WHAT IF Check report

This file was created 2011-12-15 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 pdb1ehk.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.

 747 BNG   ( 901-)  A  -         OK
 748 BNG   ( 902-)  A  -         OK
 750 HAS   ( 801-)  A  -         Atom types
 751 CUA   ( 802-)  B  -         Atom types
 753 BNG   ( 903-)  A  -         OK

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

   2 TYR   (  15-)  A  -   CE1
   2 TYR   (  15-)  A  -   CE2
   2 TYR   (  15-)  A  -   CZ
   2 TYR   (  15-)  A  -   OH
  44 ARG   (  57-)  A  -   CG
  44 ARG   (  57-)  A  -   CD
  44 ARG   (  57-)  A  -   NE
  44 ARG   (  57-)  A  -   CZ
  44 ARG   (  57-)  A  -   NH1
  44 ARG   (  57-)  A  -   NH2
 164 LYS   ( 177-)  A  -   CE
 164 LYS   ( 177-)  A  -   NZ
 317 ARG   ( 330-)  A  -   CG
 317 ARG   ( 330-)  A  -   CD
 317 ARG   ( 330-)  A  -   NE
 317 ARG   ( 330-)  A  -   CZ
 317 ARG   ( 330-)  A  -   NH1
 317 ARG   ( 330-)  A  -   NH2
 324 ARG   ( 337-)  A  -   NE
 324 ARG   ( 337-)  A  -   CZ
 324 ARG   ( 337-)  A  -   NH1
 324 ARG   ( 337-)  A  -   NH2
 398 LYS   ( 411-)  A  -   CD
 398 LYS   ( 411-)  A  -   CE
 398 LYS   ( 411-)  A  -   NZ
And so on for a total of 130 lines.

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

 545 ASP   (   3-)  B  -   N
 619 ASN   (  77-)  B  -   C
 619 ASN   (  77-)  B  -   O

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: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

 318 GLY   ( 331-)  A    High
 320 PHE   ( 333-)  A    High
 402 ASP   ( 415-)  A    High
 481 SER   ( 494-)  A    High
 483 LEU   ( 501-)  A    High
 545 ASP   (   3-)  B    High
 547 HIS   (   5-)  B    High
 556 TYR   (  14-)  B    High
 603 GLU   (  61-)  B    High
 617 GLY   (  75-)  B    High
 618 PRO   (  76-)  B    High
 619 ASN   (  77-)  B    High
 641 GLN   (  99-)  B    High
 711 GLU   (   2-)  C    High
 712 GLU   (   3-)  C    High
 713 LYS   (   4-)  C    High

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.633 over 5256 bonds
Average difference in B over a bond : 3.52
RMS difference in B over a bond : 7.09

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.

  44 ARG   (  57-)  A
  82 ARG   (  95-)  A
  87 ARG   ( 100-)  A
 155 ARG   ( 168-)  A
 156 ARG   ( 169-)  A
 212 ARG   ( 225-)  A
 314 ARG   ( 327-)  A
 317 ARG   ( 330-)  A
 324 ARG   ( 337-)  A
 405 ARG   ( 418-)  A
 406 ARG   ( 419-)  A
 436 ARG   ( 449-)  A
 437 ARG   ( 450-)  A
 482 ARG   ( 495-)  A
 500 ARG   ( 518-)  A
 501 ARG   ( 519-)  A
 508 ARG   ( 526-)  A
 542 ARG   ( 560-)  A
 594 ARG   (  52-)  B
 601 ARG   (  59-)  B
 683 ARG   ( 141-)  B
 688 ARG   ( 146-)  B
 742 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

  10 TYR   (  23-)  A
  53 TYR   (  66-)  A
 123 TYR   ( 136-)  A
 133 TYR   ( 146-)  A
 231 TYR   ( 244-)  A
 235 TYR   ( 248-)  A
 360 TYR   ( 373-)  A
 389 TYR   ( 402-)  A
 439 TYR   ( 452-)  A
 473 TYR   ( 486-)  A
 679 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.

  11 PHE   (  24-)  A
  16 PHE   (  29-)  A
 101 PHE   ( 114-)  A
 200 PHE   ( 213-)  A
 225 PHE   ( 238-)  A
 259 PHE   ( 272-)  A
 268 PHE   ( 281-)  A
 272 PHE   ( 285-)  A
 291 PHE   ( 304-)  A
 301 PHE   ( 314-)  A
 416 PHE   ( 429-)  A
 490 PHE   ( 508-)  A
 513 PHE   ( 531-)  A
 571 PHE   (  29-)  B
 703 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.

 152 ASP   ( 165-)  A
 249 ASP   ( 262-)  A
 274 ASP   ( 287-)  A
 359 ASP   ( 372-)  A
 499 ASP   ( 517-)  A
 507 ASP   ( 525-)  A
 545 ASP   (   3-)  B
 653 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.

 190 GLU   ( 203-)  A
 204 GLU   ( 217-)  A
 308 GLU   ( 321-)  A
 492 GLU   ( 510-)  A
 557 GLU   (  15-)  B
 593 GLU   (  51-)  B
 603 GLU   (  61-)  B
 644 GLU   ( 102-)  B
 661 GLU   ( 119-)  B
 686 GLU   ( 144-)  B
 712 GLU   (   3-)  C

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

 |  0.997958 -0.000188 -0.000030|
 | -0.000188  0.998508 -0.000194|
 | -0.000030 -0.000194  0.997655|
Proposed new scale matrix

 |  0.008938  0.000002  0.000000|
 |  0.000002  0.008933  0.000002|
 |  0.000000  0.000001  0.006210|
With corresponding cell

    A    = 111.879  B   = 111.940  C    = 161.042
    Alpha=  90.022  Beta=  90.002  Gamma=  90.022

The CRYST1 cell dimensions

    A    = 112.110  B   = 112.110  C    = 161.410
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 95.957
(Under-)estimated Z-score: 7.219

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.

  59 HIS   (  72-)  A      NE2  CD2  CG  102.04   -4.5
  59 HIS   (  72-)  A      CD2  CG   ND1 112.67    6.6
 126 LEU   ( 139-)  A      N    CA   C    99.87   -4.0
 220 HIS   ( 233-)  A      CA   CB   CG  102.40  -11.4
 220 HIS   ( 233-)  A      NE2  CD2  CG  100.38   -6.1
 220 HIS   ( 233-)  A      CD2  CG   ND1 112.13    6.0
 262 LEU   ( 275-)  A      N    CA   C   124.12    4.6
 264 THR   ( 277-)  A      N    CA   C   123.50    4.4
 269 HIS   ( 282-)  A      CA   CB   CG  119.00    5.2
 269 HIS   ( 282-)  A      NE2  CD2  CG  102.43   -4.1
 269 HIS   ( 282-)  A      CD2  CG   ND1 112.15    6.1
 269 HIS   ( 282-)  A      CB   CG   CD2 123.54   -4.3
 270 HIS   ( 283-)  A      NE2  CD2  CG  102.05   -4.5
 270 HIS   ( 283-)  A      CD2  CG   ND1 112.69    6.6
 270 HIS   ( 283-)  A      CB   CG   CD2 123.46   -4.3
 285 HIS   ( 298-)  A      CG   ND1  CE1 109.61    4.0
 371 HIS   ( 384-)  A      CD2  CG   ND1 112.03    5.9
 371 HIS   ( 384-)  A      CB   CG   CD2 122.96   -4.7
 373 HIS   ( 386-)  A      NE2  CD2  CG  102.38   -4.1
 373 HIS   ( 386-)  A      CD2  CG   ND1 112.47    6.4
 550 HIS   (   8-)  B      CG   ND1  CE1 109.60    4.0
 656 HIS   ( 114-)  B      NE2  CD2  CG  102.42   -4.1
 656 HIS   ( 114-)  B      CD2  CG   ND1 112.39    6.3
 656 HIS   ( 114-)  B      CB   CG   CD2 123.61   -4.2
 699 HIS   ( 157-)  B      CD2  CG   ND1 111.98    5.9
 699 HIS   ( 157-)  B      CB   CG   CD2 123.48   -4.3

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.

  44 ARG   (  57-)  A
  82 ARG   (  95-)  A
  87 ARG   ( 100-)  A
 152 ASP   ( 165-)  A
 155 ARG   ( 168-)  A
 156 ARG   ( 169-)  A
 190 GLU   ( 203-)  A
 204 GLU   ( 217-)  A
 212 ARG   ( 225-)  A
 249 ASP   ( 262-)  A
 274 ASP   ( 287-)  A
 308 GLU   ( 321-)  A
 314 ARG   ( 327-)  A
 317 ARG   ( 330-)  A
 324 ARG   ( 337-)  A
 359 ASP   ( 372-)  A
 405 ARG   ( 418-)  A
 406 ARG   ( 419-)  A
 436 ARG   ( 449-)  A
 437 ARG   ( 450-)  A
 482 ARG   ( 495-)  A
 492 GLU   ( 510-)  A
 499 ASP   ( 517-)  A
 500 ARG   ( 518-)  A
 501 ARG   ( 519-)  A
 507 ASP   ( 525-)  A
 508 ARG   ( 526-)  A
 542 ARG   ( 560-)  A
 545 ASP   (   3-)  B
 557 GLU   (  15-)  B
 593 GLU   (  51-)  B
 594 ARG   (  52-)  B
 601 ARG   (  59-)  B
 603 GLU   (  61-)  B
 644 GLU   ( 102-)  B
 653 ASP   ( 111-)  B
 661 GLU   ( 119-)  B
 683 ARG   ( 141-)  B
 686 GLU   ( 144-)  B
 688 ARG   ( 146-)  B
 712 GLU   (   3-)  C
 742 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.

 262 LEU   ( 275-)  A    8.05
 236 THR   ( 249-)  A    6.29
 362 VAL   ( 375-)  A    5.77
 168 LEU   ( 181-)  A    5.76
 217 TRP   ( 230-)  A    5.73
 267 GLY   ( 280-)  A    5.64
  54 GLN   (  67-)  A    5.34
 228 LEU   ( 241-)  A    5.22
  40 PRO   (  53-)  A    4.86
 227 LEU   ( 240-)  A    4.75
 126 LEU   ( 139-)  A    4.62
 402 ASP   ( 415-)  A    4.54
 345 PRO   ( 358-)  A    4.48
 225 PHE   ( 238-)  A    4.48
 224 TYR   ( 237-)  A    4.42
 393 PRO   ( 406-)  A    4.25
 722 LEU   (  13-)  C    4.23
 297 LEU   ( 310-)  A    4.23
 264 THR   ( 277-)  A    4.19
  76 MET   (  89-)  A    4.13
 372 PHE   ( 385-)  A    4.02
  77 VAL   (  90-)  A    4.00

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 1.776

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.

 224 TYR   ( 237-)  A    7.82

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.

 356 PHE   ( 369-)  A    -3.5
 122 PHE   ( 135-)  A    -2.8
 650 THR   ( 108-)  B    -2.5
 652 PRO   ( 110-)  B    -2.4
 439 TYR   ( 452-)  A    -2.3
 316 GLY   ( 329-)  A    -2.3
 534 HIS   ( 552-)  A    -2.3
 436 ARG   ( 449-)  A    -2.2
 705 THR   ( 163-)  B    -2.2
 601 ARG   (  59-)  B    -2.0
 653 ASP   ( 111-)  B    -2.0
 595 VAL   (  53-)  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.

  35 ASN   (  48-)  A  Poor phi/psi
  85 ASN   (  98-)  A  Poor phi/psi
 114 ASN   ( 127-)  A  Poor phi/psi
 119 LEU   ( 132-)  A  Poor phi/psi
 122 PHE   ( 135-)  A  Poor phi/psi
 124 PRO   ( 137-)  A  PRO omega poor
 267 GLY   ( 280-)  A  Poor phi/psi
 316 GLY   ( 329-)  A  Poor phi/psi
 317 ARG   ( 330-)  A  Poor phi/psi
 327 PRO   ( 340-)  A  Poor phi/psi
 356 PHE   ( 369-)  A  Poor phi/psi
 364 ASN   ( 377-)  A  Poor phi/psi
 378 SER   ( 391-)  A  Poor phi/psi
 433 ASN   ( 446-)  A  Poor phi/psi
 489 PRO   ( 507-)  A  Poor phi/psi
 602 GLN   (  60-)  B  Poor phi/psi
 619 ASN   (  77-)  B  Poor phi/psi
 629 ALA   (  87-)  B  omega poor
 633 GLN   (  91-)  B  PRO omega poor
 635 ASN   (  93-)  B  PRO omega poor
 653 ASP   ( 111-)  B  Poor phi/psi
 714 PRO   (   5-)  C  Poor phi/psi
 732 TRP   (  23-)  C  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.080

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.

 137 SER   ( 150-)  A    0.35
 306 SER   ( 319-)  A    0.36

Warning: Unusual backbone conformations

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

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

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

   3 PRO   (  16-)  A      0
  35 ASN   (  48-)  A      0
  38 ALA   (  51-)  A      0
  50 GLN   (  63-)  A      0
  86 MET   (  99-)  A      0
  89 ASN   ( 102-)  A      0
  90 MET   ( 103-)  A      0
 116 ALA   ( 129-)  A      0
 117 THR   ( 130-)  A      0
 118 VAL   ( 131-)  A      0
 119 LEU   ( 132-)  A      0
 123 TYR   ( 136-)  A      0
 124 PRO   ( 137-)  A      0
 125 PRO   ( 138-)  A      0
 126 LEU   ( 139-)  A      0
 162 PRO   ( 175-)  A      0
 195 LEU   ( 208-)  A      0
 200 PHE   ( 213-)  A      0
 202 LEU   ( 215-)  A      0
 217 TRP   ( 230-)  A      0
 218 THR   ( 231-)  A      0
 236 THR   ( 249-)  A      0
 248 SER   ( 261-)  A      0
 249 ASP   ( 262-)  A      0
 262 LEU   ( 275-)  A      0
And so on for a total of 178 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 0.415

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]

   3 PRO   (  16-)  A    0.48 HIGH
  27 PRO   (  40-)  A    0.51 HIGH
  40 PRO   (  53-)  A    0.50 HIGH
  47 PRO   (  60-)  A    0.49 HIGH
  80 PRO   (  93-)  A    0.48 HIGH
  88 PRO   ( 101-)  A    0.46 HIGH
 110 PRO   ( 123-)  A    0.48 HIGH
 124 PRO   ( 137-)  A    0.48 HIGH
 125 PRO   ( 138-)  A    0.51 HIGH
 162 PRO   ( 175-)  A    0.49 HIGH
 167 PRO   ( 180-)  A    0.49 HIGH
 197 PRO   ( 210-)  A    0.48 HIGH
 208 PRO   ( 221-)  A    0.49 HIGH
 229 PRO   ( 242-)  A    0.49 HIGH
 239 PRO   ( 252-)  A    0.50 HIGH
 250 PRO   ( 263-)  A    0.51 HIGH
 265 PRO   ( 278-)  A    0.50 HIGH
 275 PRO   ( 288-)  A    0.52 HIGH
 279 PRO   ( 292-)  A    0.50 HIGH
 295 PRO   ( 308-)  A    0.48 HIGH
 327 PRO   ( 340-)  A    0.48 HIGH
 331 PRO   ( 344-)  A    0.49 HIGH
 336 PRO   ( 349-)  A    0.48 HIGH
 369 PRO   ( 382-)  A    0.47 HIGH
 393 PRO   ( 406-)  A    0.47 HIGH
 399 PRO   ( 412-)  A    0.49 HIGH
 435 PRO   ( 448-)  A    0.45 HIGH
 444 PRO   ( 457-)  A    0.49 HIGH
 448 PRO   ( 461-)  A    0.49 HIGH
 453 PRO   ( 466-)  A    0.49 HIGH
 487 PRO   ( 505-)  A    0.49 HIGH
 489 PRO   ( 507-)  A    0.48 HIGH
 497 PRO   ( 515-)  A    0.50 HIGH
 526 PRO   ( 544-)  A    0.49 HIGH
 537 PRO   ( 555-)  A    0.48 HIGH
 539 PRO   ( 557-)  A    0.46 HIGH
 588 PRO   (  46-)  B    0.49 HIGH
 597 PRO   (  55-)  B    0.50 HIGH
 605 PRO   (  63-)  B    0.50 HIGH
 609 PRO   (  67-)  B    0.49 HIGH
 618 PRO   (  76-)  B    0.50 HIGH
 634 PRO   (  92-)  B    0.49 HIGH
 636 PRO   (  94-)  B    0.50 HIGH
 640 PRO   (  98-)  B    0.50 HIGH
 652 PRO   ( 110-)  B    0.48 HIGH
 671 PRO   ( 129-)  B    0.49 HIGH
 684 PRO   ( 142-)  B    0.50 HIGH
 714 PRO   (   5-)  C    0.49 HIGH

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.

 220 HIS   ( 233-)  A      NE2 <->  224 TYR   ( 237-)  A      CE2    1.67    1.43  INTRA BL
 220 HIS   ( 233-)  A      CE1 <->  224 TYR   ( 237-)  A      CE2    0.90    2.30  INTRA BL
 220 HIS   ( 233-)  A      CD2 <->  224 TYR   ( 237-)  A      CE2    0.71    2.49  INTRA BL
 220 HIS   ( 233-)  A      NE2 <->  224 TYR   ( 237-)  A      CZ     0.65    2.45  INTRA BL
 220 HIS   ( 233-)  A      NE2 <->  224 TYR   ( 237-)  A      CD2    0.63    2.47  INTRA BL
 220 HIS   ( 233-)  A      CE1 <->  224 TYR   ( 237-)  A      CZ     0.29    2.91  INTRA BL
 220 HIS   ( 233-)  A      CD2 <->  224 TYR   ( 237-)  A      CD2    0.25    2.95  INTRA BL
 452 VAL   ( 465-)  A      CG1 <->  453 PRO   ( 466-)  A      CD     0.23    2.97  INTRA BF
  39 TYR   (  52-)  A      N   <->   40 PRO   (  53-)  A      CD     0.22    2.78  INTRA BF
 373 HIS   ( 386-)  A      NE2 <->  752 HEM   ( 800-)  A      NA     0.21    2.79  INTRA BL
 392 LEU   ( 405-)  A      N   <->  393 PRO   ( 406-)  A      CD     0.21    2.79  INTRA BF
 407 LEU   ( 420-)  A      O   <->  410 ALA   ( 423-)  A      N      0.20    2.50  INTRA BF
 713 LYS   (   4-)  C      O   <->  715 LYS   (   6-)  C      N      0.19    2.51  INTRA BF
 663 THR   ( 121-)  B      CB  <->  665 ILE   ( 123-)  B      CD1    0.19    3.01  INTRA BF
 422 MET   ( 435-)  A      CG  <->  426 LEU   ( 439-)  A      CD2    0.18    3.02  INTRA BF
 312 ARG   ( 325-)  A      NH1 <->  712 GLU   (   3-)  C      C      0.18    2.92  INTRA BF
 581 THR   (  39-)  B      CG2 <->  582 HIS   (  40-)  B      N      0.18    2.82  INTRA BF
 249 ASP   ( 262-)  A      N   <->  250 PRO   ( 263-)  A      CD     0.17    2.83  INTRA BL
 165 VAL   ( 178-)  A      CG1 <->  503 VAL   ( 521-)  A      CG1    0.17    3.03  INTRA BL
 369 PRO   ( 382-)  A      O   <->  373 HIS   ( 386-)  A      ND1    0.17    2.53  INTRA BL
 425 GLY   ( 438-)  A      CA  <->  457 ASN   ( 470-)  A      ND2    0.16    2.94  INTRA BF
  34 GLY   (  47-)  A      N   <->   35 ASN   (  48-)  A      N      0.15    2.45  INTRA BF
 436 ARG   ( 449-)  A      NH2 <->  750 HAS   ( 801-)  A      O2A    0.15    2.55  INTRA BL
 423 ALA   ( 436-)  A      O   <->  427 HIS   ( 440-)  A      ND1    0.15    2.55  INTRA BL
 393 PRO   ( 406-)  A      CG  <->  400 ILE   ( 413-)  A      CD1    0.15    3.05  INTRA BF
And so on for a total of 132 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

 317 ARG   ( 330-)  A      -7.94
 683 ARG   ( 141-)  B      -6.53
 314 ARG   ( 327-)  A      -6.31
 202 LEU   ( 215-)  A      -5.89
 594 ARG   (  52-)  B      -5.81
 682 LYS   ( 140-)  B      -5.79
  50 GLN   (  63-)  A      -5.70
 601 ARG   (  59-)  B      -5.47
 442 GLN   ( 455-)  A      -5.47
 241 GLN   ( 254-)  A      -5.46
 319 LEU   ( 332-)  A      -5.36
 436 ARG   ( 449-)  A      -5.34
 270 HIS   ( 283-)  A      -5.17
   2 TYR   (  15-)  A      -5.06
 437 ARG   ( 450-)  A      -5.03

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.

 601 ARG   (  59-)  B       603 - GLU     61- ( B)         -4.69

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.

  84 LEU   (  97-)  A   -2.68
 612 ALA   (  70-)  B   -2.51

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.

 359 ASP   ( 372-)  A     -  362 VAL   ( 375-)  A        -1.92

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

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.

 755 HOH   ( 822 )  B      O
 756 HOH   (  65 )  C      O
Metal-coordinating Histidine residue 220 fixed to   1
Metal-coordinating Histidine residue 269 fixed to   1
Metal-coordinating Histidine residue 270 fixed to   1
Metal-coordinating Histidine residue 699 fixed to   1
Metal-coordinating Histidine residue 656 fixed to   1
Metal-coordinating Histidine residue  59 fixed to   1
Metal-coordinating Histidine residue 373 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.

  35 ASN   (  48-)  A
  73 GLN   (  86-)  A
 161 ASN   ( 174-)  A
 285 HIS   ( 298-)  A
 364 ASN   ( 377-)  A
 449 HIS   ( 462-)  A
 457 ASN   ( 470-)  A
 534 HIS   ( 552-)  A
 611 GLN   (  69-)  B
 615 GLN   (  73-)  B
 633 GLN   (  91-)  B
 664 ASN   ( 122-)  B
 693 GLN   ( 151-)  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.

  28 PHE   (  41-)  A      N
  29 GLN   (  42-)  A      NE2
  39 TYR   (  52-)  A      OH
  51 SER   (  64-)  A      N
  52 TYR   (  65-)  A      OH
  53 TYR   (  66-)  A      N
  63 ASN   (  76-)  A      ND2
 117 THR   ( 130-)  A      N
 224 TYR   ( 237-)  A      OH
 245 LYS   ( 258-)  A      N
 248 SER   ( 261-)  A      N
 249 ASP   ( 262-)  A      N
 266 VAL   ( 279-)  A      N
 277 ILE   ( 290-)  A      N
 317 ARG   ( 330-)  A      N
 322 TRP   ( 335-)  A      N
 324 ARG   ( 337-)  A      N
 353 ASN   ( 366-)  A      ND2
 356 PHE   ( 369-)  A      N
 364 ASN   ( 377-)  A      N
 375 GLN   ( 388-)  A      NE2
 436 ARG   ( 449-)  A      NH1
 437 ARG   ( 450-)  A      N
 437 ARG   ( 450-)  A      NE
 437 ARG   ( 450-)  A      NH2
 457 ASN   ( 470-)  A      ND2
 486 ALA   ( 504-)  A      N
 543 LEU   ( 561-)  A      N
 547 HIS   (   5-)  B      N
 548 LYS   (   6-)  B      N
 666 ASN   ( 124-)  B      ND2
 681 PHE   ( 139-)  B      N
 683 ARG   ( 141-)  B      N
 692 ASN   ( 150-)  B      N
 692 ASN   ( 150-)  B      ND2
 694 TYR   ( 152-)  B      N
 696 GLY   ( 154-)  B      N
 700 GLN   ( 158-)  B      N
 701 ASN   ( 159-)  B      N
 705 THR   ( 163-)  B      N
 715 LYS   (   6-)  C      N
 742 ARG   (  33-)  C      NE
 742 ARG   (  33-)  C      NH2
Only metal coordination for   59 HIS  (  72-) A      NE2
Only metal coordination for  220 HIS  ( 233-) A      ND1
Only metal coordination for  269 HIS  ( 282-) A      NE2
Only metal coordination for  270 HIS  ( 283-) A      NE2
Only metal coordination for  373 HIS  ( 386-) A      NE2
Only metal coordination for  656 HIS  ( 114-) B      ND1
Only metal coordination for  699 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.

  29 GLN   (  42-)  A      OE1
 190 GLU   ( 203-)  A      OE1
 241 GLN   ( 254-)  A      OE1
 359 ASP   ( 372-)  A      OD1
 363 HIS   ( 376-)  A      ND1
 371 HIS   ( 384-)  A      NE2
 375 GLN   ( 388-)  A      OE1
 427 HIS   ( 440-)  A      NE2
 457 ASN   ( 470-)  A      OD1
 557 GLU   (  15-)  B      OE1
 557 GLU   (  15-)  B      OE2
 602 GLN   (  60-)  B      OE1
 664 ASN   ( 122-)  B      OD1

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.

 190 GLU   ( 203-)  A   H-bonding suggests Gln
 308 GLU   ( 321-)  A   H-bonding suggests Gln; but Alt-Rotamer
 329 ASP   ( 342-)  A   H-bonding suggests Asn; but Alt-Rotamer
 673 GLU   ( 131-)  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 :  -0.155
  2nd generation packing quality :  -0.431
  Ramachandran plot appearance   :  -2.139
  chi-1/chi-2 rotamer normality  :  -1.080
  Backbone conformation          :   0.144

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.368 (tight)
  Bond angles                    :   0.751
  Omega angle restraints         :   0.075 (tight)
  Side chain planarity           :   0.609 (tight)
  Improper dihedral distribution :   0.669
  B-factor distribution          :   1.633 (loose)
  Inside/Outside distribution    :   1.146

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 : 2.40


Structure Z-scores, positive is better than average:

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

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.368 (tight)
  Bond angles                    :   0.751
  Omega angle restraints         :   0.075 (tight)
  Side chain planarity           :   0.609 (tight)
  Improper dihedral distribution :   0.669
  B-factor distribution          :   1.633 (loose)
  Inside/Outside distribution    :   1.146
==============

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.