WHAT IF Check report

This file was created 2013-12-10 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 pdb4iib.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 : 5.814
CA-only RMS fit for the two chains : 5.527

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: Ligands for which a topology was generated automatically

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

1699 BMA   ( 903-)  A  -
1700 MAN   ( 904-)  A  -
1701 MAN   ( 905-)  A  -
1702 MAN   ( 906-)  A  -
1703 BMA   ( 910-)  A  -
1704 BMA   ( 915-)  A  -
1705 MAN   ( 916-)  A  -
1706 MAN   ( 917-)  A  -
1707 MAN   ( 918-)  A  -
1708 MAN   ( 919-)  A  -
1709 MAN   ( 920-)  A  -
1710 MAN   ( 921-)  A  -
1711 MAN   ( 922-)  A  -
1712 BMA   ( 925-)  A  -
1713 BMA   ( 928-)  A  -
1714 MAN   ( 929-)  A  -
1715 MAN   ( 930-)  A  -
1716 MAN   ( 931-)  A  -
1717 MAN   ( 932-)  A  -
1718 MRD   ( 942-)  A  -
1719 BMA   ( 935-)  A  -
1720 MAN   ( 936-)  A  -
1721 MAN   ( 937-)  A  -
1722 MAN   ( 938-)  A  -
1723 MAN   ( 939-)  A  -
And so on for a total of 62 lines.

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.

1667 NAG   ( 901-)  A  -   O4  bound to 1668 NAG   ( 902-)  A  -   C1
1668 NAG   ( 902-)  A  -   O4  bound to 1699 BMA   ( 903-)  A  -   C1
1670 NAG   ( 908-)  A  -   O4  bound to 1671 NAG   ( 909-)  A  -   C1
1671 NAG   ( 909-)  A  -   O4  bound to 1703 BMA   ( 910-)  A  -   C1
1672 NAG   ( 911-)  A  -   O4  bound to 1673 NAG   ( 912-)  A  -   C1
1674 NAG   ( 913-)  A  -   O4  bound to 1675 NAG   ( 914-)  A  -   C1
1675 NAG   ( 914-)  A  -   O4  bound to 1704 BMA   ( 915-)  A  -   C1
1676 NAG   ( 923-)  A  -   O4  bound to 1677 NAG   ( 924-)  A  -   C1
1677 NAG   ( 924-)  A  -   O4  bound to 1712 BMA   ( 925-)  A  -   C1
1679 NAG   ( 926-)  A  -   O4  bound to 1680 NAG   ( 927-)  A  -   C1
1680 NAG   ( 927-)  A  -   O4  bound to 1713 BMA   ( 928-)  A  -   C1
1681 NAG   ( 933-)  A  -   O4  bound to 1682 NAG   ( 934-)  A  -   C1
1682 NAG   ( 934-)  A  -   O4  bound to 1719 BMA   ( 935-)  A  -   C1
1683 NAG   ( 915-)  B  -   O4  bound to 1684 NAG   ( 916-)  B  -   C1
1684 NAG   ( 916-)  B  -   O4  bound to 1728 BMA   ( 917-)  B  -   C1
1685 NAG   ( 918-)  B  -   O4  bound to 1686 NAG   ( 919-)  B  -   C1
1686 NAG   ( 919-)  B  -   O4  bound to 1729 BMA   ( 920-)  B  -   C1
1687 NAG   ( 901-)  B  -   O4  bound to 1688 NAG   ( 902-)  B  -   C1
1688 NAG   ( 902-)  B  -   O4  bound to 1737 BMA   ( 903-)  B  -   C1
1689 NAG   ( 928-)  B  -   O4  bound to 1690 NAG   ( 929-)  B  -   C1
1690 NAG   ( 929-)  B  -   O4  bound to 1741 BMA   ( 930-)  B  -   C1
1691 NAG   ( 931-)  B  -   O4  bound to 1692 NAG   ( 932-)  B  -   C1
1692 NAG   ( 932-)  B  -   O4  bound to 1742 BMA   ( 933-)  B  -   C1
1694 NAG   ( 909-)  B  -   O4  bound to 1695 NAG   ( 910-)  B  -   C1
1695 NAG   ( 910-)  B  -   O4  bound to 1747 BMA   ( 911-)  B  -   C1
1696 NAG   ( 938-)  B  -   O4  bound to 1697 NAG   ( 939-)  B  -   C1
1697 NAG   ( 939-)  B  -   O4  bound to 1761 BMA   ( 940-)  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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

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

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.

 327 ARG   ( 348-)  A
 417 ARG   ( 438-)  A
 619 ARG   ( 640-)  A
1161 ARG   ( 348-)  B
1199 ARG   ( 386-)  B
1251 ARG   ( 438-)  B
1508 ARG   ( 702-)  B
1626 ARG   ( 820-)  B

Warning: Tyrosine convention problem

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

   8 TYR   (  29-)  A
 101 TYR   ( 122-)  A
 234 TYR   ( 255-)  A
 490 TYR   ( 511-)  A
 539 TYR   ( 560-)  A
 586 TYR   ( 607-)  A
 613 TYR   ( 634-)  A
 638 TYR   ( 659-)  A
 670 TYR   ( 696-)  A
 758 TYR   ( 784-)  A
 842 TYR   (  29-)  B
 935 TYR   ( 122-)  B
1074 TYR   ( 261-)  B
1324 TYR   ( 511-)  B
1373 TYR   ( 560-)  B
1420 TYR   ( 607-)  B
1447 TYR   ( 634-)  B
1502 TYR   ( 696-)  B
1590 TYR   ( 784-)  B

Warning: Phenylalanine convention problem

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

   7 PHE   (  28-)  A
  85 PHE   ( 106-)  A
 140 PHE   ( 161-)  A
 255 PHE   ( 276-)  A
 334 PHE   ( 355-)  A
 481 PHE   ( 502-)  A
 616 PHE   ( 637-)  A
 680 PHE   ( 706-)  A
 774 PHE   ( 800-)  A
 919 PHE   ( 106-)  B
 945 PHE   ( 132-)  B
1089 PHE   ( 276-)  B
1168 PHE   ( 355-)  B
1315 PHE   ( 502-)  B
1444 PHE   ( 631-)  B
1450 PHE   ( 637-)  B
1512 PHE   ( 706-)  B
1606 PHE   ( 800-)  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.

 540 ASP   ( 561-)  A

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.

 183 GLU   ( 204-)  A
 488 GLU   ( 509-)  A
 652 GLU   ( 678-)  A
 672 GLU   ( 698-)  A
 783 GLU   ( 809-)  A
 852 GLU   (  39-)  B
1418 GLU   ( 605-)  B
1484 GLU   ( 678-)  B

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.

   1 LEU   (  22-)  A      N    CA    1.57    5.7
   3 PHE   (  24-)  A      CA   CB    1.62    4.4
   9 PRO   (  30-)  A      CA   CB    1.62    4.3
  12 TRP   (  33-)  A      NE1  CE2   1.32   -4.3
  31 SER   (  52-)  A      N    CA    1.54    4.2
  58 GLY   (  79-)  A      CA   C     1.58    4.4
 104 GLY   ( 125-)  A      N    CA    1.52    4.6
 104 GLY   ( 125-)  A      CA   C     1.58    4.4
 108 GLY   ( 129-)  A      N    CA    1.52    4.1
 130 SER   ( 151-)  A      CA   CB    1.45   -4.0
 131 PRO   ( 152-)  A      C    O     1.32    4.4
 133 GLY   ( 154-)  A      CA   C     1.58    4.5
 172 LEU   ( 193-)  A      CA   CB    1.61    4.2
 184 ALA   ( 205-)  A      CA   C     1.61    4.1
 188 GLY   ( 209-)  A      N    CA    1.52    4.0
 191 ILE   ( 212-)  A      CA   CB    1.62    4.3
 202 LYS   ( 223-)  A      CA   C     1.62    4.5
 260 TRP   ( 281-)  A      NE1  CE2   1.31   -5.8
 281 ASP   ( 302-)  A      CB   CG    1.62    4.1
 315 ARG   ( 336-)  A      CZ   NH1   1.40    4.3
 436 PRO   ( 457-)  A      CD   N     1.53    4.3
 438 LEU   ( 459-)  A      C    O     1.31    4.0
 438 LEU   ( 459-)  A      CB   CG    1.62    4.3
 448 GLU   ( 469-)  A      CD   OE2   1.17   -4.3
 457 TYR   ( 478-)  A      CA   CB    1.61    4.1
And so on for a total of 66 lines.

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

 |  0.989935 -0.001100  0.002180|
 | -0.001100  0.989944  0.003080|
 |  0.002180  0.003080  0.989148|
Proposed new scale matrix

 |  0.012295  0.000014 -0.000027|
 |  0.000009  0.008211 -0.000026|
 | -0.000010 -0.000014  0.004548|
With corresponding cell

    A    =  81.336  B   = 121.795  C    = 219.861
    Alpha=  89.643  Beta=  89.748  Gamma=  90.127

The CRYST1 cell dimensions

    A    =  82.162  B   = 123.024  C    = 222.254
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 6016.048
(Under-)estimated Z-score: 57.164

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.

  25 ARG   (  46-)  A      CA   CB   CG  105.89   -4.1
  52 CYS   (  73-)  A      CA   CB   SG  104.05   -4.5
  55 GLN   (  76-)  A     -C    N    CA  113.02   -4.8
  67 MET   (  88-)  A      CA   CB   CG  103.96   -5.1
 103 ARG   ( 124-)  A      CB   CG   CD  102.23   -5.9
 151 PHE   ( 172-)  A      CA   CB   CG  117.92    4.1
 179 ARG   ( 200-)  A      CB   CG   CD  105.39   -4.4
 247 LYS   ( 268-)  A      CA   CB   CG  104.90   -4.6
 263 HIS   ( 284-)  A      CG   ND1  CE1 109.88    4.3
 364 GLN   ( 385-)  A      CB   CG   CD  104.78   -4.6
 367 HIS   ( 388-)  A      CG   ND1  CE1 109.72    4.1
 415 SER   ( 436-)  A      CA   CB   OG  101.98   -4.6
 466 SER   ( 487-)  A      CA   CB   OG  101.89   -4.6
 481 PHE   ( 502-)  A      CA   CB   CG  108.69   -5.1
 504 THR   ( 525-)  A      CA   CB   OG1 102.77   -4.6
 510 ASP   ( 531-)  A     -C    N    CA  114.47   -4.0
 592 ARG   ( 613-)  A      CG   CD   NE  119.41    5.2
 614 ARG   ( 635-)  A      CB   CG   CD  104.26   -4.9
 705 GLU   ( 731-)  A      CB   CG   CD  119.71    4.2
 749 VAL   ( 775-)  A      CA   CB   CG2 103.42   -4.2
 765 ASN   ( 791-)  A     -C    N    CA  112.94   -4.9
 782 SER   ( 808-)  A      CA   CB   OG   96.60   -7.3
 784 GLU   ( 810-)  A      C    CA   CB  102.06   -4.2
 789 THR   ( 815-)  A      N    CA   CB  117.82    4.3
 827 HIS   ( 853-)  A      C    CA   CB  102.41   -4.0
And so on for a total of 63 lines.

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.

 183 GLU   ( 204-)  A
 327 ARG   ( 348-)  A
 417 ARG   ( 438-)  A
 488 GLU   ( 509-)  A
 540 ASP   ( 561-)  A
 619 ARG   ( 640-)  A
 652 GLU   ( 678-)  A
 672 GLU   ( 698-)  A
 783 GLU   ( 809-)  A
 852 GLU   (  39-)  B
1161 ARG   ( 348-)  B
1199 ARG   ( 386-)  B
1251 ARG   ( 438-)  B
1418 GLU   ( 605-)  B
1484 GLU   ( 678-)  B
1508 ARG   ( 702-)  B
1626 ARG   ( 820-)  B

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 749 VAL   ( 775-)  A      CB    -6.3   -41.17   -32.96
1143 VAL   ( 330-)  B      CB    -6.1   -40.93   -32.96
The average deviation= 1.958

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.

1592 SER   ( 786-)  B    5.22
 515 ALA   ( 536-)  A    4.80
 473 LYS   ( 494-)  A    4.24
 760 SER   ( 786-)  A    4.23
 312 MET   ( 333-)  A    4.01
 942 GLY   ( 129-)  B    4.00

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 510 ASP   ( 531-)  A    6.90
 193 ASP   ( 214-)  A    6.67
1017 GLU   ( 204-)  B    6.59
 132 ASP   ( 153-)  A    6.22
 494 ASP   ( 515-)  A    6.04
 214 ASP   ( 235-)  A    5.76
1027 ASP   ( 214-)  B    5.47
1328 ASP   ( 515-)  B    5.33
 138 GLU   ( 159-)  A    5.31
 521 ASN   ( 542-)  A    5.10
 483 ASN   ( 504-)  A    4.99
1566 ASP   ( 760-)  B    4.96
1499 ASP   ( 693-)  B    4.91
 253 GLN   ( 274-)  A    4.90
1062 ASN   ( 249-)  B    4.85
 977 ASP   ( 164-)  B    4.83
 377 ASP   ( 398-)  A    4.76
 852 GLU   (  39-)  B    4.70
1203 GLU   ( 390-)  B    4.70
 912 ASP   (  99-)  B    4.60
 402 GLU   ( 423-)  A    4.58
1397 ASP   ( 584-)  B    4.54
1460 GLU   ( 647-)  B    4.50
1071 GLN   ( 258-)  B    4.45
1393 ASN   ( 580-)  B    4.43
1446 ASP   ( 633-)  B    4.42
 169 HIS   ( 190-)  A    4.41
 384 ASN   ( 405-)  A    4.31
1003 HIS   ( 190-)  B    4.20
1296 ASN   ( 483-)  B    4.20
 407 ASN   ( 428-)  A    4.19
1066 ASN   ( 253-)  B    4.04
1236 GLU   ( 423-)  B    4.03

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.

1410 PRO   ( 597-)  B    -2.9
1012 PHE   ( 199-)  B    -2.9
 576 PRO   ( 597-)  A    -2.8
 122 PRO   ( 143-)  A    -2.8
1183 PRO   ( 370-)  B    -2.7
 683 PRO   ( 709-)  A    -2.7
1515 PRO   ( 709-)  B    -2.7
 178 PHE   ( 199-)  A    -2.6
 349 PRO   ( 370-)  A    -2.4
 956 PRO   ( 143-)  B    -2.4
1271 TYR   ( 458-)  B    -2.4
1612 LYS   ( 806-)  B    -2.3
 908 LEU   (  95-)  B    -2.3
1113 PRO   ( 300-)  B    -2.3
1172 THR   ( 359-)  B    -2.3
 279 PRO   ( 300-)  A    -2.2
 851 GLY   (  38-)  B    -2.2
1468 THR   ( 655-)  B    -2.2
 417 ARG   ( 438-)  A    -2.2
1290 VAL   ( 477-)  B    -2.2
 456 VAL   ( 477-)  A    -2.2
 741 VAL   ( 767-)  A    -2.1
1251 ARG   ( 438-)  B    -2.1
1411 PHE   ( 598-)  B    -2.1
 959 GLY   ( 146-)  B    -2.1
 125 GLY   ( 146-)  A    -2.1
 748 ARG   ( 774-)  A    -2.1
1157 VAL   ( 344-)  B    -2.1
  29 ILE   (  50-)  A    -2.1
  74 LEU   (  95-)  A    -2.1
 634 THR   ( 655-)  A    -2.1
 338 THR   ( 359-)  A    -2.1
 553 PRO   ( 574-)  A    -2.1
1621 THR   ( 815-)  B    -2.0
 785 THR   ( 811-)  A    -2.0
1439 PHE   ( 626-)  B    -2.0
 577 PHE   ( 598-)  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.

   8 TYR   (  29-)  A  PRO omega poor
  48 GLU   (  69-)  A  Poor phi/psi
  50 GLU   (  71-)  A  Poor phi/psi
  63 ASN   (  84-)  A  Poor phi/psi
  71 ASP   (  92-)  A  omega poor
  78 ASP   (  99-)  A  Poor phi/psi
  79 SER   ( 100-)  A  Poor phi/psi
  95 TRP   ( 116-)  A  omega poor
 121 GLY   ( 142-)  A  PRO omega poor
 125 GLY   ( 146-)  A  PRO omega poor
 128 GLY   ( 149-)  A  Poor phi/psi
 140 PHE   ( 161-)  A  Poor phi/psi
 168 LYS   ( 189-)  A  omega poor
 170 TYR   ( 191-)  A  omega poor
 172 LEU   ( 193-)  A  Poor phi/psi
 178 PHE   ( 199-)  A  Poor phi/psi
 207 MET   ( 228-)  A  Poor phi/psi, omega poor
 225 CYS   ( 246-)  A  omega poor
 232 ASN   ( 253-)  A  Poor phi/psi
 258 SER   ( 279-)  A  omega poor
 278 MET   ( 299-)  A  PRO omega poor
 285 ASP   ( 306-)  A  Poor phi/psi
 287 ALA   ( 308-)  A  Poor phi/psi
 291 TRP   ( 312-)  A  Poor phi/psi
 336 SER   ( 357-)  A  omega poor
And so on for a total of 96 lines.

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.

1394 SER   ( 581-)  B    0.37
 560 SER   ( 581-)  A    0.39

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!

   8 TYR   (  29-)  A      0
  10 SER   (  31-)  A      0
  14 ASN   (  35-)  A      0
  16 GLN   (  37-)  A      0
  18 GLU   (  39-)  A      0
  19 TRP   (  40-)  A      0
  42 THR   (  63-)  A      0
  45 THR   (  66-)  A      0
  47 TRP   (  68-)  A      0
  48 GLU   (  69-)  A      0
  49 LEU   (  70-)  A      0
  50 GLU   (  71-)  A      0
  51 LYS   (  72-)  A      0
  52 CYS   (  73-)  A      0
  59 VAL   (  80-)  A      0
  70 GLN   (  91-)  A      0
  71 ASP   (  92-)  A      0
  72 SER   (  93-)  A      0
  74 LEU   (  95-)  A      0
  77 ARG   (  98-)  A      0
  78 ASP   (  99-)  A      0
  79 SER   ( 100-)  A      0
  80 ASP   ( 101-)  A      0
  81 TYR   ( 102-)  A      0
  95 TRP   ( 116-)  A      0
And so on for a total of 736 lines.

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!

 630 GLY   ( 651-)  A   1.62   39
1464 GLY   ( 651-)  B   1.59   37

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]

   5 PRO   (  26-)  A    0.15 LOW
  60 PRO   (  81-)  A    0.15 LOW
 349 PRO   ( 370-)  A    0.50 HIGH
 353 PRO   ( 374-)  A    0.19 LOW
 716 PRO   ( 742-)  A    0.47 HIGH
 721 PRO   ( 747-)  A    0.20 LOW
 812 PRO   ( 838-)  A    0.56 HIGH
 839 PRO   (  26-)  B    0.10 LOW
 894 PRO   (  81-)  B    0.16 LOW
 956 PRO   ( 143-)  B    0.45 HIGH
 965 PRO   ( 152-)  B    0.45 HIGH
1457 PRO   ( 644-)  B    0.49 HIGH
1553 PRO   ( 747-)  B    0.16 LOW
1657 PRO   ( 851-)  B    0.19 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].

 332 PRO   ( 353-)  A  -120.4 half-chair C-delta/C-gamma (-126 degrees)
 730 PRO   ( 756-)  A  -117.8 half-chair C-delta/C-gamma (-126 degrees)
1166 PRO   ( 353-)  B  -112.1 envelop C-gamma (-108 degrees)
1376 PRO   ( 563-)  B  -117.0 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.

1697 NAG   ( 939-)  B      O4  <-> 1761 BMA   ( 940-)  B      C1     0.97    1.43  INTRA B3
1752 MAN   ( 942-)  B      O6  <-> 1760 MAN   ( 945-)  B      C1     0.88    1.52  INTRA B3
1697 NAG   ( 939-)  B      C4  <-> 1761 BMA   ( 940-)  B      C1     0.85    2.35  INTRA
1752 MAN   ( 942-)  B      C6  <-> 1760 MAN   ( 945-)  B      C1     0.76    2.44  INTRA
1699 BMA   ( 903-)  A      C3  <-> 1700 MAN   ( 904-)  A      C5     0.65    2.45  INTRA
 793 ARG   ( 819-)  A      NH1 <->  834 GLN   ( 860-)  A      C      0.57    2.53  INTRA
 521 ASN   ( 542-)  A      ND2 <-> 1763 HOH   (1640 )  A      O      0.43    2.27  INTRA
1200 ASN   ( 387-)  B      CG  <-> 1764 HOH   (1673 )  B      O      0.33    2.47  INTRA
1426 ARG   ( 613-)  B      NH1 <-> 1764 HOH   (1057 )  B      O      0.31    2.39  INTRA
1200 ASN   ( 387-)  B      ND2 <-> 1764 HOH   (1673 )  B      O      0.27    2.43  INTRA
 217 ARG   ( 238-)  A      NE  <-> 1763 HOH   (1872 )  A      O      0.27    2.43  INTRA
1625 ARG   ( 819-)  B      NH1 <-> 1666 GLN   ( 860-)  B      C      0.24    2.86  INTRA
 816 HIS   ( 842-)  A      ND1 <->  827 HIS   ( 853-)  A      ND1    0.24    2.76  INTRA
 217 ARG   ( 238-)  A      NH2 <-> 1763 HOH   (1847 )  A      O      0.23    2.47  INTRA
 706 HIS   ( 732-)  A      ND1 <-> 1763 HOH   (1270 )  A      O      0.21    2.49  INTRA
  25 ARG   (  46-)  A      NH1 <-> 1763 HOH   (1948 )  A      O      0.20    2.50  INTRA
1476 HIS   ( 663-)  B      ND1 <-> 1764 HOH   (2051 )  B      O      0.20    2.50  INTRA
1285 LYS   ( 472-)  B      NZ  <-> 1764 HOH   (1477 )  B      O      0.17    2.53  INTRA
 598 ASN   ( 619-)  A      N   <-> 1763 HOH   (1622 )  A      O      0.16    2.54  INTRA
1415 LYS   ( 602-)  B      NZ  <-> 1764 HOH   (1882 )  B      O      0.16    2.54  INTRA
1754 MAN   ( 944-)  B      O6  <-> 1764 HOH   (1997 )  B      O      0.15    2.25  INTRA BF
 403 ASP   ( 424-)  A      OD2 <->  528 HIS   ( 549-)  A      ND1    0.14    2.56  INTRA BL
1669 NAG   ( 907-)  A      N2  <-> 1763 HOH   (1626 )  A      O      0.14    2.56  INTRA BF
 831 PRO   ( 857-)  A      CD  <-> 1763 HOH   (1336 )  A      O      0.14    2.66  INTRA
1492 GLY   ( 686-)  B      N   <-> 1764 HOH   (1455 )  B      O      0.13    2.57  INTRA
And so on for a total of 116 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.

 661 GLN   ( 687-)  A      -7.57
1493 GLN   ( 687-)  B      -7.48
 748 ARG   ( 774-)  A      -7.42
1580 ARG   ( 774-)  B      -6.87
 698 TYR   ( 724-)  A      -6.78
1530 TYR   ( 724-)  B      -6.67
 832 LYS   ( 858-)  A      -6.53
 330 GLN   ( 351-)  A      -6.11
1164 GLN   ( 351-)  B      -6.10
1664 LYS   ( 858-)  B      -6.09
 837 PHE   (  24-)  B      -6.02
   3 PHE   (  24-)  A      -6.02
 706 HIS   ( 732-)  A      -5.99
1538 HIS   ( 732-)  B      -5.98
 329 TYR   ( 350-)  A      -5.80
1163 TYR   ( 350-)  B      -5.62
 217 ARG   ( 238-)  A      -5.58
1051 ARG   ( 238-)  B      -5.58
 647 ASN   ( 668-)  A      -5.58
1308 GLN   ( 495-)  B      -5.47
1643 TYR   ( 837-)  B      -5.45
 474 GLN   ( 495-)  A      -5.41
1597 ASN   ( 791-)  B      -5.40
1199 ARG   ( 386-)  B      -5.40
1324 TYR   ( 511-)  B      -5.26
1426 ARG   ( 613-)  B      -5.17
1415 LYS   ( 602-)  B      -5.14
 519 ASN   ( 540-)  A      -5.09
1353 ASN   ( 540-)  B      -5.08
 592 ARG   ( 613-)  A      -5.08
 963 ARG   ( 150-)  B      -5.06
1423 TYR   ( 610-)  B      -5.04
 589 TYR   ( 610-)  A      -5.03
 581 LYS   ( 602-)  A      -5.01
 490 TYR   ( 511-)  A      -5.01
 765 ASN   ( 791-)  A      -5.01

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.

1336 ASN   ( 523-)  B   -3.12
 502 ASN   ( 523-)  A   -3.11
 262 ALA   ( 283-)  A   -2.78
1096 ALA   ( 283-)  B   -2.74
1547 SER   ( 741-)  B   -2.60
 715 SER   ( 741-)  A   -2.58
1637 ASP   ( 831-)  B   -2.56
1198 GLN   ( 385-)  B   -2.55
1639 VAL   ( 833-)  B   -2.54
 364 GLN   ( 385-)  A   -2.53

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.

 328 LEU   ( 349-)  A     -  331 PRO   ( 352-)  A        -1.79
 583 ARG   ( 604-)  A     -  586 TYR   ( 607-)  A        -1.77
 804 GLN   ( 830-)  A     -  807 VAL   ( 833-)  A        -1.55

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.

1763 HOH   (1458 )  A      O     63.59  -24.16   36.10
1763 HOH   (2026 )  A      O     47.70  -10.81  -26.23
1763 HOH   (2027 )  A      O     46.43   -9.09  -24.09
1764 HOH   (1563 )  B      O     97.13   12.90  -13.60
1764 HOH   (1612 )  B      O     28.93   35.39    2.30
1764 HOH   (1700 )  B      O     70.30   31.74   -4.85
1764 HOH   (1803 )  B      O     57.82   16.86   13.24

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.

1763 HOH   (1328 )  A      O
1763 HOH   (1511 )  A      O
1763 HOH   (1579 )  A      O
1763 HOH   (1642 )  A      O
1763 HOH   (1785 )  A      O
1763 HOH   (1822 )  A      O
1764 HOH   (1538 )  B      O
1764 HOH   (1562 )  B      O
1764 HOH   (1680 )  B      O
1764 HOH   (2089 )  B      O
1764 HOH   (2096 )  B      O
Bound group on Asn; dont flip   40 ASN  (  61-) A
Bound to: 1667 NAG  ( 901-) A
Bound group on Asn; dont flip  190 ASN  ( 211-) A
Bound to: 1669 NAG  ( 907-) A
Bound group on Asn; dont flip  231 ASN  ( 252-) A
Bound to: 1670 NAG  ( 908-) A
Bound group on Asn; dont flip  294 ASN  ( 315-) A
Bound to: 1672 NAG  ( 911-) A
Bound group on Asn; dont flip  301 ASN  ( 322-) A
Bound to: 1674 NAG  ( 913-) A
Bound group on Asn; dont flip  421 ASN  ( 442-) A
Bound to: 1676 NAG  ( 923-) A
Bound group on Asn; dont flip  502 ASN  ( 523-) A
Bound to: 1679 NAG  ( 926-) A
Bound group on Asn; dont flip  543 ASN  ( 564-) A
Bound to: 1681 NAG  ( 933-) A
Bound group on Asn; dont flip  686 ASN  ( 712-) A
Bound to: 1678 NAG  ( 940-) A
Bound group on Asn; dont flip  874 ASN  (  61-) B
Bound to: 1687 NAG  ( 901-) B
Bound group on Asn; dont flip 1024 ASN  ( 211-) B
Bound to: 1693 NAG  ( 908-) B
Bound group on Asn; dont flip 1065 ASN  ( 252-) B
Bound to: 1694 NAG  ( 909-) B
Bound group on Asn; dont flip 1128 ASN  ( 315-) B
Bound to: 1683 NAG  ( 915-) B
Bound group on Asn; dont flip 1135 ASN  ( 322-) B
Bound to: 1685 NAG  ( 918-) B
Bound group on Asn; dont flip 1255 ASN  ( 442-) B
Bound to: 1689 NAG  ( 928-) B
Bound group on Asn; dont flip 1336 ASN  ( 523-) B
Bound to: 1691 NAG  ( 931-) B
Bound group on Asn; dont flip 1377 ASN  ( 564-) B
Bound to: 1696 NAG  ( 938-) B
Bound group on Asn; dont flip 1518 ASN  ( 712-) B
Bound to: 1698 NAG  ( 946-) B

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.

  32 GLN   (  53-)  A
 109 GLN   ( 130-)  A
 173 ASN   ( 194-)  A
 823 GLN   ( 849-)  A
 866 GLN   (  53-)  B
1007 ASN   ( 194-)  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.

  71 ASP   (  92-)  A      N
  77 ARG   (  98-)  A      NH1
  79 SER   ( 100-)  A      OG
 193 ASP   ( 214-)  A      N
 208 TYR   ( 229-)  A      N
 238 ASN   ( 259-)  A      N
 254 GLY   ( 275-)  A      N
 265 SER   ( 286-)  A      N
 281 ASP   ( 302-)  A      N
 334 PHE   ( 355-)  A      N
 339 ARG   ( 360-)  A      NH1
 408 SER   ( 429-)  A      OG
 484 SER   ( 505-)  A      OG
 485 ASP   ( 506-)  A      N
 490 TYR   ( 511-)  A      N
 531 GLY   ( 552-)  A      N
 533 VAL   ( 554-)  A      N
 551 GLY   ( 572-)  A      N
 582 THR   ( 603-)  A      N
 625 TYR   ( 646-)  A      OH
 684 TRP   ( 710-)  A      N
 765 ASN   ( 791-)  A      N
 892 GLY   (  79-)  B      N
 905 ASP   (  92-)  B      N
 911 ARG   (  98-)  B      NH1
And so on for a total of 53 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.

 119 GLN   ( 140-)  A      OE1
 243 ASN   ( 264-)  A      OD1
 285 ASP   ( 306-)  A      OD1
 420 ASP   ( 441-)  A      OD2
 621 GLU   ( 642-)  A      OE1
 953 GLN   ( 140-)  B      OE1
1119 ASP   ( 306-)  B      OD1
1254 ASP   ( 441-)  B      OD2
1319 ASP   ( 506-)  B      OD2
1422 ASP   ( 609-)  B      OD2
1455 GLU   ( 642-)  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.

1763 HOH   (1099 )  A      O  0.87  K  4 NCS 1/1
1763 HOH   (1135 )  A      O  1.12  K  4 NCS 1/1
1763 HOH   (1228 )  A      O  0.86 NA  5 *1 and *2 NCS 1/1
1763 HOH   (1239 )  A      O  1.09  K  5
1763 HOH   (1242 )  A      O  0.97  K  4 NCS 1/1
1763 HOH   (1273 )  A      O  1.14  K  5
1763 HOH   (1311 )  A      O  1.09  K  4 NCS 1/1
1763 HOH   (1482 )  A      O  0.90  K  5 NCS 1/1
1763 HOH   (1497 )  A      O  0.93  K  4
1763 HOH   (1530 )  A      O  0.99  K  5
1763 HOH   (1534 )  A      O  0.98  K  4 NCS 1/1
1763 HOH   (1660 )  A      O  1.15  K  4 Ion-B NCS 1/1
1763 HOH   (1808 )  A      O  0.95  K  4 Ion-B NCS 1/1
1763 HOH   (1987 )  A      O  0.94  K  4 NCS 1/1
1764 HOH   (1139 )  B      O  1.00  K  5 NCS 1/1
1764 HOH   (1227 )  B      O  0.96  K  5 NCS 1/1
1764 HOH   (1252 )  B      O  1.00 NA  4 *1 and *2 NCS 1/1
1764 HOH   (1262 )  B      O  0.99  K  4 NCS 1/1
1764 HOH   (1338 )  B      O  1.01  K  4 NCS 1/1
1764 HOH   (1358 )  B      O  1.13  K  4
1764 HOH   (1365 )  B      O  1.00  K  5 NCS 1/1
1764 HOH   (1398 )  B      O  1.06  K  5 Ion-B NCS 1/1
1764 HOH   (1453 )  B      O  0.79 NA  4 *1 and *2 NCS 1/1
1764 HOH   (1488 )  B      O  1.02  K  5 Ion-B NCS 1/1
1764 HOH   (1745 )  B      O  0.92  K  4 Ion-B NCS 1/1
1764 HOH   (1776 )  B      O  1.01  K  5 NCS 1/1
1764 HOH   (2021 )  B      O  1.14  K  4 Ion-B
1764 HOH   (2030 )  B      O  0.82 NA  4 *1 and *2 Ion-B NCS 1/1
1764 HOH   (2082 )  B      O  1.05  K  4 Ion-B
1764 HOH   (2091 )  B      O  0.95  K  5 ION-B NCS 1/1
1764 HOH   (2097 )  B      O  0.78 NA  4 *1 and *2 Ion-B NCS 1/1

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.

  71 ASP   (  92-)  A   H-bonding suggests Asn; Ligand-contact
 160 ASP   ( 181-)  A   H-bonding suggests Asn; but Alt-Rotamer
 193 ASP   ( 214-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 285 ASP   ( 306-)  A   H-bonding suggests Asn
 485 ASP   ( 506-)  A   H-bonding suggests Asn
 588 ASP   ( 609-)  A   H-bonding suggests Asn
 593 GLU   ( 614-)  A   H-bonding suggests Gln
 775 ASP   ( 801-)  A   H-bonding suggests Asn
 905 ASP   (  92-)  B   H-bonding suggests Asn; Ligand-contact
1027 ASP   ( 214-)  B   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1119 ASP   ( 306-)  B   H-bonding suggests Asn
1319 ASP   ( 506-)  B   H-bonding suggests Asn
1422 ASP   ( 609-)  B   H-bonding suggests Asn
1607 ASP   ( 801-)  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 :  -1.084
  2nd generation packing quality :  -1.940
  Ramachandran plot appearance   :  -0.740
  chi-1/chi-2 rotamer normality  :  -0.696
  Backbone conformation          :  -0.667

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.348
  Bond angles                    :   1.165
  Omega angle restraints         :   1.152
  Side chain planarity           :   1.996
  Improper dihedral distribution :   1.578 (loose)
  B-factor distribution          :   0.661
  Inside/Outside distribution    :   1.039

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 : 1.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.7
  2nd generation packing quality :  -1.5
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -0.4
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.348
  Bond angles                    :   1.165
  Omega angle restraints         :   1.152
  Side chain planarity           :   1.996
  Improper dihedral distribution :   1.578 (loose)
  B-factor distribution          :   0.661
  Inside/Outside distribution    :   1.039
==============

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.