WHAT IF Check report

This file was created 2012-03-27 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 pdb3s8g.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

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

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

 755 HAS   ( 801-)  A  -         Atom types
 757 PER   ( 563-)  A  -         Size
 758 OLC   ( 564-)  A  -         OK
 759 OLC   ( 565-)  A  -         OK
 760 OLC   ( 566-)  A  -         OK
 761 OLC   ( 568-)  B  -         OK
 762 OLC   ( 574-)  A  -         OK
 763 OLC   ( 577-)  A  -         OK
 764 CUA   ( 802-)  B  -         Atom types
 765 OLC   ( 169-)  B  -         OK
 766 OLC   ( 170-)  A  -         OK
 768 A20   (  35-)  C  -         OK
 769 A19   ( 172-)  A  -         OK
 770 OLC   ( 171-)  B  -         OK
 771 A18   ( 578-)  A  -         OK
 772 A17   ( 576-)  A  -         OK
 773 A16   ( 575-)  A  -         OK
 774 A15   ( 573-)  A  -         OK
 775 A14   ( 572-)  A  -         OK
 776 A13   ( 571-)  A  -         OK
 777 A12   ( 570-)  A  -         OK
 778 A11   ( 569-)  A  -         OK
 779 A10   ( 567-)  A  -         OK

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 574 SER   (  22-)  B  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 574 SER   (  22-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

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'.

   2 ARG   (  10-)  A      CG
   2 ARG   (  10-)  A      CD
   2 ARG   (  10-)  A      NE
   2 ARG   (  10-)  A      CZ
   2 ARG   (  10-)  A      NH1
   2 ARG   (  10-)  A      NH2
   5 GLU   (  13-)  A      CG
   5 GLU   (  13-)  A      CD
   5 GLU   (  13-)  A      OE1
   5 GLU   (  13-)  A      OE2
  49 ARG   (  57-)  A      CD
  49 ARG   (  57-)  A      NE
  49 ARG   (  57-)  A      CZ
  49 ARG   (  57-)  A      NH1
  49 ARG   (  57-)  A      NH2
 329 ARG   ( 337-)  A      CD
 329 ARG   ( 337-)  A      NE
 329 ARG   ( 337-)  A      CZ
 329 ARG   ( 337-)  A      NH1
 329 ARG   ( 337-)  A      NH2
 557 HIS   (   5-)  B      CG
 557 HIS   (   5-)  B      ND1
 557 HIS   (   5-)  B      CD2
 557 HIS   (   5-)  B      CE1
 557 HIS   (   5-)  B      NE2
 561 LYS   (   9-)  B      CG
 561 LYS   (   9-)  B      CD
 561 LYS   (   9-)  B      CE
 561 LYS   (   9-)  B      NZ
 613 GLU   (  61-)  B      CG
 613 GLU   (  61-)  B      CD
 613 GLU   (  61-)  B      OE1
 613 GLU   (  61-)  B      OE2

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: 45

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

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.

  87 ARG   (  95-)  A
  92 ARG   ( 100-)  A
 161 ARG   ( 169-)  A
 317 ARG   ( 325-)  A
 319 ARG   ( 327-)  A
 410 ARG   ( 418-)  A
 442 ARG   ( 450-)  A
 487 ARG   ( 495-)  A
 518 ARG   ( 526-)  A
 552 ARG   ( 560-)  A
 604 ARG   (  52-)  B
 611 ARG   (  59-)  B
 688 ARG   ( 136-)  B
 750 ARG   (  33-)  C

Warning: Tyrosine convention problem

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

  15 TYR   (  23-)  A
  58 TYR   (  66-)  A
 128 TYR   ( 136-)  A
 138 TYR   ( 146-)  A
 236 TYR   ( 244-)  A
 240 TYR   ( 248-)  A
 365 TYR   ( 373-)  A
 394 TYR   ( 402-)  A
 444 TYR   ( 452-)  A
 452 TYR   ( 460-)  A
 631 TYR   (  79-)  B
 634 TYR   (  82-)  B
 642 TYR   (  90-)  B
 689 TYR   ( 137-)  B

Warning: Phenylalanine convention problem

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

  16 PHE   (  24-)  A
  21 PHE   (  29-)  A
  30 PHE   (  38-)  A
  33 PHE   (  41-)  A
  53 PHE   (  61-)  A
 106 PHE   ( 114-)  A
 127 PHE   ( 135-)  A
 186 PHE   ( 194-)  A
 205 PHE   ( 213-)  A
 230 PHE   ( 238-)  A
 264 PHE   ( 272-)  A
 273 PHE   ( 281-)  A
 277 PHE   ( 285-)  A
 296 PHE   ( 304-)  A
 314 PHE   ( 322-)  A
 361 PHE   ( 369-)  A
 421 PHE   ( 429-)  A
 461 PHE   ( 469-)  A
 481 PHE   ( 489-)  A
 500 PHE   ( 508-)  A
 523 PHE   ( 531-)  A
 542 PHE   ( 550-)  A
 581 PHE   (  29-)  B
 640 PHE   (  88-)  B
 657 PHE   ( 105-)  B
 713 PHE   ( 161-)  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.

  42 ASP   (  50-)  A
 157 ASP   ( 165-)  A
 254 ASP   ( 262-)  A
 279 ASP   ( 287-)  A
 283 ASP   ( 291-)  A
 364 ASP   ( 372-)  A
 407 ASP   ( 415-)  A
 517 ASP   ( 525-)  A
 555 ASP   (   3-)  B
 663 ASP   ( 111-)  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.

  88 GLU   (  96-)  A
 120 GLU   ( 128-)  A
 195 GLU   ( 203-)  A
 313 GLU   ( 321-)  A
 488 GLU   ( 496-)  A
 508 GLU   ( 516-)  A
 556 GLU   (   4-)  B
 567 GLU   (  15-)  B
 603 GLU   (  51-)  B
 654 GLU   ( 102-)  B
 671 GLU   ( 119-)  B
 696 GLU   ( 144-)  B

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.627
RMS-deviation in bond distances: 0.015

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

 |  0.994293 -0.000262 -0.000904|
 | -0.000262  0.993621  0.001266|
 | -0.000904  0.001266  0.993680|
Proposed new scale matrix

 |  0.006943 -0.000005  0.005445|
 |  0.000003  0.010203 -0.000013|
 |  0.000012 -0.000017  0.013448|
With corresponding cell

    A    = 144.142  B   =  98.010  C    =  94.568
    Alpha=  89.866  Beta= 128.157  Gamma=  90.030

The CRYST1 cell dimensions

    A    = 144.963  B   =  98.636  C    =  95.060
    Alpha=  90.000  Beta= 128.070  Gamma=  90.000

Variance: 951.299
(Under-)estimated Z-score: 22.731

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.

 225 HIS   ( 233-)  A      N    CA   CB  120.04    5.6
 225 HIS   ( 233-)  A      CA   CB   CG  108.89   -4.9
 274 HIS   ( 282-)  A      CG   ND1  CE1 109.66    4.1
 666 HIS   ( 114-)  B      CG   ND1  CE1 109.69    4.1

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.652
RMS-deviation in bond angles: 1.327

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.

  42 ASP   (  50-)  A
  87 ARG   (  95-)  A
  88 GLU   (  96-)  A
  92 ARG   ( 100-)  A
 120 GLU   ( 128-)  A
 157 ASP   ( 165-)  A
 161 ARG   ( 169-)  A
 195 GLU   ( 203-)  A
 254 ASP   ( 262-)  A
 279 ASP   ( 287-)  A
 283 ASP   ( 291-)  A
 313 GLU   ( 321-)  A
 317 ARG   ( 325-)  A
 319 ARG   ( 327-)  A
 364 ASP   ( 372-)  A
 407 ASP   ( 415-)  A
 410 ARG   ( 418-)  A
 442 ARG   ( 450-)  A
 487 ARG   ( 495-)  A
 488 GLU   ( 496-)  A
 508 GLU   ( 516-)  A
 517 ASP   ( 525-)  A
 518 ARG   ( 526-)  A
 552 ARG   ( 560-)  A
 555 ASP   (   3-)  B
 556 GLU   (   4-)  B
 567 GLU   (  15-)  B
 603 GLU   (  51-)  B
 604 ARG   (  52-)  B
 611 ARG   (  59-)  B
 654 GLU   ( 102-)  B
 663 ASP   ( 111-)  B
 671 GLU   ( 119-)  B
 688 ARG   ( 136-)  B
 696 GLU   ( 144-)  B
 750 ARG   (  33-)  C

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.

 267 LEU   ( 275-)  A    4.34

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.

 225 HIS   ( 233-)  A    4.27

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.

 361 PHE   ( 369-)  A    -3.3
 662 PRO   ( 110-)  B    -2.8
 127 PHE   ( 135-)  A    -2.5
 130 PRO   ( 138-)  A    -2.4
 444 TYR   ( 452-)  A    -2.2
 722 PRO   (   5-)  C    -2.2
 125 TYR   ( 133-)  A    -2.1
 270 PRO   ( 278-)  A    -2.1
 663 ASP   ( 111-)  B    -2.1
 324 LEU   ( 332-)  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.

  40 ASN   (  48-)  A  Poor phi/psi
  81 MET   (  89-)  A  omega poor
  90 ASN   (  98-)  A  Poor phi/psi
 119 ASN   ( 127-)  A  Poor phi/psi
 124 LEU   ( 132-)  A  Poor phi/psi
 129 PRO   ( 137-)  A  PRO omega poor
 131 LEU   ( 139-)  A  omega poor
 240 TYR   ( 248-)  A  omega poor
 270 PRO   ( 278-)  A  omega poor
 361 PHE   ( 369-)  A  Poor phi/psi
 369 ASN   ( 377-)  A  Poor phi/psi
 383 SER   ( 391-)  A  Poor phi/psi
 438 ASN   ( 446-)  A  Poor phi/psi
 442 ARG   ( 450-)  A  Poor phi/psi
 499 PRO   ( 507-)  A  Poor phi/psi
 508 GLU   ( 516-)  A  Poor phi/psi
 639 ALA   (  87-)  B  omega poor
 643 GLN   (  91-)  B  PRO omega poor
 645 ASN   (  93-)  B  PRO omega poor
 663 ASP   ( 111-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.047

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.

 101 SER   ( 109-)  A    0.36
 301 SER   ( 309-)  A    0.36

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   7 TYR   (  15-)  A      0
  40 ASN   (  48-)  A      0
  43 ALA   (  51-)  A      0
  51 LEU   (  59-)  A      0
  55 GLN   (  63-)  A      0
  56 SER   (  64-)  A      0
  91 MET   (  99-)  A      0
  94 ASN   ( 102-)  A      0
  95 MET   ( 103-)  A      0
 119 ASN   ( 127-)  A      0
 121 ALA   ( 129-)  A      0
 122 THR   ( 130-)  A      0
 123 VAL   ( 131-)  A      0
 124 LEU   ( 132-)  A      0
 127 PHE   ( 135-)  A      0
 128 TYR   ( 136-)  A      0
 129 PRO   ( 137-)  A      0
 130 PRO   ( 138-)  A      0
 131 LEU   ( 139-)  A      0
 167 PRO   ( 175-)  A      0
 199 PHE   ( 207-)  A      0
 200 LEU   ( 208-)  A      0
 205 PHE   ( 213-)  A      0
 207 LEU   ( 215-)  A      0
 241 THR   ( 249-)  A      0
And so on for a total of 177 lines.

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]

  85 PRO   (  93-)  A    0.05 LOW
 332 PRO   ( 340-)  A    0.16 LOW
 374 PRO   ( 382-)  A    0.16 LOW

Warning: Unusual PRO puckering phases

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

 130 PRO   ( 138-)  A    41.5 envelop C-delta (36 degrees)
 167 PRO   ( 175-)  A  -113.3 envelop C-gamma (-108 degrees)
 226 PRO   ( 234-)  A  -120.6 half-chair C-delta/C-gamma (-126 degrees)
 300 PRO   ( 308-)  A  -124.8 half-chair C-delta/C-gamma (-126 degrees)
 336 PRO   ( 344-)  A  -120.5 half-chair C-delta/C-gamma (-126 degrees)
 507 PRO   ( 515-)  A   103.0 envelop C-beta (108 degrees)
 650 PRO   (  98-)  B    18.1 half-chair N/C-delta (18 degrees)
 662 PRO   ( 110-)  B   -62.9 half-chair C-beta/C-alpha (-54 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.

 225 HIS   ( 233-)  A      NE2 <->  229 TYR   ( 237-)  A      CE2    1.44    1.66  INTRA BL
 225 HIS   ( 233-)  A      CD2 <->  229 TYR   ( 237-)  A      CE2    0.60    2.60  INTRA BL
 225 HIS   ( 233-)  A      CE1 <->  229 TYR   ( 237-)  A      CE2    0.57    2.63  INTRA BL
 225 HIS   ( 233-)  A      NE2 <->  229 TYR   ( 237-)  A      CZ     0.55    2.55  INTRA BL
 225 HIS   ( 233-)  A      NE2 <->  229 TYR   ( 237-)  A      CD2    0.40    2.70  INTRA BL
 378 HIS   ( 386-)  A      NE2 <->  767 HEM   ( 800-)  A      NA     0.37    2.63  INTRA BL
 750 ARG   (  33-)  C      CD  <->  782 HOH   (  36 )  C      O      0.32    2.48  INTRA
 750 ARG   (  33-)  C      NH1 <->  782 HOH   (  36 )  C      O      0.29    2.41  INTRA
 645 ASN   (  93-)  B      O   <->  781 HOH   (1083 )  B      O      0.25    2.15  INTRA BL
 780 HOH   (1074 )  A      O   <->  781 HOH   (1031 )  B      O      0.23    2.17  INTRA BF
 246 GLN   ( 254-)  A    A NE2 <->  395 TRP   ( 403-)  A      CD1    0.22    2.88  INTRA
 693 ARG   ( 141-)  B      NH1 <->  766 OLC   ( 170-)  A      C24    0.21    2.89  INTRA BF
 274 HIS   ( 282-)  A      CD2 <->  275 HIS   ( 283-)  A      CD2    0.20    3.00  INTRA BL
 378 HIS   ( 386-)  A      CE1 <->  767 HEM   ( 800-)  A      NA     0.20    2.90  INTRA BL
 540 GLN   ( 548-)  A      NE2 <->  780 HOH   (1201 )  A      O      0.18    2.52  INTRA BF
 645 ASN   (  93-)  B      ND2 <->  781 HOH   (1135 )  B      O      0.18    2.52  INTRA
 233 LEU   ( 241-)  A      N   <->  234 PRO   ( 242-)  A      CD     0.17    2.83  INTRA BL
 274 HIS   ( 282-)  A      NE2 <->  275 HIS   ( 283-)  A      NE2    0.16    2.84  INTRA BL
 160 ARG   ( 168-)  A      NH2 <->  775 A14   ( 572-)  A      C6     0.15    2.95  INTRA
  83 TYR   (  91-)  A      OH  <->  399 ASN   ( 407-)  A      ND2    0.13    2.57  INTRA
  44 TYR   (  52-)  A      N   <->   45 PRO   (  53-)  A      CD     0.12    2.88  INTRA
 378 HIS   ( 386-)  A      NE2 <->  767 HEM   ( 800-)  A      ND     0.11    2.89  INTRA BL
 269 THR   ( 277-)  A      N   <->  270 PRO   ( 278-)  A      CD     0.10    2.90  INTRA BL
 392 SER   ( 400-)  A      O   <->  396 LEU   ( 404-)  A      N      0.10    2.60  INTRA
 666 HIS   ( 114-)  B      ND1 <->  712 MET   ( 160-)  B      SD     0.09    3.21  INTRA BL
 274 HIS   ( 282-)  A      CD2 <->  755 HAS   ( 801-)  A      CMD    0.09    3.11  INTRA BL
 225 HIS   ( 233-)  A      CD2 <->  229 TYR   ( 237-)  A      CD2    0.09    3.11  INTRA BL
 721 LYS   (   4-)  C      N   <->  782 HOH   (1058 )  C      O      0.08    2.62  INTRA BF
 319 ARG   ( 327-)  A      NE  <->  330 ALA   ( 338-)  A      O      0.08    2.62  INTRA
 780 HOH   ( 617 )  A      O   <->  782 HOH   (  36 )  C      O      0.07    2.33  INTRA
  64 HIS   (  72-)  A      NE2 <->  767 HEM   ( 800-)  A      NB     0.07    2.93  INTRA BL
  64 HIS   (  72-)  A      CD2 <->  767 HEM   ( 800-)  A      ND     0.07    3.03  INTRA BL
  64 HIS   (  72-)  A      NE2 <->  767 HEM   ( 800-)  A      NC     0.07    2.93  INTRA BL
 378 HIS   ( 386-)  A      NE2 <->  767 HEM   ( 800-)  A      NC     0.07    2.93  INTRA BL
 160 ARG   ( 168-)  A      NH1 <->  776 A13   ( 571-)  A      O20    0.06    2.64  INTRA
 552 ARG   ( 560-)  A      NH2 <->  780 HOH   (1042 )  A      O      0.06    2.64  INTRA
  64 HIS   (  72-)  A      NE2 <->  767 HEM   ( 800-)  A      ND     0.05    2.95  INTRA BL
 225 HIS   ( 233-)  A      CB  <->  756  CU   ( 803-)  A     CU      0.05    3.15  INTRA BL
 781 HOH   (1047 )  B      O   <->  781 HOH   (1052 )  B      O      0.04    2.16  INTRA
 287 LYS   ( 295-)  A      NZ  <->  780 HOH   (1238 )  A      O      0.04    2.66  INTRA BL
 225 HIS   ( 233-)  A      CE1 <->  229 TYR   ( 237-)  A      CZ     0.04    3.16  INTRA BL
  58 TYR   (  66-)  A      OH  <->  710 GLN   ( 158-)  B    A NE2    0.03    2.67  INTRA BL
 160 ARG   ( 168-)  A      NH1 <->  776 A13   ( 571-)  A      C22    0.03    3.07  INTRA
 509 ASP   ( 517-)  A      CG  <->  512 LEU   ( 520-)  A      CB     0.03    3.17  INTRA BF
 630 GLN   (  78-)  B      NE2 <->  654 GLU   ( 102-)  B      OE1    0.03    2.67  INTRA
 212 ASP   ( 220-)  A      OD2 <->  546 ASN   ( 554-)  A      N      0.02    2.68  INTRA
 378 HIS   ( 386-)  A      CE1 <->  767 HEM   ( 800-)  A      C1A    0.01    3.19  INTRA BL
 509 ASP   ( 517-)  A      C   <->  511 ARG   ( 519-)  A      N      0.01    2.89  INTRA BF
 535 GLY   ( 543-)  A      N   <->  536 PRO   ( 544-)  A      CD     0.01    2.99  INTRA

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

 322 ARG   ( 330-)  A      -8.17
 487 ARG   ( 495-)  A      -7.57
 693 ARG   ( 141-)  B      -7.05
 489 ARG   ( 497-)  A      -6.46
 611 ARG   (  59-)  B      -6.28
 319 ARG   ( 327-)  A      -6.24
  55 GLN   (  63-)  A      -5.76
 692 LYS   ( 140-)  B      -5.75
 447 GLN   ( 455-)  A      -5.48
 604 ARG   (  52-)  B      -5.47
 207 LEU   ( 215-)  A      -5.46
 209 GLU   ( 217-)  A      -5.44
 246 GLN   ( 254-)  A      -5.41
 441 ARG   ( 449-)  A      -5.29
 125 TYR   ( 133-)  A      -5.20
 612 GLN   (  60-)  B      -5.09
 495 GLU   ( 503-)  A      -5.01

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.

 207 LEU   ( 215-)  A       209 - GLU    217- ( A)         -4.98

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

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.

 506 GLY   ( 514-)  A   -3.01
 451 ALA   ( 459-)  A   -2.92
 622 ALA   (  70-)  B   -2.56

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.

 364 ASP   ( 372-)  A     -  367 VAL   ( 375-)  A        -1.85
 591 THR   (  39-)  B     -  594 ALA   (  42-)  B        -1.76

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

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.

 781 HOH   (1062 )  B      O    -29.50   -0.55   36.15

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.

 780 HOH   (1023 )  A      O
 780 HOH   (1185 )  A      O
 780 HOH   (1218 )  A      O
 781 HOH   (1034 )  B      O
Metal-coordinating Histidine residue 376 fixed to   1
Metal-coordinating Histidine residue 225 fixed to   1
Metal-coordinating Histidine residue 274 fixed to   1
Metal-coordinating Histidine residue 275 fixed to   1
Metal-coordinating Histidine residue 709 fixed to   1
Metal-coordinating Histidine residue 666 fixed to   1
Metal-coordinating Histidine residue  64 fixed to   1
Metal-coordinating Histidine residue 378 fixed to   1

Error: HIS, ASN, GLN side chain flips

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

 399 ASN   ( 407-)  A
 592 HIS   (  40-)  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.

  56 SER   (  64-)  A      N
  57 TYR   (  65-)  A      OH
  58 TYR   (  66-)  A      OH
  68 ASN   (  76-)  A      ND2
 103 TRP   ( 111-)  A      NE1
 122 THR   ( 130-)  A      N
 217 ARG   ( 225-)  A      NH1
 229 TYR   ( 237-)  A      OH
 250 LYS   ( 258-)  A      N
 253 SER   ( 261-)  A      N
 282 ILE   ( 290-)  A      N
 327 TRP   ( 335-)  A      N
 358 ASN   ( 366-)  A      ND2
 361 PHE   ( 369-)  A      N
 380 GLN   ( 388-)  A      NE2
 418 TRP   ( 426-)  A      NE1
 433 TRP   ( 441-)  A      NE1
 438 ASN   ( 446-)  A      ND2
 441 ARG   ( 449-)  A      NH2
 442 ARG   ( 450-)  A      N
 442 ARG   ( 450-)  A      NE
 442 ARG   ( 450-)  A      NH2
 462 ASN   ( 470-)  A      ND2
 506 GLY   ( 514-)  A      N
 510 ARG   ( 518-)  A      N
 511 ARG   ( 519-)  A      N
 553 LEU   ( 561-)  A      N
 554 TRP   ( 562-)  A      N
 558 LYS   (   6-)  B      N
 702 ASN   ( 150-)  B      N
 702 ASN   ( 150-)  B      ND2
 706 GLY   ( 154-)  B      N
 710 GLN   ( 158-)  B      N
 750 ARG   (  33-)  C      NE
 750 ARG   (  33-)  C      NH2
Only metal coordination for   64 HIS  (  72-) A      NE2
Only metal coordination for  225 HIS  ( 233-) A      ND1
Only metal coordination for  274 HIS  ( 282-) A      NE2
Only metal coordination for  275 HIS  ( 283-) A      NE2
Only metal coordination for  376 HIS  ( 384-) A      NE2
Only metal coordination for  378 HIS  ( 386-) A      NE2
Only metal coordination for  666 HIS  ( 114-) B      ND1
Only metal coordination for  709 HIS  ( 157-) B      ND1

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.

  34 GLN   (  42-)  A      OE1
  68 ASN   (  76-)  A      OD1
 195 GLU   ( 203-)  A      OE1
 364 ASP   ( 372-)  A      OD1
 380 GLN   ( 388-)  A      OE1
 462 ASN   ( 470-)  A      OD1
 567 GLU   (  15-)  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.

 781 HOH   ( 173 )  B      O  1.00  K  6 Ion-B

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.

 567 GLU   (  15-)  B   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.019
  2nd generation packing quality :  -0.714
  Ramachandran plot appearance   :   0.133
  chi-1/chi-2 rotamer normality  :   0.047
  Backbone conformation          :   0.748

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.627 (tight)
  Bond angles                    :   0.652 (tight)
  Omega angle restraints         :   0.916
  Side chain planarity           :   0.668
  Improper dihedral distribution :   0.804
  B-factor distribution          :   0.449
  Inside/Outside distribution    :   1.145

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 :   0.4
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :   0.3
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.627 (tight)
  Bond angles                    :   0.652 (tight)
  Omega angle restraints         :   0.916
  Side chain planarity           :   0.668
  Improper dihedral distribution :   0.804
  B-factor distribution          :   0.449
  Inside/Outside distribution    :   1.145
==============

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.