WHAT IF Check report

This file was created 2011-12-13 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 pdb2ayl.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 : 0.449
CA-only RMS fit for the two chains : 0.237

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

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 132581.172
Volume of the Unit Cell V= 4527288.5
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.268
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.440

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.

1119 BOG   ( 751-)  A  -         OK
1120 BOG   ( 752-)  B  -         OK
1121 BOG   ( 753-)  A  -         OK
1122 BOG   ( 754-)  A  -         OK
1123 MAN   ( 673-)  A  -         OK
1124 MAN   ( 674-)  A  -         OK
1125 MAN   ( 675-)  A  -         OK
1126 MAN   ( 683-)  A  -         OK
1127 MAN   ( 684-)  A  -         OK
1128 FLP   (1701-)  A  -         OK
1129 MNH   ( 601-)  A  -         Atom types
1132 BOG   (1751-)  B  -         OK
1133 BOG   (1750-)  B  -         OK
1135 MAN   (1673-)  B  -         OK
1136 MAN   (1674-)  B  -         OK
1137 MAN   (1675-)  B  -         OK
1138 MAN   (1683-)  B  -         OK
1139 MNH   (1601-)  B  -         Atom types
1142 FLP   (2701-)  B  -         OK
1143 MAN   (1684-)  B  -         OK
1144 BOG   (1753-)  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.

1107 NAG   ( 661-)  A  -   O4  bound to 1108 NAG   ( 662-)  A  -   C1
1109 NAG   ( 671-)  A  -   O4  bound to 1110 NAG   ( 672-)  A  -   C1
1110 NAG   ( 672-)  A  -   O4  bound to 1123 MAN   ( 673-)  A  -   C1
1111 NAG   ( 681-)  A  -   O4  bound to 1112 NAG   ( 682-)  A  -   C1
1112 NAG   ( 682-)  A  -   O4  bound to 1126 MAN   ( 683-)  A  -   C1
1113 NAG   (1661-)  B  -   O4  bound to 1114 NAG   (1662-)  B  -   C1
1115 NAG   (1671-)  B  -   O4  bound to 1116 NAG   (1672-)  B  -   C1
1116 NAG   (1672-)  B  -   O4  bound to 1135 MAN   (1673-)  B  -   C1
1117 NAG   (1681-)  B  -   O4  bound to 1118 NAG   (1682-)  B  -   C1
1118 NAG   (1682-)  B  -   O4  bound to 1138 MAN   (1683-)  B  -   C1

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

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

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) :180.000

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

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 149 ARG   ( 180-)  A
 428 ARG   ( 459-)  A
 702 ARG   (1180-)  B
 981 ARG   (1459-)  B

Warning: Tyrosine convention problem

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

  99 TYR   ( 130-)  A
 211 TYR   ( 242-)  A
 223 TYR   ( 254-)  A
 231 TYR   ( 262-)  A
 324 TYR   ( 355-)  A
 342 TYR   ( 373-)  A
 354 TYR   ( 385-)  A
 373 TYR   ( 404-)  A
 386 TYR   ( 417-)  A
 444 TYR   ( 475-)  A
 464 TYR   ( 495-)  A
 513 TYR   ( 544-)  A
 652 TYR   (1130-)  B
 764 TYR   (1242-)  B
 784 TYR   (1262-)  B
 877 TYR   (1355-)  B
 895 TYR   (1373-)  B
 907 TYR   (1385-)  B
 926 TYR   (1404-)  B
 939 TYR   (1417-)  B
 997 TYR   (1475-)  B
1017 TYR   (1495-)  B
1066 TYR   (1544-)  B

Warning: Phenylalanine convention problem

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

  57 PHE   (  88-)  A
  71 PHE   ( 102-)  A
 150 PHE   ( 181-)  A
 156 PHE   ( 187-)  A
 167 PHE   ( 198-)  A
 170 PHE   ( 201-)  A
 178 PHE   ( 209-)  A
 189 PHE   ( 220-)  A
 216 PHE   ( 247-)  A
 336 PHE   ( 367-)  A
 378 PHE   ( 409-)  A
 447 PHE   ( 478-)  A
 487 PHE   ( 518-)  A
 498 PHE   ( 529-)  A
 519 PHE   ( 550-)  A
 549 PHE   ( 580-)  A
 572 PHE   (1050-)  B
 610 PHE   (1088-)  B
 703 PHE   (1181-)  B
 709 PHE   (1187-)  B
 720 PHE   (1198-)  B
 723 PHE   (1201-)  B
 731 PHE   (1209-)  B
 742 PHE   (1220-)  B
 769 PHE   (1247-)  B
 889 PHE   (1367-)  B
 931 PHE   (1409-)  B
1000 PHE   (1478-)  B
1040 PHE   (1518-)  B
1051 PHE   (1529-)  B
1072 PHE   (1550-)  B
1102 PHE   (1580-)  B

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.

  22 ASP   (  53-)  A
 218 ASP   ( 249-)  A
 283 ASP   ( 314-)  A
 362 ASP   ( 393-)  A
 466 ASP   ( 497-)  A
 575 ASP   (1053-)  B
 771 ASP   (1249-)  B
 836 ASP   (1314-)  B
 915 ASP   (1393-)  B
1019 ASP   (1497-)  B

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.

  42 GLU   (  73-)  A
 144 GLU   ( 175-)  A
 237 GLU   ( 268-)  A
 277 GLU   ( 308-)  A
 288 GLU   ( 319-)  A
 316 GLU   ( 347-)  A
 333 GLU   ( 364-)  A
 374 GLU   ( 405-)  A
 423 GLU   ( 454-)  A
 449 GLU   ( 480-)  A
 453 GLU   ( 484-)  A
 471 GLU   ( 502-)  A
 479 GLU   ( 510-)  A
 489 GLU   ( 520-)  A
 522 GLU   ( 553-)  A
 595 GLU   (1073-)  B
 697 GLU   (1175-)  B
 761 GLU   (1239-)  B
 790 GLU   (1268-)  B
 830 GLU   (1308-)  B
 841 GLU   (1319-)  B
 861 GLU   (1339-)  B
 886 GLU   (1364-)  B
 927 GLU   (1405-)  B
1002 GLU   (1480-)  B
1006 GLU   (1484-)  B
1032 GLU   (1510-)  B
1042 GLU   (1520-)  B
1075 GLU   (1553-)  B

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.998151 -0.000133 -0.000038|
 | -0.000133  0.998760  0.000128|
 | -0.000038  0.000128  0.998719|
Proposed new scale matrix

 |  0.010127  0.000001  0.000000|
 |  0.000000  0.004847  0.000000|
 |  0.000000  0.000000  0.004520|
With corresponding cell

    A    =  98.749  B   = 206.313  C    = 221.249
    Alpha=  90.002  Beta=  90.002  Gamma=  90.009

The CRYST1 cell dimensions

    A    =  98.931  B   = 206.550  C    = 221.553
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 84.005
(Under-)estimated Z-score: 6.755

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    99.76   -4.1
 670 TYR   (1148-)  B      N    CA   C    99.58   -4.1

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.

  22 ASP   (  53-)  A
  42 GLU   (  73-)  A
 144 GLU   ( 175-)  A
 149 ARG   ( 180-)  A
 218 ASP   ( 249-)  A
 237 GLU   ( 268-)  A
 277 GLU   ( 308-)  A
 283 ASP   ( 314-)  A
 288 GLU   ( 319-)  A
 316 GLU   ( 347-)  A
 333 GLU   ( 364-)  A
 362 ASP   ( 393-)  A
 374 GLU   ( 405-)  A
 423 GLU   ( 454-)  A
 428 ARG   ( 459-)  A
 449 GLU   ( 480-)  A
 453 GLU   ( 484-)  A
 466 ASP   ( 497-)  A
 471 GLU   ( 502-)  A
 479 GLU   ( 510-)  A
 489 GLU   ( 520-)  A
 522 GLU   ( 553-)  A
 575 ASP   (1053-)  B
 595 GLU   (1073-)  B
 697 GLU   (1175-)  B
 702 ARG   (1180-)  B
 761 GLU   (1239-)  B
 771 ASP   (1249-)  B
 790 GLU   (1268-)  B
 830 GLU   (1308-)  B
 836 ASP   (1314-)  B
 841 GLU   (1319-)  B
 861 GLU   (1339-)  B
 886 GLU   (1364-)  B
 915 ASP   (1393-)  B
 927 GLU   (1405-)  B
 981 ARG   (1459-)  B
1002 GLU   (1480-)  B
1006 GLU   (1484-)  B
1019 ASP   (1497-)  B
1032 GLU   (1510-)  B
1042 GLU   (1520-)  B
1075 GLU   (1553-)  B

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.

 665 SER   (1143-)  B    5.95
 112 SER   ( 143-)  A    5.73
 150 PHE   ( 181-)  A    5.46
 538 CYS   ( 569-)  A    5.13
 315 GLU   ( 346-)  A    5.09
 868 GLU   (1346-)  B    4.76
1091 CYS   (1569-)  B    4.76
 703 PHE   (1181-)  B    4.67
 670 TYR   (1148-)  B    4.43
 117 TYR   ( 148-)  A    4.36

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.

1040 PHE   (1518-)  B    -3.3
 487 PHE   ( 518-)  A    -3.2
 583 ARG   (1061-)  B    -2.7
   8 TYR   (  39-)  A    -2.6
 561 TYR   (1039-)  B    -2.6
 354 TYR   ( 385-)  A    -2.6
 707 ARG   (1185-)  B    -2.6
1098 PRO   (1576-)  B    -2.6
 907 TYR   (1385-)  B    -2.6
 378 PHE   ( 409-)  A    -2.4
1006 GLU   (1484-)  B    -2.4
 453 GLU   ( 484-)  A    -2.3
 591 CYS   (1069-)  B    -2.3
 532 THR   ( 563-)  A    -2.3
  99 TYR   ( 130-)  A    -2.3
 545 PRO   ( 576-)  A    -2.2
 571 ARG   (1049-)  B    -2.2
 345 ARG   ( 376-)  A    -2.2
 654 ILE   (1132-)  B    -2.2
1085 THR   (1563-)  B    -2.2
 686 GLY   (1164-)  B    -2.2
 752 LEU   (1230-)  B    -2.2
 133 GLY   ( 164-)  A    -2.2
1092 LEU   (1570-)  B    -2.1
  18 ARG   (  49-)  A    -2.1
 652 TYR   (1130-)  B    -2.1
 199 LEU   ( 230-)  A    -2.1
 813 VAL   (1291-)  B    -2.1
 671 THR   (1149-)  B    -2.1
 672 ARG   (1150-)  B    -2.1
 119 ARG   ( 150-)  A    -2.1
 931 PHE   (1409-)  B    -2.1
 260 VAL   ( 291-)  A    -2.1
 467 ILE   ( 498-)  A    -2.0
  38 CYS   (  69-)  A    -2.0
 118 THR   ( 149-)  A    -2.0
1020 ILE   (1498-)  B    -2.0
 774 LEU   (1252-)  B    -2.0
 221 LEU   ( 252-)  A    -2.0
 101 ILE   ( 132-)  A    -2.0

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.

  13 GLN   (  44-)  A  Poor phi/psi
  30 ARG   (  61-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
  98 THR   ( 129-)  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
 227 ASN   ( 258-)  A  Poor phi/psi
 378 PHE   ( 409-)  A  Poor phi/psi
 381 SER   ( 412-)  A  Poor phi/psi
 428 ARG   ( 459-)  A  Poor phi/psi
 465 GLY   ( 496-)  A  Poor phi/psi
 514 TRP   ( 545-)  A  Poor phi/psi
 566 GLN   (1044-)  B  Poor phi/psi
 583 ARG   (1061-)  B  Poor phi/psi
 648 SER   (1126-)  B  PRO omega poor
 651 THR   (1129-)  B  Poor phi/psi
 752 LEU   (1230-)  B  Poor phi/psi
 769 PHE   (1247-)  B  Poor phi/psi
 771 ASP   (1249-)  B  Poor phi/psi
 780 ASN   (1258-)  B  Poor phi/psi
 931 PHE   (1409-)  B  Poor phi/psi
1067 TRP   (1545-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.347

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.

 110 SER   ( 141-)  A    0.36
 147 SER   ( 178-)  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!

   3 ASN   (  34-)  A      0
   5 CYS   (  36-)  A      0
   6 CYS   (  37-)  A      0
   8 TYR   (  39-)  A      0
   9 PRO   (  40-)  A      0
  10 CYS   (  41-)  A      0
  11 GLN   (  42-)  A      0
  12 HIS   (  43-)  A      0
  13 GLN   (  44-)  A      0
  19 PHE   (  50-)  A      0
  21 LEU   (  52-)  A      0
  22 ASP   (  53-)  A      0
  28 CYS   (  59-)  A      0
  29 THR   (  60-)  A      0
  30 ARG   (  61-)  A      0
  31 THR   (  62-)  A      0
  33 TYR   (  64-)  A      0
  34 SER   (  65-)  A      0
  38 CYS   (  69-)  A      0
  39 THR   (  70-)  A      0
  43 ILE   (  74-)  A      0
  52 ARG   (  83-)  A      0
  63 THR   (  94-)  A      0
  64 HIS   (  95-)  A      0
  74 ALA   ( 105-)  A      0
And so on for a total of 418 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 : 1.336

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!

 684 PRO   (1162-)  B   1.72   13

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].

 431 PRO   ( 462-)  A  -118.9 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.

1138 MAN   (1683-)  B      O6  <-> 1143 MAN   (1684-)  B      C1     1.00    1.40  INTRA BF
1138 MAN   (1683-)  B      C6  <-> 1143 MAN   (1684-)  B      C1     0.86    2.34  INTRA BF
  28 CYS   (  59-)  A      SG  <->   38 CYS   (  69-)  A    A SG     0.84    2.61  INTRA
 538 CYS   ( 569-)  A      SG  <->  544 CYS   ( 575-)  A      SG     0.81    2.64  INTRA BF
 581 CYS   (1059-)  B      SG  <->  591 CYS   (1069-)  B    A SG     0.70    2.75  INTRA
 896 ARG   (1374-)  B      NH1 <-> 1146 HOH   ( 153 )  B      O      0.44    2.26  INTRA BF
 905 GLN   (1383-)  B      NE2 <->  976 GLU   (1454-)  B      CD     0.43    2.67  INTRA
 321 LEU   ( 352-)  A      CD2 <->  487 PHE   ( 518-)  A      CZ     0.34    2.86  INTRA
  30 ARG   (  61-)  A      NH2 <-> 1145 HOH   (1963 )  A      O      0.33    2.37  INTRA
 737 LYS   (1215-)  B      NZ  <->  744 LYS   (1222-)  B      CD     0.32    2.78  INTRA BF
  96 PRO   ( 127-)  A      CD  <->  343 ARG   ( 374-)  A      NH2    0.32    2.78  INTRA
 534 LYS   ( 565-)  A      NZ  <->  544 CYS   ( 575-)  A      SG     0.31    2.99  INTRA BF
  95 SER   ( 126-)  A      OG  <->  343 ARG   ( 374-)  A      NH1    0.28    2.42  INTRA
 583 ARG   (1061-)  B      NH2 <-> 1146 HOH   ( 177 )  B      O      0.28    2.42  INTRA
  96 PRO   ( 127-)  A      CA  <->  343 ARG   ( 374-)  A      NH1    0.28    2.82  INTRA
1110 NAG   ( 672-)  A      C4  <-> 1123 MAN   ( 673-)  A      O2     0.24    2.56  INTRA BF
 110 SER   ( 141-)  A      O   <->  345 ARG   ( 376-)  A      NH2    0.24    2.46  INTRA
 357 HIS   ( 388-)  A      N   <->  358 PRO   ( 389-)  A      CD     0.23    2.77  INTRA BL
 896 ARG   (1374-)  B      NH2 <-> 1146 HOH   ( 595 )  B      O      0.23    2.47  INTRA BF
1110 NAG   ( 672-)  A      O3  <-> 1123 MAN   ( 673-)  A      C1     0.23    2.57  INTRA BF
 119 ARG   ( 150-)  A      CD  <->  121 LEU   ( 152-)  A      O      0.22    2.58  INTRA BL
 896 ARG   (1374-)  B      NH2 <-> 1146 HOH   ( 569 )  B      O      0.21    2.49  INTRA BF
  52 ARG   (  83-)  A      NH1 <-> 1145 HOH   (2121 )  A      O      0.20    2.50  INTRA BF
 765 GLN   (1243-)  B      NE2 <-> 1125 MAN   ( 675-)  A      C6     0.20    2.90  INTRA BF
  96 PRO   ( 127-)  A      N   <->  343 ARG   ( 374-)  A      NH1    0.20    2.80  INTRA
And so on for a total of 154 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

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.

 799 ARG   (1277-)  B      -7.81
 246 ARG   ( 277-)  A      -7.55
 139 GLN   ( 170-)  A      -7.08
 692 GLN   (1170-)  B      -7.06
  30 ARG   (  61-)  A      -6.71
 583 ARG   (1061-)  B      -6.65
 154 ARG   ( 185-)  A      -6.52
  21 LEU   (  52-)  A      -6.24
 896 ARG   (1374-)  B      -6.18
 574 LEU   (1052-)  B      -6.07
 737 LYS   (1215-)  B      -5.98
 156 PHE   ( 187-)  A      -5.97
 184 LYS   ( 215-)  A      -5.94
 343 ARG   ( 374-)  A      -5.89
 709 PHE   (1187-)  B      -5.69
 707 ARG   (1185-)  B      -5.63
 397 ARG   ( 428-)  A      -5.43
 339 GLN   ( 370-)  A      -5.43
 402 ARG   ( 433-)  A      -5.40
 950 ARG   (1428-)  B      -5.35
 892 GLN   (1370-)  B      -5.35
 965 HIS   (1443-)  B      -5.30
 412 HIS   ( 443-)  A      -5.29
 201 HIS   ( 232-)  A      -5.26
 754 HIS   (1232-)  B      -5.23
 702 ARG   (1180-)  B      -5.20
 185 MET   ( 216-)  A      -5.18
 438 ARG   ( 469-)  A      -5.17
   2 VAL   (  33-)  A      -5.15
 991 ARG   (1469-)  B      -5.11
 149 ARG   ( 180-)  A      -5.11
 555 VAL   (1033-)  B      -5.09

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.

 138 LYS   ( 169-)  A       140 - LEU    171- ( A)         -5.51
 153 ARG   ( 184-)  A       156 - PHE    187- ( A)         -5.30
 691 LYS   (1169-)  B       693 - LEU   1171- ( B)         -5.35
 706 ARG   (1184-)  B       709 - PHE   1187- ( B)         -4.99

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

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.

 658 TYR   (1136-)  B   -2.82
 105 TYR   ( 136-)  A   -2.79
 966 ILE   (1444-)  B   -2.65
 413 ILE   ( 444-)  A   -2.58
 344 ASN   ( 375-)  A   -2.55
 887 LEU   (1365-)  B   -2.54
 334 LEU   ( 365-)  A   -2.54

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

 744 LYS   (1222-)  B     -  747 GLY   (1225-)  B        -1.88

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

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1146 HOH   ( 491 )  B      O     23.49   68.04  179.80
1146 HOH   ( 734 )  B      O     32.35   -0.47  187.29
1146 HOH   ( 803 )  B      O     -1.21   34.97  178.96

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.

1145 HOH   (2072 )  A      O
1146 HOH   ( 729 )  B      O
1146 HOH   ( 883 )  B      O
Bound group on Asn; dont flip   37 ASN  (  68-) A
Bound to: 1107 NAG  ( 661-) A
Bound group on Asn; dont flip  113 ASN  ( 144-) A
Bound to: 1109 NAG  ( 671-) A
Bound group on Asn; dont flip  379 ASN  ( 410-) A
Bound to: 1111 NAG  ( 681-) A
Bound group on Asn; dont flip  590 ASN  (1068-) B
Bound to: 1113 NAG  (1661-) B
Bound group on Asn; dont flip  666 ASN  (1144-) B
Bound to: 1115 NAG  (1671-) B
Bound group on Asn; dont flip  932 ASN  (1410-) B
Bound to: 1117 NAG  (1681-) B
Marked this atom as acceptor 1128 FLP  (1701-) A    A F
Marked this atom as acceptor 1142 FLP  (2701-) B      F
Metal-coordinating Histidine residue 357 fixed to   1
Metal-coordinating Histidine residue 910 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.

  11 GLN   (  42-)  A
  64 HIS   (  95-)  A
 103 HIS   ( 134-)  A
 177 GLN   ( 208-)  A
 206 ASN   ( 237-)  A
 210 GLN   ( 241-)  A
 289 HIS   ( 320-)  A
 412 HIS   ( 443-)  A
 482 HIS   ( 513-)  A
 564 GLN   (1042-)  B
 617 HIS   (1095-)  B
 656 HIS   (1134-)  B
 730 GLN   (1208-)  B
 759 ASN   (1237-)  B
 763 GLN   (1241-)  B
 842 HIS   (1320-)  B
 897 ASN   (1375-)  B
1035 HIS   (1513-)  B

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.

  89 ARG   ( 120-)  A      NE
  89 ARG   ( 120-)  A      NH1
  95 SER   ( 126-)  A      OG
 105 TYR   ( 136-)  A      N
 154 ARG   ( 185-)  A      NE
 172 GLN   ( 203-)  A      NE2
 177 GLN   ( 208-)  A      NE2
 182 SER   ( 213-)  A      OG
 201 HIS   ( 232-)  A      N
 201 HIS   ( 232-)  A      ND1
 206 ASN   ( 237-)  A      N
 217 LYS   ( 248-)  A      N
 259 GLU   ( 290-)  A      N
 266 GLY   ( 297-)  A      N
 280 ARG   ( 311-)  A      NH1
 317 TYR   ( 348-)  A      OH
 319 GLN   ( 350-)  A      N
 326 LEU   ( 357-)  A      N
 343 ARG   ( 374-)  A      NH2
 351 ASN   ( 382-)  A      ND2
 357 HIS   ( 388-)  A      N
 446 SER   ( 477-)  A      N
 466 ASP   ( 497-)  A      N
 487 PHE   ( 518-)  A      N
 524 GLY   ( 555-)  A      N
And so on for a total of 56 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.

 308 GLU   ( 339-)  A      OE1
 726 HIS   (1204-)  B      NE2
 842 HIS   (1320-)  B      ND1
 861 GLU   (1339-)  B      OE1
 965 HIS   (1443-)  B      ND1
 976 GLU   (1454-)  B      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.

1145 HOH   (1721 )  A      O  0.99  K  5
1145 HOH   (1754 )  A      O  1.00  K  4
1145 HOH   (1968 )  A      O  0.87  K  4
1146 HOH   (  71 )  B      O  1.05  K  5
1146 HOH   (  95 )  B      O  0.89  K  5

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.

  70 ASP   ( 101-)  A   H-bonding suggests Asn
 385 ASP   ( 416-)  A   H-bonding suggests Asn; but Alt-Rotamer
 938 ASP   (1416-)  B   H-bonding suggests Asn

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 :  -1.439
  2nd generation packing quality :  -1.851
  Ramachandran plot appearance   :  -0.691
  chi-1/chi-2 rotamer normality  :  -1.347
  Backbone conformation          :  -1.043

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.280 (tight)
  Bond angles                    :   0.625 (tight)
  Omega angle restraints         :   0.243 (tight)
  Side chain planarity           :   0.230 (tight)
  Improper dihedral distribution :   0.581
  B-factor distribution          :   0.341
  Inside/Outside distribution    :   1.096

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.2
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.280 (tight)
  Bond angles                    :   0.625 (tight)
  Omega angle restraints         :   0.243 (tight)
  Side chain planarity           :   0.230 (tight)
  Improper dihedral distribution :   0.581
  B-factor distribution          :   0.341
  Inside/Outside distribution    :   1.096
==============

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.