WHAT IF Check report

This file was created 2012-01-30 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 pdb3keh.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 : 0.995
CA-only RMS fit for the two chains : 0.612

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.

1010 NDG   (1997-)  A  -

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.

 996 NAG   (1503-)  B  -   O4  bound to  997 NAG   (1504-)  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: Missing atoms

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

 995 NAG   (1998-)  A      O4
 995 NAG   (1998-)  A      C4
 995 NAG   (1998-)  A      C1
 995 NAG   (1998-)  A      O5
 995 NAG   (1998-)  A      C5
 995 NAG   (1998-)  A      C6
 995 NAG   (1998-)  A      O6
 995 NAG   (1998-)  A      C3
 995 NAG   (1998-)  A      O3
 995 NAG   (1998-)  A      C2
 995 NAG   (1998-)  A      N2
 995 NAG   (1998-)  A      C7
 995 NAG   (1998-)  A      O7

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  57 GLN   (  57-)  A    0.50
  73 GLN   (  73-)  A    0.50
 151 GLU   ( 151-)  A    0.50
 358 ASP   ( 358-)  A    0.50
 388 GLU   ( 388-)  A    0.50
 570 GLN   (  73-)  B    0.50
 599 ASN   ( 102-)  B    0.50
 608 GLU   ( 111-)  B    0.50
 609 GLU   ( 112-)  B    0.50
 708 ARG   ( 211-)  B    0.50
 767 ASN   ( 270-)  B    0.50
 855 ASP   ( 358-)  B    0.50

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.

 541 ARG   (  44-)  B

Warning: Tyrosine convention problem

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

  11 TYR   (  11-)  A
 108 TYR   ( 108-)  A
 116 TYR   ( 116-)  A
 133 TYR   ( 133-)  A
 135 TYR   ( 135-)  A
 205 TYR   ( 205-)  A
 212 TYR   ( 212-)  A
 304 TYR   ( 304-)  A
 412 TYR   ( 412-)  A
 487 TYR   ( 487-)  A
 508 TYR   (  11-)  B
 519 TYR   (  22-)  B
 605 TYR   ( 108-)  B
 613 TYR   ( 116-)  B
 632 TYR   ( 135-)  B
 702 TYR   ( 205-)  B
 709 TYR   ( 212-)  B
 801 TYR   ( 304-)  B
 810 TYR   ( 313-)  B
 909 TYR   ( 412-)  B
 915 TYR   ( 418-)  B
 984 TYR   ( 487-)  B
 989 TYR   ( 492-)  B

Warning: Phenylalanine convention problem

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

   9 PHE   (   9-)  A
  26 PHE   (  26-)  A
  75 PHE   (  75-)  A
 109 PHE   ( 109-)  A
 128 PHE   ( 128-)  A
 142 PHE   ( 142-)  A
 147 PHE   ( 147-)  A
 216 PHE   ( 216-)  A
 246 PHE   ( 246-)  A
 251 PHE   ( 251-)  A
 316 PHE   ( 316-)  A
 337 PHE   ( 337-)  A
 347 PHE   ( 347-)  A
 397 PHE   ( 397-)  A
 417 PHE   ( 417-)  A
 426 PHE   ( 426-)  A
 523 PHE   (  26-)  B
 572 PHE   (  75-)  B
 606 PHE   ( 109-)  B
 625 PHE   ( 128-)  B
 639 PHE   ( 142-)  B
 644 PHE   ( 147-)  B
 813 PHE   ( 316-)  B
 828 PHE   ( 331-)  B
 834 PHE   ( 337-)  B
 894 PHE   ( 397-)  B
 908 PHE   ( 411-)  B
 923 PHE   ( 426-)  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.

 153 ASP   ( 153-)  A
 358 ASP   ( 358-)  A
 650 ASP   ( 153-)  B
 779 ASP   ( 282-)  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.

 846 GLU   ( 349-)  B
 885 GLU   ( 388-)  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

 |  0.997758 -0.000280 -0.000402|
 | -0.000280  0.999562  0.000118|
 | -0.000402  0.000118  0.999240|
Proposed new scale matrix

 |  0.009295  0.000003  0.000004|
 |  0.000000  0.003499  0.000000|
 |  0.000004 -0.000001  0.010878|
With corresponding cell

    A    = 107.587  B   = 285.834  C    =  91.926
    Alpha=  89.995  Beta=  90.046  Gamma=  90.018

The CRYST1 cell dimensions

    A    = 107.830  B   = 285.920  C    =  92.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 55.627
(Under-)estimated Z-score: 5.497

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.

  33 ALA   (  33-)  A      C    CA   CB  102.98   -5.0
  44 ARG   (  44-)  A      CB   CG   CD  103.20   -5.4
 154 THR   ( 154-)  A      C    CA   CB  102.09   -4.2
 306 HIS   ( 306-)  A      CG   ND1  CE1 109.68    4.1
 557 HIS   (  60-)  B      CG   ND1  CE1 109.60    4.0
 642 HIS   ( 145-)  B      CG   ND1  CE1 109.67    4.1
 730 GLU   ( 233-)  B      C    CA   CB  118.91    4.6
 779 ASP   ( 282-)  B     -O   -C    N   116.15   -4.3
 779 ASP   ( 282-)  B      N    CA   CB  103.25   -4.3
 862 HIS   ( 365-)  B      CG   ND1  CE1 109.71    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.

 153 ASP   ( 153-)  A
 358 ASP   ( 358-)  A
 541 ARG   (  44-)  B
 650 ASP   ( 153-)  B
 779 ASP   ( 282-)  B
 846 GLU   ( 349-)  B
 885 GLU   ( 388-)  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.

 733 PRO   ( 236-)  B      N      7.0    20.59    -2.48
 778 LEU   ( 281-)  B      C     -6.1    -9.42     0.20
The average deviation= 1.003

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.

 406 ILE   ( 406-)  A    6.55
 158 ILE   ( 158-)  A    4.99
 109 PHE   ( 109-)  A    4.23
  84 ALA   (  84-)  A    4.16

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.

 778 LEU   ( 281-)  B    -2.8
 979 THR   ( 482-)  B    -2.7
 482 THR   ( 482-)  A    -2.6
 967 LEU   ( 470-)  B    -2.6
 907 THR   ( 410-)  B    -2.5
 924 ILE   ( 427-)  B    -2.5
 816 PRO   ( 319-)  B    -2.5
 370 SER   ( 370-)  A    -2.5
 281 LEU   ( 281-)  A    -2.4
 732 GLU   ( 235-)  B    -2.3
 353 ARG   ( 353-)  A    -2.3
 489 ILE   ( 489-)  A    -2.3
 170 ARG   ( 170-)  A    -2.2
 939 ASN   ( 442-)  B    -2.2
 912 PRO   ( 415-)  B    -2.1
  31 PHE   (  31-)  A    -2.1
 449 LEU   ( 449-)  A    -2.1
 451 HIS   ( 451-)  A    -2.1
 195 GLY   ( 195-)  A    -2.1
 647 PRO   ( 150-)  B    -2.1
 116 TYR   ( 116-)  A    -2.1
 484 SER   ( 484-)  A    -2.1
 652 LYS   ( 155-)  B    -2.1
 233 GLU   ( 233-)  A    -2.1
 787 HIS   ( 290-)  B    -2.1
 391 PRO   ( 391-)  A    -2.1
 876 THR   ( 379-)  B    -2.0
 343 VAL   ( 343-)  A    -2.0
 144 LEU   ( 144-)  A    -2.0
 447 VAL   ( 447-)  A    -2.0
 628 ARG   ( 131-)  B    -2.0
 895 VAL   ( 398-)  B    -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.

  19 ASN   (  19-)  A  Poor phi/psi
  22 TYR   (  22-)  A  omega poor
  41 GLU   (  41-)  A  omega poor
  55 PRO   (  55-)  A  omega poor
  75 PHE   (  75-)  A  Poor phi/psi
  94 LEU   (  94-)  A  omega poor
 114 ILE   ( 114-)  A  omega poor
 124 ALA   ( 124-)  A  Poor phi/psi
 125 SER   ( 125-)  A  omega poor
 133 TYR   ( 133-)  A  omega poor
 144 LEU   ( 144-)  A  Poor phi/psi
 169 GLN   ( 169-)  A  omega poor
 224 LYS   ( 224-)  A  Poor phi/psi
 233 GLU   ( 233-)  A  Poor phi/psi
 282 ASP   ( 282-)  A  Poor phi/psi, omega poor
 288 LEU   ( 288-)  A  PRO omega poor
 301 ALA   ( 301-)  A  omega poor
 312 TRP   ( 312-)  A  omega poor
 323 THR   ( 323-)  A  Poor phi/psi
 344 GLY   ( 344-)  A  Poor phi/psi
 349 GLU   ( 349-)  A  omega poor
 373 TYR   ( 373-)  A  omega poor
 374 HIS   ( 374-)  A  Poor phi/psi
 381 TRP   ( 381-)  A  Poor phi/psi
 389 GLY   ( 389-)  A  Poor phi/psi
And so on for a total of 56 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.950

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.

 370 SER   ( 370-)  A    0.38
 867 SER   ( 370-)  B    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!

   6 PRO   (   6-)  A      0
   9 PHE   (   9-)  A      0
  11 TYR   (  11-)  A      0
  12 SER   (  12-)  A      0
  19 ASN   (  19-)  A      0
  20 ALA   (  20-)  A      0
  21 THR   (  21-)  A      0
  22 TYR   (  22-)  A      0
  23 CYS   (  23-)  A      0
  24 ASP   (  24-)  A      0
  33 ALA   (  33-)  A      0
  34 LEU   (  34-)  A      0
  45 SER   (  45-)  A      0
  48 ARG   (  48-)  A      0
  49 MET   (  49-)  A      0
  57 GLN   (  57-)  A      0
  58 ALA   (  58-)  A      0
  59 ASN   (  59-)  A      0
  60 HIS   (  60-)  A      0
  61 THR   (  61-)  A      0
  63 THR   (  63-)  A      0
  65 LEU   (  65-)  A      0
  70 GLN   (  70-)  A      0
  73 GLN   (  73-)  A      0
  75 PHE   (  75-)  A      0
And so on for a total of 421 lines.

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].

  28 PRO   (  28-)  A   118.3 half-chair C-beta/C-alpha (126 degrees)
  55 PRO   (  55-)  A    -0.6 envelop N (0 degrees)
  98 PRO   (  98-)  A   103.5 envelop C-beta (108 degrees)
 139 PRO   ( 139-)  A    30.4 envelop C-delta (36 degrees)
 178 PRO   ( 178-)  A   -65.6 envelop C-beta (-72 degrees)
 182 PRO   ( 182-)  A   110.9 envelop C-beta (108 degrees)
 245 PRO   ( 245-)  A   -13.6 half-chair C-alpha/N (-18 degrees)
 319 PRO   ( 319-)  A    38.1 envelop C-delta (36 degrees)
 428 PRO   ( 428-)  A  -119.8 half-chair C-delta/C-gamma (-126 degrees)
 469 PRO   ( 469-)  A    35.1 envelop C-delta (36 degrees)
 529 PRO   (  32-)  B  -115.6 envelop C-gamma (-108 degrees)
 568 PRO   (  71-)  B  -149.1 envelop C-delta (-144 degrees)
 656 PRO   ( 159-)  B   109.8 envelop C-beta (108 degrees)
 733 PRO   ( 236-)  B   -64.5 envelop C-beta (-72 degrees)
 786 PRO   ( 289-)  B   -50.6 half-chair C-beta/C-alpha (-54 degrees)
 796 PRO   ( 299-)  B  -123.3 half-chair C-delta/C-gamma (-126 degrees)
 816 PRO   ( 319-)  B   -60.2 half-chair C-beta/C-alpha (-54 degrees)
 912 PRO   ( 415-)  B   172.3 envelop N (180 degrees)
 925 PRO   ( 428-)  B  -114.0 envelop C-gamma (-108 degrees)
 966 PRO   ( 469-)  B    44.2 envelop C-delta (36 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.

  19 ASN   (  19-)  A      ND2 <-> 1010 NDG   (1997-)  A      C1     0.82    2.28  INTRA
 474 ASP   ( 474-)  A      OD1 <->  496 ARG   ( 496-)  A      NH2    0.39    2.31  INTRA BL
 363 TYR   ( 363-)  A      OH  <->  380 ASP   ( 380-)  A      OD1    0.34    2.06  INTRA
 703 HIS   ( 206-)  B      NE2 <->  752 HIS   ( 255-)  B      CE1    0.32    2.78  INTRA BL
 496 ARG   ( 496-)  A      N   <-> 1011 HOH   ( 503 )  A      O      0.30    2.40  INTRA
 704 GLN   ( 207-)  B      NE2 <->  760 ASP   ( 263-)  B      OD1    0.29    2.41  INTRA
 860 TYR   ( 363-)  B      OH  <->  877 ASP   ( 380-)  B      OD1    0.25    2.15  INTRA
 618 VAL   ( 121-)  B      N   <->  672 LEU   ( 175-)  B      O      0.22    2.48  INTRA BL
 244 TYR   ( 244-)  A      CD2 <->  248 CYS   ( 248-)  A      SG     0.22    3.18  INTRA
 500 PRO   (   3-)  B      O   <->  519 TYR   (  22-)  B      OH     0.22    2.18  INTRA
 121 VAL   ( 121-)  A      N   <->  175 LEU   ( 175-)  A      O      0.21    2.49  INTRA BL
  96 LEU   (  96-)  A      O   <->  101 GLN   ( 101-)  A      NE2    0.21    2.49  INTRA
 572 PHE   (  75-)  B      O   <->  929 GLN   ( 432-)  B      NE2    0.21    2.49  INTRA BL
 206 HIS   ( 206-)  A      NE2 <->  255 HIS   ( 255-)  A      NE2    0.21    2.79  INTRA
 388 GLU   ( 388-)  A      C   <->  396 ASN   ( 396-)  A      ND2    0.20    2.90  INTRA
  74 LYS   (  74-)  A      CB  <->  432 GLN   ( 432-)  A      NE2    0.19    2.91  INTRA BL
 896 ASP   ( 399-)  B      OD1 <->  911 GLN   ( 414-)  B      NE2    0.19    2.51  INTRA
 209 TRP   ( 209-)  A      CZ3 <->  212 TYR   ( 212-)  A      CD1    0.18    3.02  INTRA
  30 THR   (  30-)  A      CG2 <->   31 PHE   (  31-)  A      N      0.18    2.82  INTRA BF
 298 ASP   ( 298-)  A      OD1 <->  300 GLU   ( 300-)  A      N      0.17    2.53  INTRA BF
 778 LEU   ( 281-)  B      O   <->  806 ALA   ( 309-)  B      O      0.17    2.08  INTRA BL
 779 ASP   ( 282-)  B      OD1 <->  808 HIS   ( 311-)  B      NE2    0.17    2.53  INTRA BL
 188 ASN   ( 188-)  A      ND2 <->  192 ASN   ( 192-)  A      O      0.16    2.54  INTRA
 538 GLU   (  41-)  B      OE2 <->  987 HIS   ( 490-)  B      NE2    0.16    2.54  INTRA BL
 345 SER   ( 345-)  A      O   <->  346 LYS   ( 346-)  A      C      0.16    2.44  INTRA BF
And so on for a total of 139 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.

 814 LEU   ( 317-)  B      -6.99
 317 LEU   ( 317-)  A      -6.96
 938 LYS   ( 441-)  B      -6.83
 666 GLN   ( 169-)  B      -6.62
 441 LYS   ( 441-)  A      -6.45
 993 ARG   ( 496-)  B      -6.02
 200 GLN   ( 200-)  A      -5.92
 697 GLN   ( 200-)  B      -5.87
 169 GLN   ( 169-)  A      -5.75
 759 ARG   ( 262-)  B      -5.66
 262 ARG   ( 262-)  A      -5.50
  44 ARG   (  44-)  A      -5.42
 557 HIS   (  60-)  B      -5.35
 992 ARG   ( 495-)  B      -5.35
 531 LEU   (  34-)  B      -5.34
 347 PHE   ( 347-)  A      -5.26
 170 ARG   ( 170-)  A      -5.24
 844 PHE   ( 347-)  B      -5.23
  31 PHE   (  31-)  A      -5.22
 541 ARG   (  44-)  B      -5.13
 194 LYS   ( 194-)  A      -5.13
 627 ILE   ( 130-)  B      -5.12
 123 MET   ( 123-)  A      -5.11
 130 ILE   ( 130-)  A      -5.09
 496 ARG   ( 496-)  A      -5.04
 691 LYS   ( 194-)  B      -5.04
 620 MET   ( 123-)  B      -5.00

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.

 557 HIS   (  60-)  B       560 - THR     63- ( B)         -4.75

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.

 126 CYS   ( 126-)  A   -2.59
  62 GLY   (  62-)  A   -2.57

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.

1011 HOH   ( 502 )  A      O      2.70   53.41    7.57

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.

1012 HOH   ( 499 )  B      O
Bound group on Asn; dont flip  516 ASN  (  19-) B
Bound to:  996 NAG  (1503-) B
Bound group on Asn; dont flip  643 ASN  ( 146-) B
Bound to:  998 NAG  (1505-) 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.

 169 GLN   ( 169-)  A
 223 HIS   ( 223-)  A
 720 HIS   ( 223-)  B
 752 HIS   ( 255-)  B
 771 HIS   ( 274-)  B
 803 HIS   ( 306-)  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.

   2 ARG   (   2-)  A      N
   5 ILE   (   5-)  A      N
   9 PHE   (   9-)  A      N
  11 TYR   (  11-)  A      N
  20 ALA   (  20-)  A      N
  24 ASP   (  24-)  A      N
  31 PHE   (  31-)  A      N
  35 GLY   (  35-)  A      N
  43 THR   (  43-)  A      OG1
  48 ARG   (  48-)  A      NE
 120 ARG   ( 120-)  A      NH1
 129 SER   ( 129-)  A      OG
 130 ILE   ( 130-)  A      N
 131 ARG   ( 131-)  A      N
 134 THR   ( 134-)  A      OG1
 140 ASP   ( 140-)  A      N
 141 ASP   ( 141-)  A      N
 147 PHE   ( 147-)  A      N
 160 LEU   ( 160-)  A      N
 174 LEU   ( 174-)  A      N
 179 TRP   ( 179-)  A      N
 181 SER   ( 181-)  A      OG
 184 TRP   ( 184-)  A      N
 197 LEU   ( 197-)  A      N
 209 TRP   ( 209-)  A      NE1
And so on for a total of 90 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.

  24 ASP   (  24-)  A      OD1
 153 ASP   ( 153-)  A      OD1
 169 GLN   ( 169-)  A      OE1
 233 GLU   ( 233-)  A      OE1
 263 ASP   ( 263-)  A      OD2
 311 HIS   ( 311-)  A      NE2
 419 HIS   ( 419-)  A      NE2
 650 ASP   ( 153-)  B      OD1
 730 GLU   ( 233-)  B      OE1
 730 GLU   ( 233-)  B      OE2
 916 HIS   ( 419-)  B      NE2

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.

 137 ASP   ( 137-)  A   H-bonding suggests Asn
 203 ASP   ( 203-)  A   H-bonding suggests Asn
 218 ASP   ( 218-)  A   H-bonding suggests Asn; but Alt-Rotamer
 233 GLU   ( 233-)  A   H-bonding suggests Gln
 380 ASP   ( 380-)  A   H-bonding suggests Asn; but Alt-Rotamer
 624 ASP   ( 127-)  B   H-bonding suggests Asn; Ligand-contact
 700 ASP   ( 203-)  B   H-bonding suggests Asn; but Alt-Rotamer
 715 ASP   ( 218-)  B   H-bonding suggests Asn
 730 GLU   ( 233-)  B   H-bonding suggests Gln; but Alt-Rotamer

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 :  -0.875
  2nd generation packing quality :  -1.584
  Ramachandran plot appearance   :  -2.662
  chi-1/chi-2 rotamer normality  :  -3.950 (poor)
  Backbone conformation          :  -0.774

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.660 (tight)
  Bond angles                    :   0.808
  Omega angle restraints         :   1.272
  Side chain planarity           :   0.510 (tight)
  Improper dihedral distribution :   0.827
  B-factor distribution          :   0.419
  Inside/Outside distribution    :   1.034

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 : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.660 (tight)
  Bond angles                    :   0.808
  Omega angle restraints         :   1.272
  Side chain planarity           :   0.510 (tight)
  Improper dihedral distribution :   0.827
  B-factor distribution          :   0.419
  Inside/Outside distribution    :   1.034
==============

WHAT IF
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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.