WHAT IF Check report

This file was created 2011-12-17 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 pdb1pxx.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.156
CA-only RMS fit for the two chains : 0.102

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.148
CA-only RMS fit for the two chains : 0.101

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.129
CA-only RMS fit for the two chains : 0.088

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.144
CA-only RMS fit for the two chains : 0.100

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and D

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

2229 DIF   ( 701-)  A  -         OK
2231 DIF   (1701-)  B  -         OK
2233 DIF   (2701-)  C  -         OK
2235 A10   (3703-)  C  -         Fragmented
2237 DIF   (3701-)  D  -         OK
2238 BOG   ( 703-)  B  -         OK

Administrative problems that can generate validation failures

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.

2210 NAG   ( 671-)  A  -   O4  bound to 2211 NAG   ( 672-)  A  -   C1
2211 NAG   ( 672-)  A  -   O4  bound to 2212 NAG   ( 673-)  A  -   C1
2215 NAG   (1671-)  B  -   O4  bound to 2216 NAG   (1672-)  B  -   C1
2216 NAG   (1672-)  B  -   O4  bound to 2217 NAG   (1673-)  B  -   C1
2220 NAG   (2671-)  C  -   O4  bound to 2221 NAG   (2672-)  C  -   C1
2221 NAG   (2672-)  C  -   O4  bound to 2222 NAG   (2673-)  C  -   C1
2225 NAG   (3671-)  D  -   O4  bound to 2226 NAG   (3672-)  D  -   C1
2226 NAG   (3672-)  D  -   O4  bound to 2227 NAG   (3673-)  D  -   C1

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

   1 ALA   (  33-)  A  -
   2 ASN   (  34-)  A  -

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

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   1 ALA   (  33-)  A      N
   2 ASN   (  34-)  A      N

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

  33 TYR   (  65-)  A
 116 TYR   ( 147-)  A
 223 TYR   ( 254-)  A
 231 TYR   ( 262-)  A
 244 TYR   ( 275-)  A
 342 TYR   ( 373-)  A
 354 TYR   ( 385-)  A
 371 TYR   ( 402-)  A
 444 TYR   ( 475-)  A
 464 TYR   ( 495-)  A
 513 TYR   ( 544-)  A
 575 TYR   (1055-)  B
 585 TYR   (1065-)  B
 611 TYR   (1091-)  B
 651 TYR   (1130-)  B
 668 TYR   (1147-)  B
 775 TYR   (1254-)  B
 783 TYR   (1262-)  B
 796 TYR   (1275-)  B
 894 TYR   (1373-)  B
 906 TYR   (1385-)  B
 930 TYR   (1409-)  B
 996 TYR   (1475-)  B
1016 TYR   (1495-)  B
1065 TYR   (1544-)  B
1137 TYR   (2065-)  C
1203 TYR   (2130-)  C
1220 TYR   (2147-)  C
1327 TYR   (2254-)  C
1335 TYR   (2262-)  C
1348 TYR   (2275-)  C
1446 TYR   (2373-)  C
1458 TYR   (2385-)  C
1475 TYR   (2402-)  C
1482 TYR   (2409-)  C
1548 TYR   (2475-)  C
1568 TYR   (2495-)  C
1617 TYR   (2544-)  C
1740 TYR   (3115-)  D
1772 TYR   (3147-)  D
1879 TYR   (3254-)  D
1887 TYR   (3262-)  D
1900 TYR   (3275-)  D
1998 TYR   (3373-)  D
2010 TYR   (3385-)  D
2027 TYR   (3402-)  D
2100 TYR   (3475-)  D
2120 TYR   (3495-)  D
2169 TYR   (3544-)  D

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

  20 PHE   (  52-)  A
  64 PHE   (  96-)  A
 156 PHE   ( 187-)  A
 178 PHE   ( 209-)  A
 216 PHE   ( 247-)  A
 254 PHE   ( 285-)  A
 336 PHE   ( 367-)  A
 498 PHE   ( 529-)  A
 519 PHE   ( 550-)  A
 546 PHE   ( 577-)  A
 549 PHE   ( 580-)  A
 572 PHE   (1052-)  B
 616 PHE   (1096-)  B
 708 PHE   (1187-)  B
 730 PHE   (1209-)  B
 768 PHE   (1247-)  B
 806 PHE   (1285-)  B
 888 PHE   (1367-)  B
1050 PHE   (1529-)  B
1071 PHE   (1550-)  B
1101 PHE   (1580-)  B
1124 PHE   (2052-)  C
1260 PHE   (2187-)  C
1282 PHE   (2209-)  C
1320 PHE   (2247-)  C
1358 PHE   (2285-)  C
1440 PHE   (2367-)  C
1602 PHE   (2529-)  C
1623 PHE   (2550-)  C
1650 PHE   (2577-)  C
1653 PHE   (2580-)  C
1676 PHE   (3052-)  D
1720 PHE   (3096-)  D
1812 PHE   (3187-)  D
1834 PHE   (3209-)  D
1872 PHE   (3247-)  D
1910 PHE   (3285-)  D
1992 PHE   (3367-)  D
2154 PHE   (3529-)  D
2175 PHE   (3550-)  D
2202 PHE   (3577-)  D
2205 PHE   (3580-)  D

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

 142 ASP   ( 173-)  A
 208 ASP   ( 239-)  A
 218 ASP   ( 249-)  A
 362 ASP   ( 393-)  A
 466 ASP   ( 497-)  A
 694 ASP   (1173-)  B
 760 ASP   (1239-)  B
 770 ASP   (1249-)  B
 914 ASP   (1393-)  B
1018 ASP   (1497-)  B
1246 ASP   (2173-)  C
1312 ASP   (2239-)  C
1322 ASP   (2249-)  C
1466 ASP   (2393-)  C
1570 ASP   (2497-)  C
1798 ASP   (3173-)  D
1864 ASP   (3239-)  D
1874 ASP   (3249-)  D
2018 ASP   (3393-)  D
2122 ASP   (3497-)  D

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

 109 GLU   ( 140-)  A
 139 GLU   ( 170-)  A
 145 GLU   ( 176-)  A
 277 GLU   ( 308-)  A
 295 GLU   ( 326-)  A
 308 GLU   ( 339-)  A
 333 GLU   ( 364-)  A
 370 GLU   ( 401-)  A
 426 GLU   ( 457-)  A
 449 GLU   ( 480-)  A
 453 GLU   ( 484-)  A
 455 GLU   ( 486-)  A
 459 GLU   ( 490-)  A
 471 GLU   ( 502-)  A
 489 GLU   ( 520-)  A
 661 GLU   (1140-)  B
 691 GLU   (1170-)  B
 697 GLU   (1176-)  B
 829 GLU   (1308-)  B
 847 GLU   (1326-)  B
 885 GLU   (1364-)  B
 922 GLU   (1401-)  B
 978 GLU   (1457-)  B
1001 GLU   (1480-)  B
1005 GLU   (1484-)  B
And so on for a total of 57 lines.

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 909 HIS   (1388-)  B      CG   CD2   1.41    4.5

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.

 117 TYR   ( 148-)  A      N    CA   C    96.67   -5.2
 357 HIS   ( 388-)  A      CD2  CG   ND1 110.81    4.7
 654 HIS   (1133-)  B      CG   ND1  CE1 109.60    4.0
 669 TYR   (1148-)  B      N    CA   C    95.57   -5.6
 841 HIS   (1320-)  B      CG   ND1  CE1 109.71    4.1
 872 HIS   (1351-)  B      CG   ND1  CE1 109.67    4.1
 907 HIS   (1386-)  B      CG   ND1  CE1 109.62    4.0
 909 HIS   (1388-)  B      CA   CB   CG  109.21   -4.6
 909 HIS   (1388-)  B      CD2  CG   ND1 111.26    5.2
1162 HIS   (2090-)  C      CG   ND1  CE1 109.63    4.0
1221 TYR   (2148-)  C      N    CA   C    96.46   -5.3
1305 HIS   (2232-)  C      CG   ND1  CE1 109.70    4.1
1461 HIS   (2388-)  C      CA   CB   CG  107.71   -6.1
1461 HIS   (2388-)  C      CD2  CG   ND1 111.81    5.7
1773 TYR   (3148-)  D      N    CA   C    96.38   -5.3
2011 HIS   (3386-)  D      CG   ND1  CE1 109.71    4.1
2013 HIS   (3388-)  D      NE2  CD2  CG  102.37   -4.1
2013 HIS   (3388-)  D      CD2  CG   ND1 111.23    5.1

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

 109 GLU   ( 140-)  A
 139 GLU   ( 170-)  A
 142 ASP   ( 173-)  A
 145 GLU   ( 176-)  A
 208 ASP   ( 239-)  A
 218 ASP   ( 249-)  A
 277 GLU   ( 308-)  A
 295 GLU   ( 326-)  A
 308 GLU   ( 339-)  A
 333 GLU   ( 364-)  A
 362 ASP   ( 393-)  A
 370 GLU   ( 401-)  A
 426 GLU   ( 457-)  A
 449 GLU   ( 480-)  A
 453 GLU   ( 484-)  A
 455 GLU   ( 486-)  A
 459 GLU   ( 490-)  A
 466 ASP   ( 497-)  A
 471 GLU   ( 502-)  A
 489 GLU   ( 520-)  A
 661 GLU   (1140-)  B
 691 GLU   (1170-)  B
 694 ASP   (1173-)  B
 697 GLU   (1176-)  B
 760 ASP   (1239-)  B
And so on for a total of 77 lines.

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 669 TYR   (1148-)  B    5.96
1773 TYR   (3148-)  D    5.65
1221 TYR   (2148-)  C    5.62
 117 TYR   ( 148-)  A    5.54
 642 SER   (1121-)  B    5.38
1746 SER   (3121-)  D    5.20
1194 SER   (2121-)  C    5.13
 536 LEU   ( 567-)  A    4.97
  90 SER   ( 121-)  A    4.91
 275 LEU   ( 306-)  A    4.64
1644 ASN   (2571-)  C    4.50
 540 ASN   ( 571-)  A    4.28
 972 SER   (1451-)  B    4.26
 701 LYS   (1180-)  B    4.25
 150 VAL   ( 181-)  A    4.24
2076 SER   (3451-)  D    4.23
 434 GLU   ( 465-)  A    4.21
 827 LEU   (1306-)  B    4.19
1931 LEU   (3306-)  D    4.12
 482 ARG   ( 513-)  A    4.12
1822 MET   (3197-)  D    4.12
2111 GLU   (3486-)  D    4.11
1092 ASN   (1571-)  B    4.09
 203 TYR   ( 234-)  A    4.09
 148 GLU   ( 179-)  A    4.05

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.532

Torsion-related checks

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.

 378 TYR   ( 409-)  A    -3.2
1179 PRO   (2106-)  C    -3.1
  75 PRO   ( 106-)  A    -3.1
2034 TYR   (3409-)  D    -3.0
1731 PRO   (3106-)  D    -2.9
1168 PHE   (2096-)  C    -2.9
 627 PRO   (1106-)  B    -2.8
1132 THR   (2060-)  C    -2.8
1557 GLU   (2484-)  C    -2.5
1005 GLU   (1484-)  B    -2.5
2109 GLU   (3484-)  D    -2.5
1651 THR   (2578-)  C    -2.5
1482 TYR   (2409-)  C    -2.5
 616 PHE   (1096-)  B    -2.5
 453 GLU   ( 484-)  A    -2.5
1680 LYS   (3056-)  D    -2.4
 930 TYR   (1409-)  B    -2.4
1096 CYS   (1575-)  B    -2.4
1178 ILE   (2105-)  C    -2.4
1465 PRO   (2392-)  C    -2.4
 465 SER   ( 496-)  A    -2.4
2172 PRO   (3547-)  D    -2.4
 650 THR   (1129-)  B    -2.4
1648 CYS   (2575-)  C    -2.4
2121 SER   (3496-)  D    -2.4
And so on for a total of 101 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   (  34-)  A  Impossible phi
  12 ARG   (  44-)  A  Poor phi/psi
  64 PHE   (  96-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
  98 THR   ( 129-)  A  Poor phi/psi
 134 VAL   ( 165-)  A  Poor phi/psi
 164 ASN   ( 195-)  A  Poor phi/psi
 199 LEU   ( 230-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 239 GLN   ( 270-)  A  Poor phi/psi
 342 TYR   ( 373-)  A  Poor phi/psi
 367 GLU   ( 398-)  A  Poor phi/psi
 407 ARG   ( 438-)  A  Poor phi/psi
 440 SER   ( 471-)  A  Poor phi/psi
 453 GLU   ( 484-)  A  Poor phi/psi
 465 SER   ( 496-)  A  Poor phi/psi
 484 ASP   ( 515-)  A  Poor phi/psi
 563 ASN   (1043-)  B  Poor phi/psi
 564 ARG   (1044-)  B  Poor phi/psi
 589 CYS   (1069-)  B  Poor phi/psi
 616 PHE   (1096-)  B  Poor phi/psi
 647 SER   (1126-)  B  PRO omega poor
 650 THR   (1129-)  B  Poor phi/psi
 686 VAL   (1165-)  B  Poor phi/psi
And so on for a total of 78 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 : -4.745

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.

 535 SER   ( 566-)  A    0.36

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 CYS   (  36-)  A      0
   5 CYS   (  37-)  A      0
   8 PRO   (  40-)  A      0
   9 CYS   (  41-)  A      0
  10 GLN   (  42-)  A      0
  12 ARG   (  44-)  A      0
  18 THR   (  50-)  A      0
  21 ASP   (  53-)  A      0
  22 GLN   (  54-)  A      0
  27 CYS   (  59-)  A      0
  28 THR   (  60-)  A      0
  29 ARG   (  61-)  A      0
  30 THR   (  62-)  A      0
  33 TYR   (  65-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  62 THR   (  94-)  A      0
  63 HIS   (  95-)  A      0
  64 PHE   (  96-)  A      0
  91 TYR   ( 122-)  A      0
  95 SER   ( 126-)  A      0
  96 PRO   ( 127-)  A      0
  97 PRO   ( 128-)  A      0
  98 THR   ( 129-)  A      0
  99 TYR   ( 130-)  A      0
And so on for a total of 840 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 : 1.295

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!

 683 PRO   (1162-)  B   1.74   13
 131 PRO   ( 162-)  A   1.74   13
1235 PRO   (2162-)  C   1.73   13
1787 PRO   (3162-)  D   1.73   13

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

1684 THR   (3060-)  D   1.58

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. 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]

 160 PRO   ( 191-)  A    0.20 LOW
1112 PRO   (2040-)  C    0.20 LOW
1816 PRO   (3191-)  D    0.16 LOW

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].

   8 PRO   (  40-)  A    51.8 half-chair C-delta/C-gamma (54 degrees)
  75 PRO   ( 106-)  A   132.1 half-chair C-beta/C-alpha (126 degrees)
 122 PRO   ( 153-)  A  -119.2 half-chair C-delta/C-gamma (-126 degrees)
 361 PRO   ( 392-)  A   -58.5 half-chair C-beta/C-alpha (-54 degrees)
 507 PRO   ( 538-)  A  -118.1 half-chair C-delta/C-gamma (-126 degrees)
 604 PRO   (1084-)  B   -64.2 envelop C-beta (-72 degrees)
 627 PRO   (1106-)  B   117.2 half-chair C-beta/C-alpha (126 degrees)
 674 PRO   (1153-)  B  -114.2 envelop C-gamma (-108 degrees)
 913 PRO   (1392-)  B   -58.0 half-chair C-beta/C-alpha (-54 degrees)
1059 PRO   (1538-)  B  -115.1 envelop C-gamma (-108 degrees)
1097 PRO   (1576-)  B   -36.6 envelop C-alpha (-36 degrees)
1107 PRO   (2035-)  C  -121.9 half-chair C-delta/C-gamma (-126 degrees)
1179 PRO   (2106-)  C   168.3 half-chair C-alpha/N (162 degrees)
1226 PRO   (2153-)  C  -115.5 envelop C-gamma (-108 degrees)
1264 PRO   (2191-)  C  -113.8 envelop C-gamma (-108 degrees)
1465 PRO   (2392-)  C   -57.0 half-chair C-beta/C-alpha (-54 degrees)
1611 PRO   (2538-)  C  -117.5 half-chair C-delta/C-gamma (-126 degrees)
1659 PRO   (3035-)  D  -112.2 envelop C-gamma (-108 degrees)
1731 PRO   (3106-)  D   108.9 envelop C-beta (108 degrees)
1778 PRO   (3153-)  D  -114.8 envelop C-gamma (-108 degrees)
2017 PRO   (3392-)  D   -61.8 half-chair C-beta/C-alpha (-54 degrees)
2163 PRO   (3538-)  D  -117.2 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

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. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

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). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

1196 LEU   (2123-)  C      O   <-> 1542 ARG   (2469-)  C      NH2    0.56    2.14  INTRA
1748 LEU   (3123-)  D      O   <-> 2094 ARG   (3469-)  D      NH2    0.55    2.15  INTRA
  92 LEU   ( 123-)  A      O   <->  438 ARG   ( 469-)  A      NH2    0.55    2.15  INTRA
 644 LEU   (1123-)  B      O   <->  990 ARG   (1469-)  B      NH2    0.55    2.15  INTRA
 263 LEU   ( 294-)  A      CD2 <->  378 TYR   ( 409-)  A      CD2    0.49    2.71  INTRA
1919 LEU   (3294-)  D      CD2 <-> 2034 TYR   (3409-)  D      CD2    0.47    2.73  INTRA
1178 ILE   (2105-)  C      CG2 <-> 1181 LEU   (2108-)  C      CB     0.43    2.77  INTRA
1215 PHE   (2142-)  C      O   <-> 1449 ARG   (2376-)  C      NH2    0.43    2.27  INTRA BL
 367 GLU   ( 398-)  A      CG  <->  390 GLN   ( 421-)  A      CD     0.42    2.78  INTRA BF
 919 GLU   (1398-)  B      CG  <->  942 GLN   (1421-)  B      CD     0.42    2.78  INTRA BF
1471 GLU   (2398-)  C      CG  <-> 1494 GLN   (2421-)  C      CD     0.41    2.79  INTRA BF
1738 MET   (3113-)  D      SD  <-> 1985 LYS   (3360-)  D      N      0.41    2.89  INTRA
 815 LEU   (1294-)  B      CD2 <->  930 TYR   (1409-)  B      CD1    0.40    2.80  INTRA
 663 PHE   (1142-)  B      O   <->  897 ARG   (1376-)  B      NH2    0.40    2.30  INTRA BL
1367 LEU   (2294-)  C      CD2 <-> 1482 TYR   (2409-)  C      CD1    0.39    2.81  INTRA
1395 GLU   (2322-)  C      CG  <-> 1675 GLY   (3051-)  D      C      0.38    2.82  INTRA
 511 PRO   ( 542-)  A      O   <->  581 ARG   (1061-)  B      NH1    0.37    2.33  INTRA BL
 230 VAL   ( 261-)  A      O   <->  276 ARG   ( 307-)  A      NH1    0.37    2.33  INTRA BL
1271 PHE   (2198-)  C      CZ  <-> 1425 LEU   (2352-)  C      CD1    0.36    2.84  INTRA BL
1334 VAL   (2261-)  C      O   <-> 1380 ARG   (2307-)  C      NH1    0.35    2.35  INTRA BL
2023 GLU   (3398-)  D      CG  <-> 2046 GLN   (3421-)  D      CD     0.35    2.85  INTRA BF
1133 ARG   (2061-)  C      NH1 <-> 2167 PRO   (3542-)  D      O      0.35    2.35  INTRA BL
  36 ASN   (  68-)  A      ND2 <-> 2209 NAG   ( 661-)  A      C6     0.35    2.75  INTRA BF
1618 TRP   (2545-)  C      O   <-> 1685 ARG   (3061-)  D      NH2    0.34    2.36  INTRA BL
 167 PHE   ( 198-)  A      CZ  <->  321 LEU   ( 352-)  A      CD1    0.34    2.86  INTRA BL
And so on for a total of 571 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

  29 ARG   (  61-)  A      -6.70
 581 ARG   (1061-)  B      -6.59
 247 HIS   ( 278-)  A      -6.52
 799 HIS   (1278-)  B      -6.50
1903 HIS   (3278-)  D      -6.49
1351 HIS   (2278-)  C      -6.49
1685 ARG   (3061-)  D      -6.47
1133 ARG   (2061-)  C      -6.46
1124 PHE   (2052-)  C      -6.14
 572 PHE   (1052-)  B      -5.89
  20 PHE   (  52-)  A      -5.81
 154 ARG   ( 185-)  A      -5.65
1810 ARG   (3185-)  D      -5.56
1258 ARG   (2185-)  C      -5.53
 706 ARG   (1185-)  B      -5.45
2053 ARG   (3428-)  D      -5.44
1676 PHE   (3052-)  D      -5.44
1841 ARG   (3216-)  D      -5.39
 737 ARG   (1216-)  B      -5.37
1794 LYS   (3169-)  D      -5.35
 949 ARG   (1428-)  B      -5.32
 138 LYS   ( 169-)  A      -5.32
1289 ARG   (2216-)  C      -5.32
 690 LYS   (1169-)  B      -5.31
 185 ARG   ( 216-)  A      -5.28
And so on for a total of 65 lines.

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

  20 PHE   (  52-)  A        22 - GLN     54- ( A)         -4.66
 138 LYS   ( 169-)  A       140 - LEU    171- ( A)         -4.75
 183 HIS   ( 214-)  A       185 - ARG    216- ( A)         -4.84
 690 LYS   (1169-)  B       692 - LEU   1171- ( B)         -4.74
 735 HIS   (1214-)  B       737 - ARG   1216- ( B)         -4.84
1124 PHE   (2052-)  C      1126 - GLN   2054- ( C)         -4.95
1242 LYS   (2169-)  C      1244 - LEU   2171- ( C)         -4.74
1287 HIS   (2214-)  C      1289 - ARG   2216- ( C)         -4.84
1676 PHE   (3052-)  D      1678 - GLN   3054- ( D)         -4.65
1794 LYS   (3169-)  D      1796 - LEU   3171- ( D)         -4.79
1839 HIS   (3214-)  D      1841 - ARG   3216- ( D)         -4.89

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: C

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: D

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 105 TYR   ( 136-)  A   -2.76
1761 TYR   (3136-)  D   -2.74
1990 LEU   (3365-)  D   -2.73
1438 LEU   (2365-)  C   -2.72
 886 LEU   (1365-)  B   -2.71
1209 TYR   (2136-)  C   -2.68
 334 LEU   ( 365-)  A   -2.68
 657 TYR   (1136-)  B   -2.66

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

2240 HOH   (5132 )  B      O
2242 HOH   (5218 )  D      O
2242 HOH   (5299 )  D      O
Bound group on Asn; dont flip   36 ASN  (  68-) A
Bound to: 2209 NAG  ( 661-) A
Bound group on Asn; dont flip  113 ASN  ( 144-) A
Bound to: 2210 NAG  ( 671-) A
Bound group on Asn; dont flip  379 ASN  ( 410-) A
Bound to: 2213 NAG  ( 681-) A
Bound group on Asn; dont flip  588 ASN  (1068-) B
Bound to: 2214 NAG  (1661-) B
Bound group on Asn; dont flip  665 ASN  (1144-) B
Bound to: 2215 NAG  (1671-) B
Bound group on Asn; dont flip  931 ASN  (1410-) B
Bound to: 2218 NAG  (1681-) B
Bound group on Asn; dont flip 1140 ASN  (2068-) C
Bound to: 2219 NAG  (2661-) C
Bound group on Asn; dont flip 1217 ASN  (2144-) C
Bound to: 2220 NAG  (2671-) C
Bound group on Asn; dont flip 1483 ASN  (2410-) C
Bound to: 2223 NAG  (2681-) C
Bound group on Asn; dont flip 1692 ASN  (3068-) D
Bound to: 2224 NAG  (3661-) D
Bound group on Asn; dont flip 1769 ASN  (3144-) D
Bound to: 2225 NAG  (3671-) D
Bound group on Asn; dont flip 2035 ASN  (3410-) D
Bound to: 2228 NAG  (3681-) D
Marked this atom as acceptor 2229 DIF  ( 701-) A     CL2
Marked this atom as acceptor 2229 DIF  ( 701-) A     CL4
Marked this atom as acceptor 2231 DIF  (1701-) B     CL2
Marked this atom as acceptor 2231 DIF  (1701-) B     CL4
Marked this atom as acceptor 2233 DIF  (2701-) C     CL2
Marked this atom as acceptor 2233 DIF  (2701-) C     CL4
Marked this atom as acceptor 2237 DIF  (3701-) D     CL2
Marked this atom as acceptor 2237 DIF  (3701-) D     CL4
Metal-coordinating Histidine residue 357 fixed to   1
Metal-coordinating Histidine residue 909 fixed to   1
Metal-coordinating Histidine residue1461 fixed to   1
Metal-coordinating Histidine residue2013 fixed to   1

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

 100 ASN   ( 131-)  A
 433 ASN   ( 464-)  A
 554 ASN   (1034-)  B
 615 HIS   (1095-)  B
 652 ASN   (1131-)  B
 724 GLN   (1203-)  B
 762 GLN   (1241-)  B
 848 GLN   (1327-)  B
 877 HIS   (1356-)  B
 889 ASN   (1368-)  B
 917 ASN   (1396-)  B
 985 ASN   (1464-)  B
1104 GLN   (1583-)  B
1106 ASN   (2034-)  C
1204 ASN   (2131-)  C
1400 GLN   (2327-)  C
1441 ASN   (2368-)  C
1537 ASN   (2464-)  C
1658 ASN   (3034-)  D
1756 ASN   (3131-)  D
1866 GLN   (3241-)  D
2089 ASN   (3464-)  D
2208 GLN   (3583-)  D

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   4 CYS   (  36-)  A      N
  19 GLY   (  51-)  A      N
  53 THR   (  85-)  A      N
 100 ASN   ( 131-)  A      ND2
 105 TYR   ( 136-)  A      N
 107 SER   ( 138-)  A      N
 107 SER   ( 138-)  A      OG
 108 TRP   ( 139-)  A      N
 132 MET   ( 163-)  A      N
 135 LYS   ( 166-)  A      N
 145 GLU   ( 176-)  A      N
 161 GLN   ( 192-)  A      N
 172 GLN   ( 203-)  A      NE2
 194 GLY   ( 225-)  A      N
 206 THR   ( 237-)  A      N
 214 ARG   ( 245-)  A      NH1
 214 ARG   ( 245-)  A      NH2
 217 LYS   ( 248-)  A      N
 224 GLN   ( 255-)  A      NE2
 262 GLY   ( 293-)  A      N
 264 VAL   ( 295-)  A      N
 266 GLY   ( 297-)  A      N
 291 GLU   ( 322-)  A      N
 317 TYR   ( 348-)  A      OH
 319 GLN   ( 350-)  A      N
And so on for a total of 174 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 159 ASP   ( 190-)  A      OD1
 205 GLU   ( 236-)  A      OE2
 308 GLU   ( 339-)  A      OE2
 325 HIS   ( 356-)  A      ND1
 355 HIS   ( 386-)  A      ND1
 380 ASN   ( 411-)  A      OD1
 711 ASP   (1190-)  B      OD1
 860 GLU   (1339-)  B      OE1
 907 HIS   (1386-)  B      ND1
 932 ASN   (1411-)  B      OD1
1011 GLU   (1490-)  B      OE2
1031 GLU   (1510-)  B      OE1
1104 GLN   (1583-)  B      OE1
1263 ASP   (2190-)  C      OD1
1412 GLU   (2339-)  C      OE2
1429 HIS   (2356-)  C      ND1
1459 HIS   (2386-)  C      ND1
1484 ASN   (2411-)  C      OD1
1563 GLU   (2490-)  C      OE2
1804 GLU   (3179-)  D      OE1
1815 ASP   (3190-)  D      OD1
1964 GLU   (3339-)  D      OE1
1981 HIS   (3356-)  D      ND1
2036 ASN   (3411-)  D      OD1
2208 GLN   (3583-)  D      OE1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

2242 HOH   (5108 )  D      O  1.14  K  4

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  21 ASP   (  53-)  A   H-bonding suggests Asn; but Alt-Rotamer
 291 GLU   ( 322-)  A   H-bonding suggests Gln
 573 ASP   (1053-)  B   H-bonding suggests Asn; but Alt-Rotamer
1125 ASP   (2053-)  C   H-bonding suggests Asn; but Alt-Rotamer
1395 GLU   (2322-)  C   H-bonding suggests Gln
1677 ASP   (3053-)  D   H-bonding suggests Asn; but Alt-Rotamer
1947 GLU   (3322-)  D   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.582
  2nd generation packing quality :  -1.654
  Ramachandran plot appearance   :  -2.700
  chi-1/chi-2 rotamer normality  :  -4.745 (bad)
  Backbone conformation          :  -1.120

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.428 (tight)
  Bond angles                    :   0.667
  Omega angle restraints         :   0.236 (tight)
  Side chain planarity           :   0.196 (tight)
  Improper dihedral distribution :   0.616
  B-factor distribution          :   0.935
  Inside/Outside distribution    :   1.098

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :  -0.3
  chi-1/chi-2 rotamer normality  :  -2.4
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.428 (tight)
  Bond angles                    :   0.667
  Omega angle restraints         :   0.236 (tight)
  Side chain planarity           :   0.196 (tight)
  Improper dihedral distribution :   0.616
  B-factor distribution          :   0.935
  Inside/Outside distribution    :   1.098
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.