WHAT IF Check report

This file was created 2012-01-19 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1zk6.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

Note: Ramachandran plot

Chain identifier: A; Model number 11

Note: Ramachandran plot

Chain identifier: A; Model number 12

Note: Ramachandran plot

Chain identifier: A; Model number 13

Note: Ramachandran plot

Chain identifier: A; Model number 14

Note: Ramachandran plot

Chain identifier: A; Model number 15

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 GLY   ( 116-)  A    Zero
   2 LYS   ( 117-)  A    Zero
   3 ILE   ( 118-)  A    Zero
   4 ARG   ( 119-)  A    Zero
   5 ALA   ( 120-)  A    Zero
   6 SER   ( 121-)  A    Zero
   7 HIS   ( 122-)  A    Zero
   8 ILE   ( 123-)  A    Zero
   9 LEU   ( 124-)  A    Zero
  10 VAL   ( 125-)  A    Zero
  11 ALA   ( 126-)  A    Zero
  12 ASP   ( 127-)  A    Zero
  13 LYS   ( 128-)  A    Zero
  14 LYS   ( 129-)  A    Zero
  15 THR   ( 130-)  A    Zero
  16 ALA   ( 131-)  A    Zero
  17 GLU   ( 132-)  A    Zero
  18 GLU   ( 133-)  A    Zero
  19 VAL   ( 134-)  A    Zero
  20 GLU   ( 135-)  A    Zero
  21 LYS   ( 136-)  A    Zero
  22 LYS   ( 137-)  A    Zero
  23 LEU   ( 138-)  A    Zero
  24 LYS   ( 139-)  A    Zero
  25 LYS   ( 140-)  A    Zero
And so on for a total of 1365 lines.

Geometric checks

Note: Per-model averages for bond-length check

The table below gives the per-model bond-length RMS Z-scores.

Model 1 : 0.651
Model 2 : 0.661
Model 3 : 0.650
Model 4 : 0.653
Model 5 : 0.649
Model 6 : 0.646
Model 7 : 0.655
Model 8 : 0.657
Model 9 : 0.651
Model 10 : 0.666
Model 11 : 0.652
Model 12 : 0.654
Model 13 : 0.652
Model 14 : 0.653
Model 15 : 0.656

Warning: Directionality in bond lengths

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

Since this is not an XRAY structure this effect is hard to explain.

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

   7 HIS   ( 122-)  A      CA   CB   CG  119.12    5.3
  56 GLN   ( 171-)  A      NE2  CD   OE1 118.31   -4.3
 149 ASP   ( 173-)  A     -C    N    CA  129.10    4.1
 175 HIS   ( 199-)  A      CA   CB   CG  118.42    4.6
 357 HIS   ( 199-)  A      CA   CB   CG  118.00    4.2
 371 HIS   ( 122-)  A      CA   CB   CG  119.81    6.0
 511 GLN   ( 171-)  A      NE2  CD   OE1 118.45   -4.1
 535 GLN   ( 195-)  A      NE2  CD   OE1 118.44   -4.2
 539 HIS   ( 199-)  A      CA   CB   CG  118.50    4.7
 630 HIS   ( 199-)  A      CA   CB   CG  117.84    4.0
 808 GLN   ( 195-)  A      NE2  CD   OE1 118.28   -4.3
 812 HIS   ( 199-)  A      CA   CB   CG  118.17    4.4
 899 GLN   ( 195-)  A 1    NE2  CD   OE1 118.25   -4.4
 917 HIS   ( 122-)  A 1    CA   CB   CG  118.46    4.7
 990 GLN   ( 195-)  A 1    NE2  CD   OE1 118.25   -4.4
1085 HIS   ( 199-)  A 1    CA   CB   CG  117.94    4.1
1176 HIS   ( 199-)  A 1    CA   CB   CG  118.21    4.4
1190 HIS   ( 122-)  A 1    CA   CB   CG  119.66    5.9
1241 ASP   ( 173-)  A 1   -C    N    CA  129.21    4.2
1281 HIS   ( 122-)  A 1    CA   CB   CG  118.85    5.1

Note: Per-model averages for bond-angle check

The table below gives the per-model bond-angle RMS Z-scores.

Model 1 : 0.988
Model 2 : 0.989
Model 3 : 0.967
Model 4 : 0.978
Model 5 : 0.984
Model 6 : 0.957
Model 7 : 0.978
Model 8 : 0.959
Model 9 : 0.963
Model 10 : 0.997
Model 11 : 0.990
Model 12 : 0.969
Model 13 : 0.969
Model 14 : 1.000
Model 15 : 0.979

Note: Per-model averages for chirality check

The table below gives the per-model improper dihedral RMS Z-scores.

Model 1 : 0.751
Model 2 : 0.739
Model 3 : 0.764
Model 4 : 0.761
Model 5 : 0.774
Model 6 : 0.798
Model 7 : 0.743
Model 8 : 0.775
Model 9 : 0.726
Model 10 : 0.819
Model 11 : 0.759
Model 12 : 0.780
Model 13 : 0.780
Model 14 : 0.810
Model 15 : 0.754

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

1267 HIS   ( 199-)  A 1    CB   5.50
 721 HIS   ( 199-)  A      CB   4.24
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.823

Torsion-related checks

Note: Per-model averages for Ramachandran check

The table below gives the per-model Ramachandran Z-scores.

Model 1 : -2.636
Model 2 : -1.991
Model 3 : -1.750
Model 4 : -2.105
Model 5 : -1.436
Model 6 : -1.291
Model 7 : -1.542
Model 8 : -1.224
Model 9 : -3.010
Model 10 : -2.135
Model 11 : -1.299
Model 12 : -1.451
Model 13 : -1.571
Model 14 : -1.415
Model 15 : -2.484

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

1251 LEU   ( 183-)  A 1   -2.6
 978 LEU   ( 183-)  A 1   -2.6
 705 LEU   ( 183-)  A    -2.6
 614 LEU   ( 183-)  A    -2.5
1342 LEU   ( 183-)  A 1   -2.5
 996 ILE   ( 201-)  A 1   -2.5
 887 LEU   ( 183-)  A 1   -2.4
 185 ILE   ( 118-)  A    -2.4
 905 ILE   ( 201-)  A 1   -2.4
 913 ILE   ( 118-)  A 1   -2.4
 458 ILE   ( 118-)  A    -2.4
1186 ILE   ( 118-)  A 1   -2.4
 276 ILE   ( 118-)  A    -2.4
  94 ILE   ( 118-)  A    -2.4
 822 ILE   ( 118-)  A 1   -2.4
 735 HIS   ( 122-)  A    -2.3
1004 ILE   ( 118-)  A 1   -2.3
  86 ILE   ( 201-)  A    -2.3
 723 ILE   ( 201-)  A    -2.3
 268 ILE   ( 201-)  A    -2.3
1281 HIS   ( 122-)  A 1   -2.3
  98 HIS   ( 122-)  A    -2.3
   7 HIS   ( 122-)  A    -2.2
1000 GLU   ( 205-)  A 1   -2.2
 189 HIS   ( 122-)  A    -2.2
And so on for a total of 53 lines.

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  55 GLY   ( 170-)  A  Poor phi/psi
  89 THR   ( 204-)  A  Poor phi/psi
 127 TYR   ( 151-)  A  Poor phi/psi
 146 GLY   ( 170-)  A  Poor phi/psi
 218 TYR   ( 151-)  A  Poor phi/psi
 237 GLY   ( 170-)  A  Poor phi/psi
 299 GLY   ( 141-)  A  Poor phi/psi
 308 GLU   ( 150-)  A  Poor phi/psi
 309 TYR   ( 151-)  A  Poor phi/psi
 328 GLY   ( 170-)  A  Poor phi/psi
 400 TYR   ( 151-)  A  Poor phi/psi
 419 GLY   ( 170-)  A  Poor phi/psi
 491 TYR   ( 151-)  A  Poor phi/psi
 510 GLY   ( 170-)  A  Poor phi/psi
 544 THR   ( 204-)  A  Poor phi/psi
 581 GLU   ( 150-)  A  Poor phi/psi
 601 GLY   ( 170-)  A  Poor phi/psi
 672 GLU   ( 150-)  A  Poor phi/psi
 692 GLY   ( 170-)  A  Poor phi/psi
 763 GLU   ( 150-)  A  Poor phi/psi
 783 GLY   ( 170-)  A  Poor phi/psi
 855 TYR   ( 151-)  A 1 Poor phi/psi
 908 THR   ( 204-)  A 1 Poor phi/psi
 946 TYR   ( 151-)  A 1 Poor phi/psi
 965 GLY   ( 170-)  A 1 Poor phi/psi
1037 TYR   ( 151-)  A 1 Poor phi/psi
1056 GLY   ( 170-)  A 1 Poor phi/psi
1127 GLU   ( 150-)  A 1 Poor phi/psi
1128 TYR   ( 151-)  A 1 Poor phi/psi
1181 THR   ( 204-)  A 1 Poor phi/psi
1218 GLU   ( 150-)  A 1 Poor phi/psi
1219 TYR   ( 151-)  A 1 Poor phi/psi
1238 GLY   ( 170-)  A 1 Poor phi/psi
1300 GLY   ( 141-)  A 1 Poor phi/psi
1309 GLU   ( 150-)  A 1 Poor phi/psi
1310 TYR   ( 151-)  A 1 Poor phi/psi
1329 GLY   ( 170-)  A 1 Poor phi/psi
1363 THR   ( 204-)  A 1 Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.461

Note: Per-model averages for chi-1/chi-2 angle check

The table below gives the per-model chi-1/chi-2 correlation Z-scores.

Model 1 : -1.025
Model 2 : -0.168
Model 3 : 0.259
Model 4 : -0.571
Model 5 : -0.715
Model 6 : -0.743
Model 7 : -0.288
Model 8 : -0.502
Model 9 : -0.143
Model 10 : -0.977
Model 11 : -0.637
Model 12 : -0.909
Model 13 : -0.539
Model 14 : -0.717
Model 15 : 0.761

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   4 ARG   ( 119-)  A      0
  11 ALA   ( 126-)  A      0
  25 LYS   ( 140-)  A      0
  36 TYR   ( 151-)  A      0
  37 SER   ( 152-)  A      0
  44 LYS   ( 159-)  A      0
  47 ASP   ( 162-)  A      0
  48 LEU   ( 163-)  A      0
  50 TRP   ( 165-)  A      0
  53 LYS   ( 168-)  A      0
  54 GLU   ( 169-)  A      0
  57 MET   ( 172-)  A      0
  58 ASP   ( 173-)  A      0
  68 LEU   ( 183-)  A      0
  70 THR   ( 185-)  A      0
  75 ASP   ( 190-)  A      0
  76 PRO   ( 191-)  A      0
  81 TYR   ( 196-)  A      0
  83 TYR   ( 198-)  A      0
  90 GLU   ( 205-)  A      0
  91 GLU   ( 206-)  A      0
  92 GLY   ( 116-)  A      0
  93 LYS   ( 117-)  A      0
  95 ARG   ( 119-)  A      0
  97 SER   ( 121-)  A      0
And so on for a total of 516 lines.

Note: Per-model averages for omega angle check

The table below gives the per-model omega angle standard deviations.

Model 1 : 4.631
Model 2 : 4.731
Model 3 : 4.300
Model 4 : 4.491
Model 5 : 4.441
Model 6 : 4.291
Model 7 : 4.440
Model 8 : 4.454
Model 9 : 4.429
Model 10 : 4.306
Model 11 : 4.342
Model 12 : 4.418
Model 13 : 4.505
Model 14 : 4.420
Model 15 : 4.487

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

1356 GLY   ( 197-)  A 1  2.04   14
 628 GLY   ( 197-)  A   1.95   13
 264 GLY   ( 197-)  A   1.93   12
1174 GLY   ( 197-)  A 1  1.90   10
1265 GLY   ( 197-)  A 1  1.88   14
1083 GLY   ( 197-)  A 1  1.87   15
 901 GLY   ( 197-)  A 1  1.84   19
 537 GLY   ( 197-)  A   1.78   18
 992 GLY   ( 197-)  A 1  1.70   21
 719 GLY   ( 197-)  A   1.69   16
 173 GLY   ( 197-)  A   1.55   16
 810 GLY   ( 197-)  A   1.54   15
 355 GLY   ( 197-)  A   1.51   11

Packing, accessibility and threading

Note: Per-model averages for inside/outside residue distributi ...heck















Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 10

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 11

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 12

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 15

Warning: Abnormal packing environment for some residues


Note: Quality value plot

Chain identifier: A; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Per-model averages for NQA















Note: Second generation quality Z-score plot

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 15

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: No crystallisation information

Final summary

Note: Summary report for users of a structure