WHAT IF Check report

This file was created 2012-01-12 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 pdb1rus.ent

Checks that need to be done early-on in validation

Warning: Ligands for which topology could not be determined

The 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 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.

 873 3PG   ( 500-)  A  -         Fragmented
 874 3PG   ( 500-)  B  -

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.

   1 GLN   (   3-)  A  -   CG
   1 GLN   (   3-)  A  -   CD
   1 GLN   (   3-)  A  -   OE1
   1 GLN   (   3-)  A  -   NE2
 284 SER   ( 296-)  A  -   OG
 721 GLN   ( 298-)  B  -   CG
 721 GLN   ( 298-)  B  -   CD
 721 GLN   ( 298-)  B  -   OE1
 721 GLN   ( 298-)  B  -   NE2

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.

 437 VAL   ( 457-)  A  -   C
 437 VAL   ( 457-)  A  -   O
 489 GLY   (  66-)  B  -   N
 489 GLY   (  66-)  B  -   CA
 489 GLY   (  66-)  B  -   C
 489 GLY   (  66-)  B  -   O
 490 VAL   (  67-)  B  -   N
 538 MET   ( 115-)  B  -   N

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'.

 719 SER   ( 296-)  B      OG

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:

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.

Warning: Low M-factor

The B-factor flatness, the M-factor, is very low. This is very worrisome. I suggest you consult the WHAT CHECK website and/or a seasoned crystallographer.

The M-factor = 0.011

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: Tyrosine convention problem

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

  26 TYR   (  28-)  A
  34 TYR   (  36-)  A
  36 TYR   (  38-)  A
 115 TYR   ( 127-)  A
 120 TYR   ( 132-)  A
 321 TYR   ( 341-)  A
 428 TYR   ( 448-)  A
 463 TYR   (  28-)  B
 471 TYR   (  36-)  B
 555 TYR   ( 132-)  B
 669 TYR   ( 246-)  B
 688 TYR   ( 265-)  B
 756 TYR   ( 341-)  B
 863 TYR   ( 448-)  B

Warning: Phenylalanine convention problem

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

  43 PHE   (  45-)  A
  92 PHE   ( 104-)  A
 114 PHE   ( 126-)  A
 124 PHE   ( 136-)  A
 177 PHE   ( 189-)  A
 189 PHE   ( 201-)  A
 239 PHE   ( 251-)  A
 377 PHE   ( 397-)  A
 420 PHE   ( 440-)  A
 513 PHE   (  90-)  B
 549 PHE   ( 126-)  B
 599 PHE   ( 176-)  B
 624 PHE   ( 201-)  B
 661 PHE   ( 238-)  B
 706 PHE   ( 283-)  B
 729 PHE   ( 306-)  B
 812 PHE   ( 397-)  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.

  14 ASP   (  16-)  A
  56 ASP   (  68-)  A
  63 ASP   (  75-)  A
  79 ASP   (  91-)  A
  84 ASP   (  96-)  A
 113 ASP   ( 125-)  A
 144 ASP   ( 156-)  A
 176 ASP   ( 188-)  A
 181 ASP   ( 193-)  A
 201 ASP   ( 213-)  A
 208 ASP   ( 220-)  A
 223 ASP   ( 235-)  A
 224 ASP   ( 236-)  A
 251 ASP   ( 263-)  A
 269 ASP   ( 281-)  A
 405 ASP   ( 425-)  A
 425 ASP   ( 445-)  A
 451 ASP   (  16-)  B
 498 ASP   (  75-)  B
 514 ASP   (  91-)  B
 519 ASP   (  96-)  B
 540 ASP   ( 117-)  B
 560 ASP   ( 137-)  B
 611 ASP   ( 188-)  B
 636 ASP   ( 213-)  B
 643 ASP   ( 220-)  B
 659 ASP   ( 236-)  B
 751 ASP   ( 336-)  B
 761 ASP   ( 346-)  B
 816 ASP   ( 401-)  B
 834 ASP   ( 419-)  B
 860 ASP   ( 445-)  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.

  20 GLU   (  22-)  A
  61 GLU   (  73-)  A
  67 GLU   (  79-)  A
 107 GLU   ( 119-)  A
 142 GLU   ( 154-)  A
 212 GLU   ( 224-)  A
 233 GLU   ( 245-)  A
 327 GLU   ( 347-)  A
 361 GLU   ( 381-)  A
 449 GLU   (  14-)  B
 496 GLU   (  73-)  B
 499 GLU   (  76-)  B
 502 GLU   (  79-)  B
 542 GLU   ( 119-)  B
 553 GLU   ( 130-)  B
 577 GLU   ( 154-)  B
 601 GLU   ( 178-)  B
 644 GLU   ( 221-)  B
 662 GLU   ( 239-)  B
 668 GLU   ( 245-)  B
 672 GLU   ( 249-)  B
 796 GLU   ( 381-)  B
 844 GLU   ( 429-)  B
 847 GLU   ( 432-)  B

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 151 THR   ( 163-)  A      CA   CB    1.63    5.0
 286 GLN   ( 298-)  A      N   -C     1.25   -4.2
 309 HIS   ( 321-)  A      CB   CG    1.56    4.1
 310 THR   ( 322-)  A      N    CA    1.55    4.7
 337 TRP   ( 357-)  A      NE1  CE2   1.31   -5.2
 489 GLY   (  66-)  B      N    CA    1.52    4.3
 534 ASN   ( 111-)  B      N   -C     1.24   -4.6
 607 TRP   ( 184-)  B      NE1  CE2   1.32   -4.9
 613 ILE   ( 190-)  B      N   -C     1.25   -4.2
 618 PRO   ( 195-)  B      CD   N     1.39   -5.8
 711 ARG   ( 288-)  B      CD   NE    1.56    5.5
 711 ARG   ( 288-)  B      NE   CZ    1.40    5.1
 720 PRO   ( 297-)  B      CD   N     1.41   -4.3
 744 HIS   ( 321-)  B      CB   CG    1.56    4.6
 772 TRP   ( 357-)  B      NE1  CE2   1.31   -5.3
 793 GLY   ( 378-)  B      N    CA    1.52    4.3

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

 |  0.998995  0.000233  0.000055|
 |  0.000233  0.999469 -0.000381|
 |  0.000055 -0.000381  0.998031|
Proposed new scale matrix

 |  0.015282 -0.000003  0.000560|
 | -0.000003  0.014172  0.000005|
 |  0.000000  0.000004  0.009632|
With corresponding cell

    A    =  65.435  B   =  70.564  C    = 103.891
    Alpha=  90.045  Beta=  92.100  Gamma=  89.973

The CRYST1 cell dimensions

    A    =  65.500  B   =  70.600  C    = 104.100
    Alpha=  90.000  Beta=  92.100  Gamma=  90.000

Variance: 42.162
(Under-)estimated Z-score: 4.785

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.

   1 GLN   (   3-)  A      NE2  CD   OE1 118.14   -4.5
   2 SER   (   4-)  A     -O   -C    N   131.44    5.3
   2 SER   (   4-)  A     -C    N    CA  129.90    4.6
   4 ARG   (   6-)  A      NE   CZ   NH2 110.99   -4.7
   4 ARG   (   6-)  A      NH1  CZ   NH2 126.98    4.0
   5 TYR   (   7-)  A      N    CA   CB  102.62   -4.6
   6 VAL   (   8-)  A      CA   C    O   108.29   -7.4
   7 ASN   (   9-)  A     -O   -C    N   130.30    4.6
   8 LEU   (  10-)  A      CD1  CG   CD2 101.77   -4.1
  11 LYS   (  13-)  A      CA   C    O   112.90   -4.6
  11 LYS   (  13-)  A      CA   CB   CG  124.59    5.2
  11 LYS   (  13-)  A      CG   CD   CE  120.70    4.1
  12 GLU   (  14-)  A     -CA  -C    N   126.84    5.3
  13 GLU   (  15-)  A     -O   -C    N   116.07   -4.3
  13 GLU   (  15-)  A     -C    N    CA  129.89    4.6
  13 GLU   (  15-)  A      CA   CB   CG  122.70    4.3
  14 ASP   (  16-)  A      CB   CG   OD1 107.04   -4.9
  17 ALA   (  19-)  A     -C    N    CA  135.28    7.5
  20 GLU   (  22-)  A      CA   CB   CG  124.15    5.0
  20 GLU   (  22-)  A      CG   CD   OE2 131.07    5.5
  21 HIS   (  23-)  A      CG   ND1  CE1 111.08    5.5
  22 VAL   (  24-)  A     -C    N    CA  129.37    4.3
  22 VAL   (  24-)  A      CA   C    O   113.84   -4.1
  23 LEU   (  25-)  A     -O   -C    N   112.27   -6.7
  23 LEU   (  25-)  A     -CA  -C    N   133.84    8.8
And so on for a total of 737 lines.

Warning: High bond angle deviations

Bond angles were found to deviate more than normal from the mean 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, and this is indeed observed for very high resolution X-ray structures. The fact that it is higher than 2.0 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond angle dictionary is used.

RMS Z-score for bond angles: 2.171
RMS-deviation in bond angles: 4.047

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.

  14 ASP   (  16-)  A
  20 GLU   (  22-)  A
  56 ASP   (  68-)  A
  61 GLU   (  73-)  A
  63 ASP   (  75-)  A
  67 GLU   (  79-)  A
  79 ASP   (  91-)  A
  84 ASP   (  96-)  A
 107 GLU   ( 119-)  A
 113 ASP   ( 125-)  A
 142 GLU   ( 154-)  A
 144 ASP   ( 156-)  A
 176 ASP   ( 188-)  A
 181 ASP   ( 193-)  A
 201 ASP   ( 213-)  A
 208 ASP   ( 220-)  A
 212 GLU   ( 224-)  A
 223 ASP   ( 235-)  A
 224 ASP   ( 236-)  A
 233 GLU   ( 245-)  A
 251 ASP   ( 263-)  A
 269 ASP   ( 281-)  A
 327 GLU   ( 347-)  A
 361 GLU   ( 381-)  A
 405 ASP   ( 425-)  A
And so on for a total of 56 lines.

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.

 127 PRO   ( 139-)  A      CA    -6.2    29.42    38.15
 171 PHE   ( 183-)  A      CA    -7.3    22.26    33.98
 198 LEU   ( 210-)  A      C     -7.3   -11.36     0.20
 490 VAL   (  67-)  B      CA   -14.4    12.35    33.23
 534 ASN   ( 111-)  B      C      9.6    15.39     0.27
 562 PRO   ( 139-)  B      CA    -6.9    28.43    38.15
 806 THR   ( 391-)  B      C     -7.9   -11.52     0.30
 862 ILE   ( 447-)  B      CA    -9.2    19.27    33.24
The average deviation= 1.500

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.

 533 GLY   ( 110-)  B   10.44
 569 LEU   ( 146-)  B    8.31
 440 SER   (   5-)  B    7.52
 810 GLY   ( 395-)  B    7.41
 474 VAL   (  39-)  B    6.41
  18 GLY   (  20-)  A    6.22
 851 ALA   ( 436-)  B    6.13
 818 PRO   ( 403-)  B    6.10
 478 ALA   (  43-)  B    5.99
 137 VAL   ( 149-)  A    5.80
 390 LEU   ( 410-)  A    5.64
 846 LYS   ( 431-)  B    5.51
 402 PRO   ( 422-)  A    5.43
  41 ALA   (  43-)  A    5.42
 503 LEU   (  80-)  B    5.35
 505 LYS   (  82-)  B    5.26
 555 TYR   ( 132-)  B    5.24
 386 GLY   ( 406-)  A    5.23
 479 HIS   (  44-)  B    5.12
 634 VAL   ( 211-)  B    5.08
 384 VAL   ( 404-)  A    5.08
 287 SER   ( 299-)  A    5.04
 531 THR   ( 108-)  B    5.00
 536 GLN   ( 113-)  B    4.93
 831 ALA   ( 416-)  B    4.87
And so on for a total of 67 lines.

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 : 2.166

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.232

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.

 792 PRO   ( 377-)  B    -3.0
 711 ARG   ( 288-)  B    -2.9
 276 ARG   ( 288-)  A    -2.8
   2 SER   (   4-)  A    -2.7
 268 PRO   ( 280-)  A    -2.6
 439 SER   (   4-)  B    -2.6
 484 SER   (  49-)  B    -2.6
 161 PRO   ( 173-)  A    -2.6
 586 THR   ( 163-)  B    -2.5
 596 PRO   ( 173-)  B    -2.5
  27 ILE   (  29-)  A    -2.5
 279 HIS   ( 291-)  A    -2.5
 747 THR   ( 324-)  B    -2.5
 286 GLN   ( 298-)  A    -2.5
 815 ILE   ( 400-)  B    -2.4
 806 THR   ( 391-)  B    -2.4
 720 PRO   ( 297-)  B    -2.4
 591 LYS   ( 168-)  B    -2.4
 240 GLY   ( 252-)  A    -2.4
 312 THR   ( 324-)  A    -2.4
 338 GLY   ( 358-)  A    -2.4
 129 VAL   ( 141-)  A    -2.4
 183 PRO   ( 195-)  A    -2.4
 837 PRO   ( 422-)  B    -2.4
 411 LYS   ( 431-)  A    -2.4
And so on for a total of 93 lines.

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.

   2 SER   (   4-)  A  Poor phi/psi
  48 SER   (  50-)  A  Poor phi/psi
  53 ARG   (  65-)  A  Poor phi/psi
  55 VAL   (  67-)  A  Poor phi/psi
  67 GLU   (  79-)  A  Poor phi/psi
 107 GLU   ( 119-)  A  Poor phi/psi
 130 ASN   ( 142-)  A  Poor phi/psi
 154 LYS   ( 166-)  A  PRO omega poor
 158 GLY   ( 170-)  A  Poor phi/psi
 172 TRP   ( 184-)  A  Poor phi/psi
 232 GLY   ( 244-)  A  Poor phi/psi
 240 GLY   ( 252-)  A  Poor phi/psi
 283 THR   ( 295-)  A  omega poor
 286 GLN   ( 298-)  A  Poor phi/psi
 288 LYS   ( 300-)  A  Poor phi/psi
 304 GLY   ( 316-)  A  Poor phi/psi
 315 SER   ( 335-)  A  Poor phi/psi
 338 GLY   ( 358-)  A  Poor phi/psi
 352 ASN   ( 372-)  A  Poor phi/psi
 367 ASN   ( 387-)  A  Poor phi/psi
 411 LYS   ( 431-)  A  Poor phi/psi
 424 ALA   ( 444-)  A  Poor phi/psi
 426 GLN   ( 446-)  A  Poor phi/psi
 435 LEU   ( 455-)  A  Poor phi/psi
 439 SER   (   4-)  B  Poor phi/psi
 440 SER   (   5-)  B  Poor phi/psi
 444 ASN   (   9-)  B  Poor phi/psi
 469 ALA   (  34-)  B  Poor phi/psi
 473 TYR   (  38-)  B  Poor phi/psi
 484 SER   (  49-)  B  Poor phi/psi
 485 SER   (  50-)  B  Poor phi/psi
 486 THR   (  51-)  B  Poor phi/psi
 502 GLU   (  79-)  B  Poor phi/psi
 533 GLY   ( 110-)  B  Poor phi/psi
 537 GLY   ( 114-)  B  omega poor
 538 MET   ( 115-)  B  Poor phi/psi
 540 ASP   ( 117-)  B  Poor phi/psi
 565 ASN   ( 142-)  B  Poor phi/psi
 579 ASP   ( 156-)  B  Poor phi/psi
 589 LYS   ( 166-)  B  PRO omega poor
 609 GLY   ( 186-)  B  Poor phi/psi
 617 GLU   ( 194-)  B  Poor phi/psi
 714 HIS   ( 291-)  B  Poor phi/psi
 715 GLY   ( 292-)  B  Poor phi/psi
 739 GLY   ( 316-)  B  Poor phi/psi
 750 SER   ( 335-)  B  Poor phi/psi
 759 THR   ( 344-)  B  Poor phi/psi
 773 GLY   ( 358-)  B  Poor phi/psi
 810 GLY   ( 395-)  B  Poor phi/psi
 838 VAL   ( 423-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -5.478

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -5.478

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 VAL   (   8-)  A      0
   7 ASN   (   9-)  A      0
  20 GLU   (  22-)  A      0
  21 HIS   (  23-)  A      0
  31 LYS   (  33-)  A      0
  32 ALA   (  34-)  A      0
  34 TYR   (  36-)  A      0
  47 SER   (  49-)  A      0
  48 SER   (  50-)  A      0
  49 THR   (  51-)  A      0
  50 GLY   (  52-)  A      0
  51 THR   (  53-)  A      0
  52 THR   (  64-)  A      0
  53 ARG   (  65-)  A      0
  55 VAL   (  67-)  A      0
  60 TYR   (  72-)  A      0
  61 GLU   (  73-)  A      0
  66 ARG   (  78-)  A      0
  67 GLU   (  79-)  A      0
  68 LEU   (  80-)  A      0
  78 PHE   (  90-)  A      0
  81 ASN   (  93-)  A      0
  83 THR   (  95-)  A      0
  84 ASP   (  96-)  A      0
  88 MET   ( 100-)  A      0
And so on for a total of 321 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 : 2.738

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 713 GLY   ( 290-)  B   2.73   25
 809 GLY   ( 394-)  B   2.08   44
 746 GLY   ( 323-)  B   2.03   19
 623 PRO   ( 200-)  B   1.60   16

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 475 ALA   (  40-)  B   1.84

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]

 161 PRO   ( 173-)  A    0.17 LOW
 331 PRO   ( 351-)  A    0.19 LOW
 383 PRO   ( 403-)  A    0.49 HIGH
 429 PRO   ( 449-)  A    0.18 LOW
 618 PRO   ( 195-)  B    0.47 HIGH
 837 PRO   ( 422-)  B    0.47 HIGH

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].

  30 PRO   (  32-)  A    43.1 envelop C-delta (36 degrees)
 117 PRO   ( 129-)  A    34.0 envelop C-delta (36 degrees)
 127 PRO   ( 139-)  A    51.2 half-chair C-delta/C-gamma (54 degrees)
 183 PRO   ( 195-)  A    25.6 half-chair N/C-delta (18 degrees)
 268 PRO   ( 280-)  A   -52.6 half-chair C-beta/C-alpha (-54 degrees)
 285 PRO   ( 297-)  A   131.5 half-chair C-beta/C-alpha (126 degrees)
 357 PRO   ( 377-)  A    99.4 envelop C-beta (108 degrees)
 383 PRO   ( 403-)  A    46.8 half-chair C-delta/C-gamma (54 degrees)
 467 PRO   (  32-)  B   -65.5 envelop C-beta (-72 degrees)
 576 PRO   ( 153-)  B    48.7 half-chair C-delta/C-gamma (54 degrees)
 590 PRO   ( 167-)  B   -34.3 envelop C-alpha (-36 degrees)
 596 PRO   ( 173-)  B   105.1 envelop C-beta (108 degrees)
 618 PRO   ( 195-)  B    16.9 half-chair N/C-delta (18 degrees)
 703 PRO   ( 280-)  B   -64.0 envelop C-beta (-72 degrees)
 720 PRO   ( 297-)  B    37.0 envelop C-delta (36 degrees)
 780 PRO   ( 365-)  B    51.0 half-chair C-delta/C-gamma (54 degrees)
 792 PRO   ( 377-)  B   151.3 envelop C-alpha (144 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.

 489 GLY   (  66-)  B      N   <->  509 PRO   (  86-)  B      CG     1.21    1.89  INTRA
 184 GLN   ( 196-)  A      O   <->  219 ASN   ( 231-)  A      ND2    1.03    1.67  INTRA
 750 SER   ( 335-)  B      O   <->  754 ILE   ( 339-)  B      CG1    0.87    1.93  INTRA
 281 ALA   ( 293-)  A      O   <->  287 SER   ( 299-)  A      CB     0.77    2.03  INTRA
 747 THR   ( 324-)  B      CG2 <->  748 MET   ( 325-)  B      N      0.72    2.28  INTRA
 489 GLY   (  66-)  B      C   <->  509 PRO   (  86-)  B      CG     0.72    2.48  INTRA
 438 GLN   (   3-)  B      NE2 <->  479 HIS   (  44-)  B      CA     0.67    2.43  INTRA
 750 SER   ( 335-)  B      C   <->  754 ILE   ( 339-)  B      CG1    0.66    2.54  INTRA
 276 ARG   ( 288-)  A      CD  <->  279 HIS   ( 291-)  A      NE2    0.63    2.47  INTRA
 489 GLY   (  66-)  B      N   <->  509 PRO   (  86-)  B      CB     0.63    2.47  INTRA
 744 HIS   ( 321-)  B      CB  <->  874 3PG   ( 500-)  B      O4P    0.62    2.18  INTRA
 277 ALA   ( 289-)  A      O   <->  534 ASN   ( 111-)  B      N      0.60    2.10  INTRA
 489 GLY   (  66-)  B      CA  <->  509 PRO   (  86-)  B      CG     0.60    2.60  INTRA
 273 HIS   ( 285-)  A      NE2 <->  309 HIS   ( 321-)  A      CD2    0.55    2.55  INTRA
 438 GLN   (   3-)  B      OE1 <->  482 ALA   (  47-)  B      CB     0.54    2.26  INTRA
 281 ALA   ( 293-)  A      O   <->  287 SER   ( 299-)  A      OG     0.54    1.86  INTRA
 251 ASP   ( 263-)  A      OD2 <->  277 ALA   ( 289-)  A      CB     0.52    2.28  INTRA
 713 GLY   ( 290-)  B      O   <->  715 GLY   ( 292-)  B      N      0.47    2.23  INTRA
 744 HIS   ( 321-)  B      ND1 <->  874 3PG   ( 500-)  B      O4P    0.47    2.23  INTRA
 615 ASN   ( 192-)  B      ND2 <->  619 GLN   ( 196-)  B      OE1    0.46    2.24  INTRA
 182 GLU   ( 194-)  A      CG  <->  183 PRO   ( 195-)  A      CD     0.46    2.74  INTRA
 601 GLU   ( 178-)  B      OE2 <->  640 ARG   ( 217-)  B      NH2    0.44    2.26  INTRA
 266 ARG   ( 278-)  A      CG  <->  267 PHE   ( 279-)  A      CE1    0.44    2.76  INTRA
 284 SER   ( 296-)  A      OG  <->  285 PRO   ( 297-)  A      CD     0.44    2.36  INTRA
 438 GLN   (   3-)  B      NE2 <->  479 HIS   (  44-)  B      CB     0.43    2.67  INTRA
And so on for a total of 313 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.

  53 ARG   (  65-)  A      -7.01
 276 ARG   ( 288-)  A      -6.60
 154 LYS   ( 166-)  A      -6.12
 812 PHE   ( 397-)  B      -5.81
 721 GLN   ( 298-)  B      -5.61
 398 ARG   ( 418-)  A      -5.60
 833 ARG   ( 418-)  B      -5.56
 701 ARG   ( 278-)  B      -5.46
 589 LYS   ( 166-)  B      -5.45
 536 GLN   ( 113-)  B      -5.43
 266 ARG   ( 278-)  A      -5.34
 245 HIS   ( 257-)  A      -5.26
 362 ASN   ( 382-)  A      -5.20
 578 VAL   ( 155-)  B      -5.20
 797 ASN   ( 382-)  B      -5.12

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: 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

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.

  99 ASN   ( 111-)  A
 275 HIS   ( 287-)  A
 296 HIS   ( 308-)  A
 325 GLN   ( 345-)  A
 365 ASN   ( 385-)  A
 444 ASN   (   9-)  B
 479 HIS   (  44-)  B
 535 ASN   ( 112-)  B
 536 GLN   ( 113-)  B
 654 ASN   ( 231-)  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 SER   (   4-)  A      N
   5 TYR   (   7-)  A      N
  13 GLU   (  15-)  A      N
  21 HIS   (  23-)  A      N
  55 VAL   (  67-)  A      N
  56 ASP   (  68-)  A      N
  62 VAL   (  74-)  A      N
  64 GLU   (  76-)  A      N
  69 THR   (  81-)  A      OG1
  76 ALA   (  88-)  A      N
  86 LYS   (  98-)  A      N
  88 MET   ( 100-)  A      N
  91 SER   ( 103-)  A      N
 100 ASN   ( 112-)  A      N
 100 ASN   ( 112-)  A      ND2
 101 GLN   ( 113-)  A      NE2
 102 GLY   ( 114-)  A      N
 106 VAL   ( 118-)  A      N
 120 TYR   ( 132-)  A      OH
 145 GLY   ( 157-)  A      N
 147 LEU   ( 159-)  A      N
 153 ILE   ( 165-)  A      N
 157 LEU   ( 169-)  A      N
 179 LYS   ( 191-)  A      NZ
 182 GLU   ( 194-)  A      N
And so on for a total of 118 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.

  21 HIS   (  23-)  A      ND1
 105 ASP   ( 117-)  A      OD1
 309 HIS   ( 321-)  A      ND1
 379 HIS   ( 399-)  A      ND1
 458 HIS   (  23-)  B      ND1
 540 ASP   ( 117-)  B      OD1
 604 HIS   ( 181-)  B      ND1
 616 ASP   ( 193-)  B      OD2
 686 ASP   ( 263-)  B      OD2
 744 HIS   ( 321-)  B      ND1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

 182 GLU   ( 194-)  A   H-bonding suggests Gln; but Alt-Rotamer
 237 GLU   ( 249-)  A   H-bonding suggests Gln
 425 ASP   ( 445-)  A   H-bonding suggests Asn
 540 ASP   ( 117-)  B   H-bonding suggests Asn
 553 GLU   ( 130-)  B   H-bonding suggests Gln
 636 ASP   ( 213-)  B   H-bonding suggests Asn
 643 ASP   ( 220-)  B   H-bonding suggests Asn
 860 ASP   ( 445-)  B   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.433
  2nd generation packing quality :  -2.036
  Ramachandran plot appearance   :  -4.232 (bad)
  chi-1/chi-2 rotamer normality  :  -5.478 (bad)
  Backbone conformation          :  -0.469

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.019
  Bond angles                    :   2.171 (loose)
  Omega angle restraints         :   0.498 (tight)
  Side chain planarity           :   0.685
  Improper dihedral distribution :   1.458
  B-factor distribution          :   0.365
  Inside/Outside distribution    :   0.992

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 : 2.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -1.7
  chi-1/chi-2 rotamer normality  :  -3.0 (poor)
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.019
  Bond angles                    :   2.171 (loose)
  Omega angle restraints         :   0.498 (tight)
  Side chain planarity           :   0.685
  Improper dihedral distribution :   1.458
  B-factor distribution          :   0.365
  Inside/Outside distribution    :   0.992
==============

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.