WHAT IF Check report

This file was created 2012-01-25 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 pdb2eu0.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

2280 ACE   (   3-)  A  1
2281 ACE   ( 118-)  B  1
2283 ACE   (   3-)  A  2
2284 ACE   ( 118-)  B  2
2286 ACE   (   3-)  A  3
2287 ACE   ( 118-)  B  3
2289 ACE   (   3-)  A  4
2290 ACE   ( 118-)  B  4
2292 ACE   (   3-)  A  5
2293 ACE   ( 118-)  B  5
2295 ACE   (   3-)  A  6
2296 ACE   ( 118-)  B  6
2298 ACE   (   3-)  A  7
2299 ACE   ( 118-)  B  7
2301 ACE   (   3-)  A  8
2302 ACE   ( 118-)  B  8
2304 ACE   (   3-)  A  9
2305 ACE   ( 118-)  B  9
2307 ACE   (   3-)  A 10
2308 ACE   ( 118-)  B 10
2310 ACE   (   3-)  A 11
2311 ACE   ( 118-)  B 11
2313 ACE   (   3-)  A 12
2314 ACE   ( 118-)  B 12
2316 ACE   (   3-)  A 13
2317 ACE   ( 118-)  B 13
2319 ACE   (   3-)  A 14
2320 ACE   ( 118-)  B 14
2322 ACE   (   3-)  A 15
2323 ACE   ( 118-)  B 15
2325 ACE   (   3-)  A 16
2326 ACE   ( 118-)  B 16
2328 ACE   (   3-)  A 17
2329 ACE   ( 118-)  B 17
2331 ACE   (   3-)  A 18
2332 ACE   ( 118-)  B 18
2334 ACE   (   3-)  A 19
2335 ACE   ( 118-)  B 19
2337 ACE   (   3-)  A 20
2338 ACE   ( 118-)  B 20

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

 150 SER   (  39-)  A  2   CA   225 PTR   ( 121-)  B  2   O3P
 150 SER   (  39-)  A  2   CB   225 PTR   ( 121-)  B  2   O3P
 157 THR   (  46-)  A  2   OG1  225 PTR   ( 121-)  B  2   CE1
 271 THR   (  46-)  A  3   OG1  339 PTR   ( 121-)  B  3   CE1
 376 ARG   (  37-)  A  4   NH1  453 PTR   ( 121-)  B  4   O3P
 378 SER   (  39-)  A  4   N    453 PTR   ( 121-)  B  4   O1P
 378 SER   (  39-)  A  4   CA   453 PTR   ( 121-)  B  4   P
 378 SER   (  39-)  A  4   CA   453 PTR   ( 121-)  B  4   O1P
 378 SER   (  39-)  A  4   CB   453 PTR   ( 121-)  B  4   CE2
 378 SER   (  39-)  A  4   OG   453 PTR   ( 121-)  B  4   CE2
 378 SER   (  39-)  A  4   OG   453 PTR   ( 121-)  B  4   CZ
1069 THR   (  46-)  A 10   OG1 1137 PTR   ( 121-)  B 10   CE1
1069 THR   (  46-)  A 10   OG1 1137 PTR   ( 121-)  B 10   O2P
1069 THR   (  46-)  A 10   CG2 1137 PTR   ( 121-)  B 10   P
1069 THR   (  46-)  A 10   CG2 1137 PTR   ( 121-)  B 10   O2P
1176 SER   (  39-)  A 11   OG  1251 PTR   ( 121-)  B 11   O1P
1859 SER   (  39-)  A 17   CB  1934 PTR   ( 121-)  B 17   O2P
1859 SER   (  39-)  A 17   OG  1934 PTR   ( 121-)  B 17   P
1866 THR   (  46-)  A 17   OG1 1934 PTR   ( 121-)  B 17   CD1
1866 THR   (  46-)  A 17   OG1 1934 PTR   ( 121-)  B 17   CE1
1866 THR   (  46-)  A 17   OG1 1934 PTR   ( 121-)  B 17   CZ

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

Error: Overlapping residues removed

The pairs of residues listed in the table overlapped too much.

The left-hand residue has been removed, and the right hand residue has been kept for validation. Be aware that WHAT IF calls everything a residue. Two residues are defined as overlapping if the two smallest ellipsoids encompassing the two residues interpenetrate by 33% of the longest axis. Many artefacts can actually cause this problem. The most often observed reason is alternative residue conformations expressed by two residues that accidentally both got 1.0 occupancy for all atoms.

1289 SER   (  39-)  A 12             1288 ARG   (  37-)  A 12           2.8
Delete overlapping entity  453 PTR  ( 121-) B  4
Delete overlapping entity 1288 ARG  (  37-) A 12

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

 453 PTR   ( 121-)  B  4
1288 ARG   (  37-)  A 12

Please also see the previous check
Please see the user course on the WHAT CHECK website if you want to know why this table and the previous one have not been merged.

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

   1 ASN   (   4-)  A  1   N   bound to 2279 ACE   (   3-)  A  1   C
 109 ALA   ( 119-)  B  1   N   bound to 2280 ACE   ( 118-)  B  1   C
 115 ASN   (   4-)  A  2   N   bound to 2282 ACE   (   3-)  A  2   C
 223 ALA   ( 119-)  B  2   N   bound to 2283 ACE   ( 118-)  B  2   C
 229 ASN   (   4-)  A  3   N   bound to 2285 ACE   (   3-)  A  3   C
 337 ALA   ( 119-)  B  3   N   bound to 2286 ACE   ( 118-)  B  3   C
 343 ASN   (   4-)  A  4   N   bound to 2288 ACE   (   3-)  A  4   C
 450 ALA   ( 119-)  B  4   N   bound to 2289 ACE   ( 118-)  B  4   C
 456 ASN   (   4-)  A  5   N   bound to 2291 ACE   (   3-)  A  5   C
 564 ALA   ( 119-)  B  5   N   bound to 2292 ACE   ( 118-)  B  5   C
 570 ASN   (   4-)  A  6   N   bound to 2294 ACE   (   3-)  A  6   C
 678 ALA   ( 119-)  B  6   N   bound to 2295 ACE   ( 118-)  B  6   C
 684 ASN   (   4-)  A  7   N   bound to 2297 ACE   (   3-)  A  7   C
 792 ALA   ( 119-)  B  7   N   bound to 2298 ACE   ( 118-)  B  7   C
 798 ASN   (   4-)  A  8   N   bound to 2300 ACE   (   3-)  A  8   C
 906 ALA   ( 119-)  B  8   N   bound to 2301 ACE   ( 118-)  B  8   C
 912 ASN   (   4-)  A  9   N   bound to 2303 ACE   (   3-)  A  9   C
1020 ALA   ( 119-)  B  9   N   bound to 2304 ACE   ( 118-)  B  9   C
1026 ASN   (   4-)  A 10   N   bound to 2306 ACE   (   3-)  A 10   C
1134 ALA   ( 119-)  B 10   N   bound to 2307 ACE   ( 118-)  B 10   C
1140 ASN   (   4-)  A 11   N   bound to 2309 ACE   (   3-)  A 11   C
1248 ALA   ( 119-)  B 11   N   bound to 2310 ACE   ( 118-)  B 11   C
1254 ASN   (   4-)  A 12   N   bound to 2312 ACE   (   3-)  A 12   C
1361 ALA   ( 119-)  B 12   N   bound to 2313 ACE   ( 118-)  B 12   C
1367 ASN   (   4-)  A 13   N   bound to 2315 ACE   (   3-)  A 13   C
1475 ALA   ( 119-)  B 13   N   bound to 2316 ACE   ( 118-)  B 13   C
1481 ASN   (   4-)  A 14   N   bound to 2318 ACE   (   3-)  A 14   C
1589 ALA   ( 119-)  B 14   N   bound to 2319 ACE   ( 118-)  B 14   C
1595 ASN   (   4-)  A 15   N   bound to 2321 ACE   (   3-)  A 15   C
1703 ALA   ( 119-)  B 15   N   bound to 2322 ACE   ( 118-)  B 15   C
1709 ASN   (   4-)  A 16   N   bound to 2324 ACE   (   3-)  A 16   C
1817 ALA   ( 119-)  B 16   N   bound to 2325 ACE   ( 118-)  B 16   C
1823 ASN   (   4-)  A 17   N   bound to 2327 ACE   (   3-)  A 17   C
1931 ALA   ( 119-)  B 17   N   bound to 2328 ACE   ( 118-)  B 17   C
1937 ASN   (   4-)  A 18   N   bound to 2330 ACE   (   3-)  A 18   C
2045 ALA   ( 119-)  B 18   N   bound to 2331 ACE   ( 118-)  B 18   C
2051 ASN   (   4-)  A 19   N   bound to 2333 ACE   (   3-)  A 19   C
2159 ALA   ( 119-)  B 19   N   bound to 2334 ACE   ( 118-)  B 19   C
2165 ASN   (   4-)  A 20   N   bound to 2336 ACE   (   3-)  A 20   C
2273 ALA   ( 119-)  B 20   N   bound to 2337 ACE   ( 118-)  B 20   C

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

Note: Ramachandran plot

Chain identifier: A; Model number 16

Note: Ramachandran plot

Chain identifier: A; Model number 17

Note: Ramachandran plot

Chain identifier: A; Model number 18

Note: Ramachandran plot

Chain identifier: A; Model number 19

Note: Ramachandran plot

Chain identifier: A; Model number 20

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 111 PTR   ( 121-)  B
 225 PTR   ( 121-)  B
 339 PTR   ( 121-)  B
 452 PTR   ( 121-)  B
 566 PTR   ( 121-)  B
 680 PTR   ( 121-)  B
 794 PTR   ( 121-)  B
 908 PTR   ( 121-)  B
1022 PTR   ( 121-)  B
1136 PTR   ( 121-)  B 1
1250 PTR   ( 121-)  B 1
1363 PTR   ( 121-)  B 1
1477 PTR   ( 121-)  B 1
1591 PTR   ( 121-)  B 1
1705 PTR   ( 121-)  B 1
1819 PTR   ( 121-)  B 1
1933 PTR   ( 121-)  B 1
2047 PTR   ( 121-)  B 1
2161 PTR   ( 121-)  B 1
2275 PTR   ( 121-)  B 2

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 ASN   (   4-)  A    Zero
   2 ASN   (   5-)  A    Zero
   3 LEU   (   6-)  A    Zero
   4 GLU   (   7-)  A    Zero
   5 THR   (   8-)  A    Zero
   6 TYR   (   9-)  A    Zero
   7 GLU   (  10-)  A    Zero
   8 TRP   (  11-)  A    Zero
   9 TYR   (  12-)  A    Zero
  10 ASN   (  13-)  A    Zero
  11 LYS   (  14-)  A    Zero
  12 SER   (  15-)  A    Zero
  13 ILE   (  16-)  A    Zero
  14 SER   (  17-)  A    Zero
  15 ARG   (  18-)  A    Zero
  16 ASP   (  19-)  A    Zero
  17 LYS   (  20-)  A    Zero
  18 ALA   (  21-)  A    Zero
  19 GLU   (  22-)  A    Zero
  20 LYS   (  23-)  A    Zero
  21 LEU   (  24-)  A    Zero
  22 LEU   (  25-)  A    Zero
  23 LEU   (  26-)  A    Zero
  24 ASP   (  27-)  A    Zero
  25 THR   (  28-)  A    Zero
And so on for a total of 2278 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 : 0.234
Model 2 : 0.234
Model 3 : 0.237
Model 4 : 0.239
Model 5 : 0.236
Model 6 : 0.235
Model 7 : 0.243
Model 8 : 0.247
Model 9 : 0.244
Model 10 : 0.244
Model 11 : 0.250
Model 12 : 0.264
Model 13 : 0.258
Model 14 : 0.255
Model 15 : 0.269
Model 16 : 0.265
Model 17 : 0.260
Model 18 : 0.268
Model 19 : 0.274
Model 20 : 0.270

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.

Note: Per-model averages for bond-angle check

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

Model 1 : 0.428
Model 2 : 0.426
Model 3 : 0.426
Model 4 : 0.430
Model 5 : 0.421
Model 6 : 0.433
Model 7 : 0.450
Model 8 : 0.444
Model 9 : 0.430
Model 10 : 0.449
Model 11 : 0.437
Model 12 : 0.455
Model 13 : 0.470
Model 14 : 0.461
Model 15 : 0.457
Model 16 : 0.466
Model 17 : 0.467
Model 18 : 0.475
Model 19 : 0.463
Model 20 : 0.465

Note: Per-model averages for chirality check

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

Model 1 : 0.417
Model 2 : 0.400
Model 3 : 0.411
Model 4 : 0.413
Model 5 : 0.412
Model 6 : 0.421
Model 7 : 0.443
Model 8 : 0.416
Model 9 : 0.433
Model 10 : 0.452
Model 11 : 0.434
Model 12 : 0.443
Model 13 : 0.457
Model 14 : 0.495
Model 15 : 0.485
Model 16 : 0.468
Model 17 : 0.467
Model 18 : 0.464
Model 19 : 0.475
Model 20 : 0.438

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.352

Note: Per-model averages for Ramachandran check

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

Model 1 : -4.576
Model 2 : -4.617
Model 3 : -4.708
Model 4 : -5.047
Model 5 : -4.629
Model 6 : -4.336
Model 7 : -4.085
Model 8 : -4.134
Model 9 : -4.535
Model 10 : -3.791
Model 11 : -4.637
Model 12 : -4.348
Model 13 : -4.559
Model 14 : -3.420
Model 15 : -4.186
Model 16 : -4.261
Model 17 : -4.501
Model 18 : -4.182
Model 19 : -4.163
Model 20 : -4.344

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.

1694 THR   ( 103-)  A 1   -3.7
1352 THR   ( 103-)  A 1   -3.7
 441 THR   ( 103-)  A    -3.7
 555 THR   ( 103-)  A    -3.6
2088 THR   (  41-)  A 1   -3.6
2150 THR   ( 103-)  A 1   -3.6
1239 THR   ( 103-)  A 1   -3.6
1466 THR   ( 103-)  A 1   -3.6
2264 THR   ( 103-)  A 2   -3.6
2036 THR   ( 103-)  A 1   -3.6
1125 THR   ( 103-)  A 1   -3.6
 669 THR   ( 103-)  A    -3.5
 607 THR   (  41-)  A    -3.5
1011 THR   ( 103-)  A    -3.5
 214 THR   ( 103-)  A    -3.5
1518 THR   (  41-)  A 1   -3.4
 783 THR   ( 103-)  A    -3.4
1580 THR   ( 103-)  A 1   -3.4
1860 THR   (  41-)  A 1   -3.4
1888 THR   (  69-)  A 1   -3.3
2230 THR   (  69-)  A 2   -3.2
1345 TYR   (  96-)  A 1   -3.2
 328 THR   ( 103-)  A    -3.2
 749 THR   (  69-)  A    -3.2
1778 PRO   (  73-)  A 1   -3.1
And so on for a total of 515 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.

   2 ASN   (   5-)  A  Poor phi/psi
   8 TRP   (  11-)  A  Poor phi/psi
  11 LYS   (  14-)  A  Poor phi/psi
  39 PRO   (  42-)  A  Poor phi/psi
  40 GLY   (  43-)  A  Poor phi/psi
  52 ILE   (  55-)  A  Poor phi/psi
  55 ASN   (  58-)  A  Poor phi/psi
  69 SER   (  72-)  A  PRO omega poor
  71 LYS   (  74-)  A  Poor phi/psi
  76 ALA   (  79-)  A  Poor phi/psi
  78 LYS   (  81-)  A  Poor phi/psi
  95 GLY   (  98-)  A  Poor phi/psi
  97 GLY   ( 100-)  A  Poor phi/psi
  99 VAL   ( 102-)  A  Poor phi/psi
 100 THR   ( 103-)  A  Poor phi/psi
 101 ARG   ( 104-)  A  Poor phi/psi
 112 GLU   ( 122-)  B  Poor phi/psi
 116 ASN   (   5-)  A  Poor phi/psi
 122 TRP   (  11-)  A  Poor phi/psi
 125 LYS   (  14-)  A  Poor phi/psi
 128 SER   (  17-)  A  Poor phi/psi
 153 PRO   (  42-)  A  Poor phi/psi
 154 GLY   (  43-)  A  Poor phi/psi
 180 THR   (  69-)  A  Poor phi/psi
 182 ASP   (  71-)  A  Poor phi/psi
And so on for a total of 392 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -8.055

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 : -8.180
Model 2 : -8.055
Model 3 : -8.021
Model 4 : -7.927
Model 5 : -7.685
Model 6 : -8.220
Model 7 : -8.052
Model 8 : -8.043
Model 9 : -8.427
Model 10 : -8.421
Model 11 : -8.051
Model 12 : -8.083
Model 13 : -8.177
Model 14 : -7.603
Model 15 : -7.901
Model 16 : -7.759
Model 17 : -8.132
Model 18 : -8.020
Model 19 : -8.047
Model 20 : -8.305

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 614 SER   (  48-)  A    0.36
1143 GLU   (   7-)  A 1   0.36
WARNING: Attached group deleted: 157
WARNING: Attached group deleted: 271
WARNING: Attached group deleted: 376
WARNING: Attached group deleted: 1068
WARNING: Attached group deleted: 1175
WARNING: Attached group deleted: 1865

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!

   6 TYR   (   9-)  A      0
   7 GLU   (  10-)  A      0
   8 TRP   (  11-)  A      0
   9 TYR   (  12-)  A      0
  10 ASN   (  13-)  A      0
  11 LYS   (  14-)  A      0
  12 SER   (  15-)  A      0
  25 THR   (  28-)  A      0
  28 GLU   (  31-)  A      0
  30 ALA   (  33-)  A      0
  31 PHE   (  34-)  A      0
  38 THR   (  41-)  A      0
  39 PRO   (  42-)  A      0
  51 ILE   (  54-)  A      0
  52 ILE   (  55-)  A      0
  54 GLU   (  57-)  A      0
  55 ASN   (  58-)  A      0
  56 PRO   (  59-)  A      0
  67 ASN   (  70-)  A      0
  68 ASP   (  71-)  A      0
  69 SER   (  72-)  A      0
  71 LYS   (  74-)  A      0
  72 ARG   (  75-)  A      0
  73 TYR   (  76-)  A      0
  75 VAL   (  78-)  A      0
And so on for a total of 1287 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.080

Note: Per-model averages for omega angle check

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

Model 1 : 0.993
Model 2 : 0.952
Model 3 : 1.021
Model 4 : 0.980
Model 5 : 0.996
Model 6 : 1.103
Model 7 : 1.015
Model 8 : 1.104
Model 9 : 1.072
Model 10 : 1.132
Model 11 : 1.088
Model 12 : 1.055
Model 13 : 1.246
Model 14 : 1.270
Model 15 : 1.220
Model 16 : 1.177
Model 17 : 1.065
Model 18 : 1.144
Model 19 : 1.198
Model 20 : 1.069

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!

1804 GLY   (  99-)  A 1  3.24   10
1348 GLY   (  99-)  A 1  2.26   13
1976 GLY   (  43-)  A 1  1.70   15
1347 GLY   (  98-)  A 1  1.67   28
1121 GLY   (  99-)  A 1  1.61   14
 437 GLY   (  99-)  A   1.55   15

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  39 PRO   (  42-)  A   114.0 envelop C-beta (108 degrees)
  70 PRO   (  73-)  A   -50.2 half-chair C-beta/C-alpha (-54 degrees)
 105 PRO   ( 108-)  A    38.9 envelop C-delta (36 degrees)
 113 PRO   ( 123-)  B   116.5 envelop C-beta (108 degrees)
 114 PRO   ( 124-)  B  -126.6 half-chair C-delta/C-gamma (-126 degrees)
 153 PRO   (  42-)  A   115.4 envelop C-beta (108 degrees)
 170 PRO   (  59-)  A   104.4 envelop C-beta (108 degrees)
 219 PRO   ( 108-)  A    43.4 envelop C-delta (36 degrees)
 267 PRO   (  42-)  A   114.0 envelop C-beta (108 degrees)
 333 PRO   ( 108-)  A    25.0 half-chair N/C-delta (18 degrees)
 341 PRO   ( 123-)  B  -121.5 half-chair C-delta/C-gamma (-126 degrees)
 342 PRO   ( 124-)  B   126.3 half-chair C-beta/C-alpha (126 degrees)
 380 PRO   (  42-)  A   112.1 envelop C-beta (108 degrees)
 397 PRO   (  59-)  A    32.0 envelop C-delta (36 degrees)
 446 PRO   ( 108-)  A    32.2 envelop C-delta (36 degrees)
 454 PRO   ( 123-)  B   111.4 envelop C-beta (108 degrees)
 455 PRO   ( 124-)  B   116.2 envelop C-beta (108 degrees)
 525 PRO   (  73-)  A    45.3 half-chair C-delta/C-gamma (54 degrees)
 560 PRO   ( 108-)  A    47.1 half-chair C-delta/C-gamma (54 degrees)
 639 PRO   (  73-)  A   -65.8 envelop C-beta (-72 degrees)
 674 PRO   ( 108-)  A   -51.2 half-chair C-beta/C-alpha (-54 degrees)
 722 PRO   (  42-)  A   -14.9 half-chair C-alpha/N (-18 degrees)
 753 PRO   (  73-)  A   -24.9 half-chair C-alpha/N (-18 degrees)
 788 PRO   ( 108-)  A    22.1 half-chair N/C-delta (18 degrees)
 796 PRO   ( 123-)  B    22.3 half-chair N/C-delta (18 degrees)
And so on for a total of 73 lines.

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively).

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. However, as this seems to be an NMR structure, this is unlikely to happen in this report.

 384 THR   (  46-)  A      CB   <->   452 PTR   ( 121-)  B      CE1  1.26    1.94
1182 THR   (  46-)  A 1    CG2  <->  1250 PTR   ( 121-)  B 1    CE1  1.20    2.00
 403 HIS   (  65-)  A      CB   <->   452 PTR   ( 121-)  B      CB   1.19    2.01
 403 HIS   (  65-)  A      CB   <->   452 PTR   ( 121-)  B      CG   1.18    2.02
 376 ARG   (  37-)  A      CD   <->   452 PTR   ( 121-)  B      O3P  1.15    1.65
1979 THR   (  46-)  A 1    OG1  <->  2047 PTR   ( 121-)  B 1    CE1  1.14    1.66
 416 VAL   (  78-)  A      C    <->   455 PRO   ( 124-)  B      CB   1.13    2.07
1979 THR   (  46-)  A 1    CB   <->  2047 PTR   ( 121-)  B 1    CE1  1.12    2.08
1295 THR   (  46-)  A 1    OG1  <->  1363 PTR   ( 121-)  B 1    CE1  1.10    1.70
1899 GLU   (  80-)  A 1    OE2  <->  2329 NH2   ( 125-)  B 1    N    1.09    1.61
 403 HIS   (  65-)  A      CB   <->   452 PTR   ( 121-)  B      CD1  1.03    2.17
1653 LYS   (  62-)  A 1    NZ   <->  2323 NH2   ( 125-)  B 1    N    1.00    2.00
2086 SER   (  39-)  A 1    CB   <->  2161 PTR   ( 121-)  B 1    O1P  0.99    1.81
 384 THR   (  46-)  A      CG2  <->   452 PTR   ( 121-)  B      CE1  0.98    2.22
 517 HIS   (  65-)  A      N    <->  2293 NH2   ( 125-)  B      N    0.97    2.03
 831 ARG   (  37-)  A      CZ   <->   908 PTR   ( 121-)  B      O3P  0.96    1.84
1087 HIS   (  65-)  A 1    CB   <->  1136 PTR   ( 121-)  B 1    CB   0.96    2.24
2207 THR   (  46-)  A 2    CG2  <->  2275 PTR   ( 121-)  B 2    CE1  0.92    2.28
 498 THR   (  46-)  A      CG2  <->   566 PTR   ( 121-)  B      CE2  0.90    2.30
 812 ARG   (  18-)  A      NH1  <->   908 PTR   ( 121-)  B      P    0.89    2.41
1177 THR   (  41-)  A 1    CG2  <->  1249 ASP   ( 120-)  B 1    OD2  0.88    1.92
1972 SER   (  39-)  A 1    OG   <->  2047 PTR   ( 121-)  B 1    CE2  0.88    1.92
 262 ARG   (  37-)  A      NH2  <->   339 PTR   ( 121-)  B      O1P  0.84    1.86
2093 THR   (  46-)  A 1    OG1  <->  2161 PTR   ( 121-)  B 1    CE1  0.84    1.96
1087 HIS   (  65-)  A 1    CB   <->  1136 PTR   ( 121-)  B 1    CG   0.84    2.36
And so on for a total of 8372 lines.

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

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 16

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 17

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 18

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 19

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 20

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential 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: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: A; Model number 17

Note: Quality value plot

Chain identifier: A; Model number 18

Note: Quality value plot

Chain identifier: A; Model number 19

Note: Quality value plot

Chain identifier: A; Model number 20

Warning: Low packing Z-score for some residues


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

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 16

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 17

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 18

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 19

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 20

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: Buried unsatisfied hydrogen bond acceptors


Warning: No crystallisation information

Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure