data_1YPC

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  1YPC
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    1YPC
_pdbx_vrpt_summary.PDB_deposition_date         1993-01-10
_pdbx_vrpt_summary.PDB_revision_number         5
_pdbx_vrpt_summary.PDB_revision_date           2024-02-14
_pdbx_vrpt_summary.report_creation_date        2024-02-06:00:53
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer  "CHYMOTRYPSIN INHIBITOR 2"  
2  water    water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  1.7  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore           
2  Ramachandran_outlier_percent  
3  rotamer_outliers_percent      
#
loop_
_pdbx_vrpt_percentile_conditions.id
_pdbx_vrpt_percentile_conditions.percentile_list_id
_pdbx_vrpt_percentile_conditions.type_id
_pdbx_vrpt_percentile_conditions.rank
_pdbx_vrpt_percentile_conditions.number_entries_total
_pdbx_vrpt_percentile_conditions.res_high
_pdbx_vrpt_percentile_conditions.res_low
1  1  1   99.96  141614     ?     ?  
2  2  1   99.85    4695  1.70  1.70  
3  1  2  100.00  138981     ?     ?  
4  2  2  100.00    4610  1.70  1.70  
5  1  3   58.54  138945     ?     ?  
6  2  3   43.17    4610  1.70  1.70  
#
loop_
_pdbx_vrpt_percentile_entity_view.ordinal
_pdbx_vrpt_percentile_entity_view.conditions_id
_pdbx_vrpt_percentile_entity_view.type_id
_pdbx_vrpt_percentile_entity_view.label_asym_id
_pdbx_vrpt_percentile_entity_view.PDB_model_num
_pdbx_vrpt_percentile_entity_view.entity_id
_pdbx_vrpt_percentile_entity_view.auth_asym_id
_pdbx_vrpt_percentile_entity_view.rank
1  3  2  A  1  1  I  100.00  
2  4  2  A  1  1  I  100.00  
3  5  3  A  1  1  I   60.43  
4  6  3  A  1  1  I   45.64  
#
_pdbx_vrpt_summary_entity_geometry.ordinal          1
_pdbx_vrpt_summary_entity_geometry.PDB_model_num    1
_pdbx_vrpt_summary_entity_geometry.entity_id        1
_pdbx_vrpt_summary_entity_geometry.label_asym_id    A
_pdbx_vrpt_summary_entity_geometry.auth_asym_id     I
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ      1.34
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.94
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   538
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  726
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       1.82
_pdbx_vrpt_summary_geometry.clashscore                     0.00
_pdbx_vrpt_summary_geometry.num_H_reduce                   563
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 538
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.94
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                726
_pdbx_vrpt_summary_geometry.angles_RMSZ                    1.34
#
_pdbx_vrpt_summary_diffraction.exp_method           x-ray
_pdbx_vrpt_summary_diffraction.ordinal              1
_pdbx_vrpt_summary_diffraction.PDB_resolution_high  1.70
_pdbx_vrpt_summary_diffraction.PDB_R                0.17
#
loop_
_pdbx_vrpt_model_instance.id
_pdbx_vrpt_model_instance.PDB_model_num
_pdbx_vrpt_model_instance.entity_id
_pdbx_vrpt_model_instance.label_asym_id
_pdbx_vrpt_model_instance.label_seq_id
_pdbx_vrpt_model_instance.label_comp_id
_pdbx_vrpt_model_instance.auth_asym_id
_pdbx_vrpt_model_instance.auth_seq_id
_pdbx_vrpt_model_instance.label_alt_id
_pdbx_vrpt_model_instance.PDB_ins_code
_pdbx_vrpt_model_instance.count_bond_outliers
_pdbx_vrpt_model_instance.count_angle_outliers
  1  1  1  A   1  MET  I   20  .  ?        ?     ?  
  2  1  1  A   2  LYS  I   21  .  ?        ?     ?  
  3  1  1  A   3  THR  I   22  .  ?        ?     ?  
  4  1  1  A   4  GLU  I   23  A  ?        ?     ?  
  5  1  1  A   4  GLU  I   23  B  ?        ?     ?  
  6  1  1  A   5  TRP  I   24  .  ?        ?     ?  
  7  1  1  A   6  PRO  I   25  .  ?        ?     ?  
  8  1  1  A   7  GLU  I   26  .  ?        ?     ?  
  9  1  1  A   8  LEU  I   27  .  ?        ?     ?  
 10  1  1  A   9  VAL  I   28  .  ?        ?     ?  
 11  1  1  A  10  GLY  I   29  .  ?        ?     ?  
 12  1  1  A  11  LYS  I   30  .  ?        ?     ?  
 13  1  1  A  12  SER  I   31  .  ?        ?     ?  
 14  1  1  A  13  VAL  I   32  .  ?        ?     ?  
 15  1  1  A  14  ALA  I   33  .  ?        ?     ?  
 16  1  1  A  15  ALA  I   34  .  ?        ?     ?  
 17  1  1  A  16  ALA  I   35  .  ?        ?     ?  
 18  1  1  A  17  LYS  I   36  .  ?        ?     ?  
 19  1  1  A  18  LYS  I   37  A  ?        ?     ?  
 20  1  1  A  18  LYS  I   37  B  ?        ?     ?  
 21  1  1  A  19  VAL  I   38  .  ?        ?     ?  
 22  1  1  A  20  ILE  I   39  .  ?        ?     ?  
 23  1  1  A  21  LEU  I   40  .  ?        ?     ?  
 24  1  1  A  22  GLN  I   41  .  ?        ?     ?  
 25  1  1  A  23  ASP  I   42  .  ?        ?     ?  
 26  1  1  A  24  LYS  I   43  .  ?        ?     ?  
 27  1  1  A  25  PRO  I   44  .  ?        ?     ?  
 28  1  1  A  26  GLU  I   45  .  ?        ?     ?  
 29  1  1  A  27  ALA  I   46  .  ?        ?     ?  
 30  1  1  A  28  GLN  I   47  .  ?        ?     ?  
 31  1  1  A  29  ILE  I   48  .  ?        ?     ?  
 32  1  1  A  30  ILE  I   49  .  ?        ?     ?  
 33  1  1  A  31  VAL  I   50  .  ?        ?     ?  
 34  1  1  A  32  LEU  I   51  .  ?        ?     ?  
 35  1  1  A  33  PRO  I   52  .  ?        ?     ?  
 36  1  1  A  34  VAL  I   53  .  ?        ?     ?  
 37  1  1  A  35  GLY  I   54  .  ?        ?     ?  
 38  1  1  A  36  THR  I   55  .  ?        ?     ?  
 39  1  1  A  37  ILE  I   56  .  ?        ?     ?  
 40  1  1  A  38  VAL  I   57  .  ?        ?     ?  
 41  1  1  A  39  THR  I   58  .  ?        ?     ?  
 42  1  1  A  40  MET  I   59  .  ?        ?     ?  
 43  1  1  A  41  GLU  I   60  .  ?        ?     ?  
 44  1  1  A  42  TYR  I   61  .  ?        ?     ?  
 45  1  1  A  43  ARG  I   62  .  ?        ?     ?  
 46  1  1  A  44  ILE  I   63  .  ?        ?     ?  
 47  1  1  A  45  ASP  I   64  .  ?        ?     ?  
 48  1  1  A  46  ARG  I   65  .  ?        ?     ?  
 49  1  1  A  47  VAL  I   66  .  ?        ?     ?  
 50  1  1  A  48  ARG  I   67  .  ?        ?     ?  
 51  1  1  A  49  LEU  I   68  .  ?        ?     ?  
 52  1  1  A  50  PHE  I   69  .  ?        ?     ?  
 53  1  1  A  51  VAL  I   70  .  ?        ?     ?  
 54  1  1  A  52  ASP  I   71  .  ?        ?     1  
 55  1  1  A  53  LYS  I   72  .  ?        ?     ?  
 56  1  1  A  54  LEU  I   73  .  ?        ?     ?  
 57  1  1  A  55  ASP  I   74  .  ?        ?     ?  
 58  1  1  A  56  ASN  I   75  .  ?        ?     ?  
 59  1  1  A  57  ILE  I   76  .  ?        ?     ?  
 60  1  1  A  58  ALA  I   77  .  ?        ?     ?  
 61  1  1  A  59  GLN  I   78  .  ?        ?     ?  
 62  1  1  A  60  VAL  I   79  .  ?        ?     ?  
 63  1  1  A  61  PRO  I   80  .  ?        ?     ?  
 64  1  1  A  62  ARG  I   81  A  ?        2     1  
 65  1  1  A  62  ARG  I   81  B  ?        2     1  
 66  1  1  A  63  VAL  I   82  .  ?        ?     ?  
 67  1  1  A  64  GLY  I   83  .  ?        ?     ?  
 68  1  2  B   .  HOH  I  101  .  ?        ?     ?  
 69  1  2  B   .  HOH  I  102  .  ?        ?     ?  
 70  1  2  B   .  HOH  I  103  .  ?        ?     ?  
 71  1  2  B   .  HOH  I  104  .  ?        ?     ?  
 72  1  2  B   .  HOH  I  105  .  ?        ?     ?  
 73  1  2  B   .  HOH  I  106  .  ?        ?     ?  
 74  1  2  B   .  HOH  I  107  .  ?        ?     ?  
 75  1  2  B   .  HOH  I  108  .  ?        ?     ?  
 76  1  2  B   .  HOH  I  109  .  ?        ?     ?  
 77  1  2  B   .  HOH  I  110  .  ?        ?     ?  
 78  1  2  B   .  HOH  I  111  .  ?        ?     ?  
 79  1  2  B   .  HOH  I  112  .  ?        ?     ?  
 80  1  2  B   .  HOH  I  113  .  ?        ?     ?  
 81  1  2  B   .  HOH  I  114  .  ?        ?     ?  
 82  1  2  B   .  HOH  I  115  .  ?        ?     ?  
 83  1  2  B   .  HOH  I  116  .  ?        ?     ?  
 84  1  2  B   .  HOH  I  117  .  ?        ?     ?  
 85  1  2  B   .  HOH  I  118  .  ?        ?     ?  
 86  1  2  B   .  HOH  I  119  .  ?        ?     ?  
 87  1  2  B   .  HOH  I  120  .  ?        ?     ?  
 88  1  2  B   .  HOH  I  121  .  ?        ?     ?  
 89  1  2  B   .  HOH  I  122  .  ?        ?     ?  
 90  1  2  B   .  HOH  I  123  .  ?        ?     ?  
 91  1  2  B   .  HOH  I  124  .  ?        ?     ?  
 92  1  2  B   .  HOH  I  125  .  ?        ?     ?  
 93  1  2  B   .  HOH  I  126  .  ?        ?     ?  
 94  1  2  B   .  HOH  I  127  .  ?        ?     ?  
 95  1  2  B   .  HOH  I  128  .  ?        ?     ?  
 96  1  2  B   .  HOH  I  129  .  ?        ?     ?  
 97  1  2  B   .  HOH  I  130  .  ?        ?     ?  
 98  1  2  B   .  HOH  I  131  .  ?        ?     ?  
 99  1  2  B   .  HOH  I  132  .  ?        ?     ?  
100  1  2  B   .  HOH  I  133  .  ?        ?     ?  
101  1  2  B   .  HOH  I  134  .  ?        ?     ?  
102  1  2  B   .  HOH  I  135  .  ?        ?     ?  
103  1  2  B   .  HOH  I  136  .  ?        ?     ?  
104  1  2  B   .  HOH  I  137  .  ?        ?     ?  
105  1  2  B   .  HOH  I  138  .  ?        ?     ?  
106  1  2  B   .  HOH  I  139  .  ?        ?     ?  
107  1  2  B   .  HOH  I  140  .  ?        ?     ?  
108  1  2  B   .  HOH  I  141  .  ?        ?     ?  
109  1  2  B   .  HOH  I  142  .  ?        ?     ?  
110  1  2  B   .  HOH  I  143  .  ?        ?     ?  
111  1  2  B   .  HOH  I  144  .  ?        ?     ?  
112  1  2  B   .  HOH  I  145  .  ?        ?     ?  
113  1  2  B   .  HOH  I  146  .  ?        ?     ?  
114  1  2  B   .  HOH  I  147  .  ?        ?     ?  
115  1  2  B   .  HOH  I  148  .  ?        ?     ?  
116  1  2  B   .  HOH  I  149  .  ?        ?     ?  
117  1  2  B   .  HOH  I  150  .  ?        ?     ?  
118  1  2  B   .  HOH  I  151  .  ?        ?     ?  
119  1  2  B   .  HOH  I  152  .  ?        ?     ?  
120  1  2  B   .  HOH  I  153  .  ?        ?     ?  
121  1  2  B   .  HOH  I  154  .  ?        ?     ?  
122  1  2  B   .  HOH  I  155  .  ?        ?     ?  
123  1  2  B   .  HOH  I  156  .  ?        ?     ?  
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.rotamer_class
_pdbx_vrpt_model_instance_geometry.phi
_pdbx_vrpt_model_instance_geometry.psi
_pdbx_vrpt_model_instance_geometry.ramachandran_class
_pdbx_vrpt_model_instance_geometry.num_H_reduce
_pdbx_vrpt_model_instance_geometry.num_bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.num_angles_RMSZ
_pdbx_vrpt_model_instance_geometry.angles_RMSZ
_pdbx_vrpt_model_instance_geometry.program_for_bond_angle_geometry
 1   1  ttt           ?       ?  ?         8   8  0.47  10  1.25  molprobity  
 2   2  tttt      -82.3   133.4  Favored  13   9  0.84  11  1.72  molprobity  
 3   3  p        -127.5     6.4  Favored   7   7  1.15  10  1.38  molprobity  
 4   4  mt-10    -143.6   145.4  Favored   4   9  1.18  12  1.73  molprobity  
 5   5  mt-10    -143.6   145.4  Favored   4   9  1.18  12  1.73  molprobity  
 6   6  m-90     -128.3    68.0  Favored  10  16  0.62  24  0.64  molprobity  
 7   7  Cg_endo   -57.9   -29.4  Favored   7   8  0.65  11  0.70  molprobity  
 8   8  pm0       -65.0   -11.8  Favored   6   9  1.29  12  1.61  molprobity  
 9   9  mt        -93.9    -0.7  Favored  11   8  0.67  11  1.01  molprobity  
10  10  t         -62.3   131.6  Favored   9   7  0.77  10  1.28  molprobity  
11  11  ?          91.0    -5.3  Favored   3   4  0.65   5  0.92  molprobity  
12  12  mmtt      -86.8   161.7  Favored  13   9  0.47  11  0.93  molprobity  
13  13  p         -75.0   165.2  Favored   5   6  0.77   8  1.09  molprobity  
14  14  t         -62.4   -44.4  Favored   9   7  0.62  10  0.71  molprobity  
15  15  ?         -57.6   -46.2  Favored   5   5  0.54   7  0.55  molprobity  
16  16  ?         -66.6   -43.4  Favored   5   5  0.78   7  0.43  molprobity  
17  17  ?         -60.9   -45.9  Favored   5   5  0.56   7  0.83  molprobity  
18  18  mttt      -59.4   -40.5  Favored  13   9  0.55  11  0.93  molprobity  
19  19  tttm      -58.0   -41.1  Favored  11   9  0.63  11  0.70  molprobity  
20  20  tttm      -58.0   -41.1  Favored  11   9  0.63  11  0.70  molprobity  
21  21  t         -75.0   -46.1  Favored   9   7  0.48  10  1.13  molprobity  
22  22  mt        -59.1   -44.2  Favored  11   8  0.76  11  1.04  molprobity  
23  23  mt        -69.0   -13.6  Favored  11   8  0.58  11  1.46  molprobity  
24  24  mm-40     -79.6   -39.9  Favored   8   9  0.47  12  0.91  molprobity  
25  25  m-20      -78.2   -37.7  Favored   4   8  0.51  11  1.27  molprobity  
26  26  tttp     -137.8    80.5  Favored  13   9  0.62  12  1.60  molprobity  
27  27  Cg_endo   -53.9   -29.6  Favored   7   8  0.71  11  1.12  molprobity  
28  28  mt-10    -104.4    25.1  Favored   6   9  1.57  12  0.87  molprobity  
29  29  ?         -65.4   142.2  Favored   5   5  0.42   7  1.55  molprobity  
30  30  tp60      -96.4   104.4  Favored   8   9  0.79  12  1.61  molprobity  
31  31  mt       -102.2   120.8  Favored  11   8  0.80  11  1.25  molprobity  
32  32  mt       -116.3   139.5  Favored  11   8  0.84  11  1.22  molprobity  
33  33  t        -111.2   131.6  Favored   9   7  0.53  10  0.71  molprobity  
34  34  mt       -141.9   149.5  Favored  11   8  0.35  12  1.18  molprobity  
35  35  Cg_exo    -64.2   139.0  Favored   7   8  0.73  11  0.91  molprobity  
36  36  p         -58.3   140.7  Favored   9   7  0.53  10  1.40  molprobity  
37  37  ?          97.2   -12.4  Favored   3   4  1.16   5  0.34  molprobity  
38  38  m         -61.3   132.0  Favored   7   7  0.97  10  1.10  molprobity  
39  39  mm        -76.2   124.8  Favored  11   8  0.82  11  0.86  molprobity  
40  40  m        -120.1   166.8  Favored   9   7  0.48  10  1.11  molprobity  
41  41  p         -86.1   170.1  Favored   7   7  1.06  10  0.99  molprobity  
42  42  ?         -88.2     1.2  Favored   2   5  0.89   7  1.32  molprobity  
43  43  OUTLIER   -58.7   139.2  Favored   6   9  1.23  12  1.66  molprobity  
44  44  t80      -100.4   118.1  Favored   9  13  0.57  18  0.72  molprobity  
45  45  mmm-85   -118.3   105.3  Favored  13  11  0.46  14  1.07  molprobity  
46  46  tt        -63.7   -18.3  Favored  11   8  1.03  11  1.03  molprobity  
47  47  p-10      -85.2   -21.0  Favored   4   8  0.38  11  1.39  molprobity  
48  48  ttp180    -97.5   146.2  Favored  13  11  0.41  14  2.06  molprobity  
49  49  t        -133.9   111.0  Favored   9   7  0.66  10  1.28  molprobity  
50  50  mtt180    -89.9   135.8  Favored  13  11  0.67  14  1.97  molprobity  
51  51  mt       -110.3   113.9  Favored  11   8  0.62  11  1.45  molprobity  
52  52  m-85      -94.0   117.4  Favored   9  12  0.84  16  1.19  molprobity  
53  53  m        -113.7   156.0  Favored   9   7  0.36  10  1.30  molprobity  
54  54  p30       -90.6  -176.1  Favored   4   8  0.62  11  2.88  molprobity  
55  55  mmtp      -70.0    -8.2  Favored  13   9  0.56  11  0.94  molprobity  
56  56  mt        -99.0     2.9  Favored  11   8  0.62  11  1.14  molprobity  
57  57  t0         70.3    27.4  Favored   4   8  0.66  11  0.98  molprobity  
58  58  m-20     -104.8   154.1  Favored   6   8  0.43  11  0.91  molprobity  
59  59  mm        -62.8   123.0  Favored  11   8  0.75  11  0.66  molprobity  
60  60  ?        -103.1   -17.3  Favored   5   5  0.87   7  1.09  molprobity  
61  61  mt-30    -137.2   158.9  Favored   8   9  1.28  12  1.69  molprobity  
62  62  t         -61.1   119.0  Favored   9   7  0.68  11  1.03  molprobity  
63  63  Cg_exo    -67.7   137.8  Favored   7   8  0.44  11  1.21  molprobity  
64  64  ptt-85   -147.3   152.6  Favored  11  11  2.83  14  2.63  molprobity  
65  65  ptt-85   -147.3   152.6  Favored  11  11  2.83  14  2.63  molprobity  
66  66  t         -67.4   139.0  Favored   9   7  0.55  10  1.14  molprobity  
67  67  ?             ?       ?  ?         3   4  1.02   2  2.27  molprobity  
#
loop_
_pdbx_vrpt_instance_intra_bond_outliers.ordinal
_pdbx_vrpt_instance_intra_bond_outliers.instance_id
_pdbx_vrpt_instance_intra_bond_outliers.atom_1
_pdbx_vrpt_instance_intra_bond_outliers.atom_2
_pdbx_vrpt_instance_intra_bond_outliers.obs
_pdbx_vrpt_instance_intra_bond_outliers.mean
_pdbx_vrpt_instance_intra_bond_outliers.stdev
_pdbx_vrpt_instance_intra_bond_outliers.Z
1  64  CA  CB  1.691  1.535  0.022   7.08  
2  64  CG  CD  1.381  1.515  0.025  -5.34  
3  65  CA  CB  1.691  1.535  0.022   7.08  
4  65  CG  CD  1.381  1.515  0.025  -5.34  
#
loop_
_pdbx_vrpt_instance_intra_angle_outliers.ordinal
_pdbx_vrpt_instance_intra_angle_outliers.instance_id
_pdbx_vrpt_instance_intra_angle_outliers.atom_1
_pdbx_vrpt_instance_intra_angle_outliers.atom_2
_pdbx_vrpt_instance_intra_angle_outliers.atom_3
_pdbx_vrpt_instance_intra_angle_outliers.obs
_pdbx_vrpt_instance_intra_angle_outliers.mean
_pdbx_vrpt_instance_intra_angle_outliers.stdev
_pdbx_vrpt_instance_intra_angle_outliers.Z
1  54  CB  CG  OD1  125.407  118.300  0.900   7.90  
2  64  NE  CZ  NH2  117.035  120.300  0.500  -6.53  
3  65  NE  CZ  NH2  117.035  120.300  0.500  -6.53  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity   4.02b-467                                                             Y  
2  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
