordination   : angle       2.59793 (   18)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 192
  time to evaluate  : 0.409 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.8132 (m110) cc_final: 0.7840 (t160)
REVERT: C   90 ASP cc_start: 0.8445 (t70) cc_final: 0.8235 (t70)
REVERT: D   93 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7716 (mp0)
REVERT: G   73 ASN cc_start: 0.8571 (m110) cc_final: 0.8014 (t0)
REVERT: H   34 LYS cc_start: 0.8850 (mptt) cc_final: 0.8579 (mptt)
REVERT: K 1125 ASP cc_start: 0.7894 (p0) cc_final: 0.7681 (p0)
  outliers start: 10
  outliers final: 5
  residues processed: 194
  average time/residue: 0.8318
  time to fit residues: 173.2124
Evaluate side-chains
  189 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 183
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain K residue 1093 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 41 optimal weight:    0.4980
   chunk 21 optimal weight:    3.9990
   chunk 105 optimal weight:    0.1980
   chunk 74 optimal weight:    6.9990
   chunk 72 optimal weight:   20.0000
   chunk 75 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   chunk 103 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.143389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.098381 restraints weight = 31919.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.45
r_work: 0.3230 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  15842  Z= 0.186
  Angle     :  0.611  11.549  22879  Z= 0.349
  Chirality :  0.037   0.288   2580
  Planarity :  0.004   0.050   1709
  Dihedral  : 31.221 176.377   4864
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 20.44 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.57 (0.27), residues: 966
  helix:  2.48 (0.21), residues: 563
  sheet: -2.20 (0.69), residues: 38
  loop : -0.95 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E  42 
 TYR   0.010   0.001   TYR G  57 
 PHE   0.018   0.002   PHE K1139 
 TRP   0.004   0.001   TRP K1075 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (15830)
  covalent geometry    : angle       0.60707 (22861)
  hydrogen bonds       : bond        0.03902 (  891)
  hydrogen bonds       : angle       2.86615 ( 2189)
  metal coordination   : bond        0.00409 (   12)
  metal coordination   : angle       2.64144 (   18)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 184
  time to evaluate  : 0.387 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.8186 (m110) cc_final: 0.7885 (t160)
REVERT: D   93 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7764 (mp0)
REVERT: D  113 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8162 (tt0)
REVERT: G   73 ASN cc_start: 0.8574 (m110) cc_final: 0.8018 (t0)
REVERT: H   34 LYS cc_start: 0.8847 (mptt) cc_final: 0.8576 (mptt)
REVERT: K 1125 ASP cc_start: 0.7954 (p0) cc_final: 0.7722 (p0)
  outliers start: 8
  outliers final: 6
  residues processed: 186
  average time/residue: 0.7914
  time to fit residues: 157.9102
Evaluate side-chains
  190 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 182
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain K residue 1093 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 116 optimal weight:    9.9990
   chunk 99 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 109 optimal weight:    6.9990
   chunk 92 optimal weight:    5.9990
   chunk 101 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 105 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
H  49 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.142308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.097055 restraints weight = 33270.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.44
r_work: 0.3203 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8738
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  15842  Z= 0.205
  Angle     :  0.621  11.399  22879  Z= 0.353
  Chirality :  0.038   0.291   2580
  Planarity :  0.004   0.045   1709
  Dihedral  : 31.300 175.397   4864
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 20.80 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.49 (0.27), residues: 966
  helix:  2.39 (0.21), residues: 561
  sheet: -2.13 (0.70), residues: 38
  loop : -0.94 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K1060 
 TYR   0.010   0.001   TYR G  57 
 PHE   0.009   0.001   PHE K1201 
 TRP   0.005   0.001   TRP K1075 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (15830)
  covalent geometry    : angle       0.61579 (22861)
  hydrogen bonds       : bond        0.04212 (  891)
  hydrogen bonds       : angle       2.91568 ( 2189)
  metal coordination   : bond        0.00526 (   12)
  metal coordination   : angle       2.96429 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7462.89 seconds
wall clock time: 126 minutes 55.89 seconds (7615.89 seconds total)