WHAT IF Check report

This file was created 2012-01-25 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 pdb2icw.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.541
CA-only RMS fit for the two chains : 0.032

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: C and F

All-atom RMS fit for the two chains : 0.242
CA-only RMS fit for the two chains : 0.021

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: G and H

All-atom RMS fit for the two chains : 0.612
CA-only RMS fit for the two chains : 0.226

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: G and H

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: I and K

All-atom RMS fit for the two chains : 0.664
CA-only RMS fit for the two chains : 0.036

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: I and K

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: J and L

All-atom RMS fit for the two chains : 0.677
CA-only RMS fit for the two chains : 0.024

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: J and L

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

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

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.

  34 MSE   (  36-)  A    High
 283 SER   ( 104-)  B    High
 284 LYS   ( 105-)  B    High
 285 THR   ( 106-)  B    High
 305 PHE   ( 132-)  B    High
 306 ARG   ( 133-)  B    High
 307 ASN   ( 134-)  B    High
 308 GLY   ( 135-)  B    High
 309 GLN   ( 136-)  B    High
 310 GLU   ( 137-)  B    High
 311 GLU   ( 138-)  B    High
 312 LYS   ( 139-)  B    High
 313 ALA   ( 140-)  B    High
 335 GLU   ( 162-)  B    High
 336 THR   ( 163-)  B    High
 337 VAL   ( 164-)  B    High
 338 PRO   ( 165-)  B    High
 339 ARG   ( 166-)  B    High
 340 SER   ( 167-)  B    High
 341 GLY   ( 168-)  B    High
 342 GLU   ( 169-)  B    High
 360 GLU   ( 187-)  B    High
 361 TRP   ( 188-)  B    High
 362 ARG   ( 189-)  B    High
 363 ALA   ( 190-)  B    High
And so on for a total of 229 lines.

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

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

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

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.

 185 ARG   (   6-)  B
 208 ARG   (  29-)  B
 227 ARG   (  48-)  B
 250 ARG   (  71-)  B
 259 ARG   (  80-)  B
 272 ARG   (  93-)  B
 303 ARG   ( 130-)  B
 306 ARG   ( 133-)  B
 362 ARG   ( 189-)  B
 418 ARG   (  44-)  D
 424 ARG   (  50-)  D
 514 ARG   ( 140-)  D
 561 ARG   (   6-)  E
 603 ARG   (  48-)  E
 626 ARG   (  71-)  E
 739 ARG   ( 189-)  E
 855 ARG   ( 102-)  G
1023 ARG   (  57-)  H
1057 ARG   (  91-)  H
1188 ARG   (   9-)  I
1200 ARG   (  21-)  I
1219 ARG   (  40-)  I
1261 ARG   (  82-)  I
1357 ARG   (  68-)  J
1477 ARG   (  76-)  K
1518 ARG   (   9-)  L
1615 ARG   ( 106-)  L

Warning: Tyrosine convention problem

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

 211 TYR   (  32-)  B
 239 TYR   (  60-)  B
 257 TYR   (  78-)  B
 366 TYR   ( 308-)  C
 535 TYR   ( 161-)  D
 587 TYR   (  32-)  E
 602 TYR   (  47-)  E
 615 TYR   (  60-)  E
 633 TYR   (  78-)  E
 743 TYR   ( 308-)  F
 819 TYR   (  66-)  G
 947 TYR   ( 194-)  G
1038 TYR   (  72-)  H
1154 TYR   ( 188-)  H
1214 TYR   (  35-)  I
1217 TYR   (  38-)  I
1267 TYR   (  88-)  I
1322 TYR   (  33-)  J
1389 TYR   ( 100-)  J
1432 TYR   (  31-)  K
1436 TYR   (  35-)  K
1439 TYR   (  38-)  K
1489 TYR   (  88-)  K
1542 TYR   (  33-)  L
1609 TYR   ( 100-)  L

Warning: Phenylalanine convention problem

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

  22 PHE   (  24-)  A
  46 PHE   (  48-)  A
  49 PHE   (  51-)  A
 106 PHE   ( 108-)  A
 110 PHE   ( 112-)  A
 135 PHE   ( 137-)  A
 192 PHE   (  13-)  B
 295 PHE   ( 122-)  B
 398 PHE   (  24-)  D
 422 PHE   (  48-)  D
 482 PHE   ( 108-)  D
 568 PHE   (  13-)  E
 572 PHE   (  17-)  E
 672 PHE   ( 122-)  E
 777 PHE   (  24-)  G
 813 PHE   (  60-)  G
 833 PHE   (  80-)  G
 874 PHE   ( 121-)  G
 964 PHE   ( 211-)  G
 990 PHE   (  24-)  H
1026 PHE   (  60-)  H
1087 PHE   ( 121-)  H
1145 PHE   ( 179-)  H
1363 PHE   (  74-)  J
1379 PHE   (  90-)  J
1390 PHE   ( 101-)  J
1583 PHE   (  74-)  L
1610 PHE   ( 101-)  L

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.

  23 ASP   (  25-)  A
  27 ASP   (  29-)  A
  33 ASP   (  35-)  A
  64 ASP   (  66-)  A
 108 ASP   ( 110-)  A
 179 ASP   ( 181-)  A
 181 ASP   (   2-)  B
 236 ASP   (  57-)  B
 245 ASP   (  66-)  B
 255 ASP   (  76-)  B
 399 ASP   (  25-)  D
 403 ASP   (  29-)  D
 409 ASP   (  35-)  D
 440 ASP   (  66-)  D
 484 ASP   ( 110-)  D
 555 ASP   ( 181-)  D
 557 ASP   (   2-)  E
 612 ASP   (  57-)  E
 621 ASP   (  66-)  E
 631 ASP   (  76-)  E
 818 ASP   (  65-)  G
 868 ASP   ( 115-)  G
 870 ASP   ( 117-)  G
 966 ASP   ( 213-)  G
1031 ASP   (  65-)  H
1081 ASP   ( 115-)  H
1083 ASP   ( 117-)  H
1136 ASP   ( 170-)  H
1179 ASP   ( 213-)  H
1232 ASP   (  53-)  I
1263 ASP   (  84-)  I
1327 ASP   (  38-)  J
1408 ASP   (   7-)  K
1454 ASP   (  53-)  K
1485 ASP   (  84-)  K
1547 ASP   (  38-)  L

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.

   2 GLU   (   4-)  A
  28 GLU   (  30-)  A
  44 GLU   (  46-)  A
  45 GLU   (  47-)  A
  86 GLU   (  88-)  A
  96 GLU   (  98-)  A
 139 GLU   ( 141-)  A
 193 GLU   (  14-)  B
 201 GLU   (  22-)  B
 207 GLU   (  28-)  B
 231 GLU   (  52-)  B
 238 GLU   (  59-)  B
 266 GLU   (  87-)  B
 310 GLU   ( 137-)  B
 335 GLU   ( 162-)  B
 360 GLU   ( 187-)  B
 378 GLU   (   4-)  D
 395 GLU   (  21-)  D
 404 GLU   (  30-)  D
 414 GLU   (  40-)  D
 421 GLU   (  47-)  D
 472 GLU   (  98-)  D
 508 GLU   ( 134-)  D
 515 GLU   ( 141-)  D
 569 GLU   (  14-)  E
And so on for a total of 60 lines.

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

 |  0.998780 -0.000373 -0.000184|
 | -0.000373  0.999307 -0.000504|
 | -0.000184 -0.000504  0.999234|
Proposed new scale matrix

 |  0.016278  0.005252  0.002855|
 |  0.000005  0.012113  0.004941|
 |  0.000002  0.000005  0.009245|
With corresponding cell

    A    =  61.441  B   =  86.774  C    = 116.938
    Alpha= 110.310  Beta=  92.323  Gamma= 107.899

The CRYST1 cell dimensions

    A    =  61.516  B   =  86.822  C    = 116.981
    Alpha= 110.270  Beta=  92.320  Gamma= 107.870

Variance: 50.693
(Under-)estimated Z-score: 5.247

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.

   7 GLN   (   9-)  A      N    CA   C    99.72   -4.1
 383 GLN   (   9-)  D      N    CA   C    99.29   -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.

   2 GLU   (   4-)  A
  23 ASP   (  25-)  A
  27 ASP   (  29-)  A
  28 GLU   (  30-)  A
  33 ASP   (  35-)  A
  44 GLU   (  46-)  A
  45 GLU   (  47-)  A
  64 ASP   (  66-)  A
  86 GLU   (  88-)  A
  96 GLU   (  98-)  A
 108 ASP   ( 110-)  A
 139 GLU   ( 141-)  A
 179 ASP   ( 181-)  A
 181 ASP   (   2-)  B
 185 ARG   (   6-)  B
 193 GLU   (  14-)  B
 201 GLU   (  22-)  B
 207 GLU   (  28-)  B
 208 ARG   (  29-)  B
 227 ARG   (  48-)  B
 231 GLU   (  52-)  B
 236 ASP   (  57-)  B
 238 GLU   (  59-)  B
 245 ASP   (  66-)  B
 250 ARG   (  71-)  B
And so on for a total of 123 lines.

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.

1031 ASP   (  65-)  H    4.61
 928 GLU   ( 175-)  G    4.51
1141 GLU   ( 175-)  H    4.50
 818 ASP   (  65-)  G    4.24
 383 GLN   (   9-)  D    4.10

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.

1229 TYR   (  50-)  I    -3.2
1451 TYR   (  50-)  K    -2.7
 525 LEU   ( 151-)  D    -2.6
 487 THR   ( 113-)  D    -2.6
 111 THR   ( 113-)  A    -2.6
 527 PHE   ( 153-)  D    -2.6
 594 ARG   (  39-)  E    -2.6
 390 PRO   (  16-)  D    -2.6
  14 PRO   (  16-)  A    -2.5
 504 THR   ( 130-)  D    -2.5
 151 PHE   ( 153-)  A    -2.5
1210 TYR   (  31-)  I    -2.4
1596 SER   (  87-)  L    -2.4
  98 ARG   ( 100-)  A    -2.4
1474 PHE   (  73-)  K    -2.3
1432 TYR   (  31-)  K    -2.3
1587 LEU   (  78-)  L    -2.3
 518 LEU   ( 144-)  D    -2.3
 142 LEU   ( 144-)  A    -2.3
 182 THR   (   3-)  B    -2.3
1208 THR   (  29-)  I    -2.3
 217 VAL   (  38-)  B    -2.3
1093 ASN   ( 127-)  H    -2.3
 582 LEU   (  27-)  E    -2.3
1226 LEU   (  47-)  I    -2.3
And so on for a total of 76 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.

  13 ASN   (  15-)  A  PRO omega poor
  76 ASN   (  78-)  A  Poor phi/psi
  77 TYR   (  79-)  A  Poor phi/psi
  98 ARG   ( 100-)  A  Poor phi/psi
 111 THR   ( 113-)  A  PRO omega poor
 113 PRO   ( 115-)  A  Poor phi/psi
 122 ASN   ( 124-)  A  Poor phi/psi
 141 HIS   ( 143-)  A  Poor phi/psi
 212 ASN   (  33-)  B  Poor phi/psi
 291 SER   ( 118-)  B  Poor phi/psi
 296 TYR   ( 123-)  B  PRO omega poor
 307 ASN   ( 134-)  B  Poor phi/psi
 312 LYS   ( 139-)  B  Poor phi/psi
 326 TRP   ( 153-)  B  Poor phi/psi
 389 ASN   (  15-)  D  PRO omega poor
 406 PHE   (  32-)  D  Poor phi/psi
 452 ASN   (  78-)  D  Poor phi/psi
 453 TYR   (  79-)  D  Poor phi/psi
 474 ARG   ( 100-)  D  Poor phi/psi
 487 THR   ( 113-)  D  PRO omega poor
 489 PRO   ( 115-)  D  Poor phi/psi
 498 ASN   ( 124-)  D  Poor phi/psi
 517 HIS   ( 143-)  D  Poor phi/psi
 574 ASN   (  19-)  E  Poor phi/psi
 588 ASN   (  33-)  E  Poor phi/psi
And so on for a total of 73 lines.

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 643 SER   (  88-)  E    0.36
 872 SER   ( 119-)  G    0.40

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!

   9 GLU   (  11-)  A      0
  13 ASN   (  15-)  A      0
  19 GLU   (  21-)  A      0
  21 MSE   (  23-)  A      0
  24 PHE   (  26-)  A      0
  29 ILE   (  31-)  A      0
  30 PHE   (  32-)  A      0
  31 HIS   (  33-)  A      0
  34 MSE   (  36-)  A      0
  49 PHE   (  51-)  A      0
  71 MSE   (  73-)  A      0
  75 SER   (  77-)  A      0
  76 ASN   (  78-)  A      0
  77 TYR   (  79-)  A      0
  97 LEU   (  99-)  A      0
  98 ARG   ( 100-)  A      0
 101 ASN   ( 103-)  A      0
 108 ASP   ( 110-)  A      0
 109 LYS   ( 111-)  A      0
 110 PHE   ( 112-)  A      0
 111 THR   ( 113-)  A      0
 112 PRO   ( 114-)  A      0
 113 PRO   ( 115-)  A      0
 114 VAL   ( 116-)  A      0
 121 ARG   ( 123-)  A      0
And so on for a total of 608 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 : 1.244

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!

 949 GLY   ( 196-)  G   1.84   15
 685 GLY   ( 135-)  E   1.53   14
 308 GLY   ( 135-)  B   1.51   14

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]

  14 PRO   (  16-)  A    0.46 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.

1182 VAL   (   3-)  I      CG2 <-> 1269 CYS   (  90-)  I      SG     0.41    2.99  INTRA BF
1385 GLY   (  96-)  J      O   <-> 1387 THR   (  98-)  J      N      0.41    2.29  INTRA BF
 906 LEU   ( 153-)  G      O   <->  908 ASP   ( 155-)  G      N      0.39    2.31  INTRA BF
1605 GLY   (  96-)  L      O   <-> 1607 THR   (  98-)  L      N      0.38    2.32  INTRA BF
 804 LYS   (  51-)  G      NZ  <->  861 ASP   ( 108-)  G      OD1    0.38    2.32  INTRA BL
 835 LYS   (  82-)  G      NZ  <-> 1639 HOH   ( 244 )  G      O      0.32    2.38  INTRA BL
 142 LEU   ( 144-)  A      CD1 <->  213 GLN   (  34-)  B      NE2    0.31    2.79  INTRA BL
 272 ARG   (  93-)  B      NH1 <->  326 TRP   ( 153-)  B      O      0.30    2.40  INTRA BL
1549 GLY   (  40-)  L      C   <-> 1550 HIS   (  41-)  L      ND1    0.30    2.70  INTRA BF
1353 TYR   (  64-)  J      CD1 <-> 1367 LEU   (  78-)  J      CD2    0.30    2.90  INTRA BL
 165 HIS   ( 167-)  A      ND1 <->  167 GLY   ( 169-)  A      N      0.29    2.71  INTRA BL
1404 VAL   (   3-)  K      CG2 <-> 1423 CYS   (  22-)  K      SG     0.29    3.11  INTRA BF
1126 ILE   ( 160-)  H      CG2 <-> 1537 ASN   (  28-)  L      CB     0.28    2.92  INTRA BF
1357 ARG   (  68-)  J      NH1 <-> 1359 SER   (  70-)  J      O      0.28    2.42  INTRA BL
1119 LEU   ( 153-)  H      O   <-> 1121 ASP   ( 155-)  H      N      0.26    2.44  INTRA BF
 920 PHE   ( 167-)  G      O   <->  922 SER   ( 169-)  G      N      0.26    2.44  INTRA BF
 463 VAL   (  89-)  D      O   <->  550 LYS   ( 176-)  D      NZ     0.24    2.46  INTRA BF
 583 GLU   (  28-)  E      OE1 <->  626 ARG   (  71-)  E      NE     0.24    2.46  INTRA BL
1133 PHE   ( 167-)  H      O   <-> 1135 SER   ( 169-)  H      N      0.23    2.47  INTRA BF
 344 TYR   ( 171-)  B      O   <->  361 TRP   ( 188-)  B      N      0.23    2.47  INTRA BF
 538 ARG   ( 164-)  D      NH2 <-> 1636 HOH   ( 221 )  D      O      0.23    2.47  INTRA BL
 945 ARG   ( 192-)  G      NH2 <-> 1385 GLY   (  96-)  J      C      0.23    2.87  INTRA BF
 576 THR   (  21-)  E      O   <->  635 ARG   (  80-)  E      NH1    0.22    2.48  INTRA BL
 945 ARG   ( 192-)  G      NH2 <-> 1386 GLY   (  97-)  J      N      0.22    2.63  INTRA BF
1157 LYS   ( 191-)  H      NZ  <-> 1161 GLU   ( 195-)  H      OE2    0.22    2.48  INTRA BF
And so on for a total of 383 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

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.

1219 ARG   (  40-)  I      -8.52
1441 ARG   (  40-)  K      -8.12
 284 LYS   ( 105-)  B      -6.75
 907 ARG   ( 154-)  G      -6.65
1427 TYR   (  26-)  K      -6.15
1229 TYR   (  50-)  I      -6.09
  98 ARG   ( 100-)  A      -6.07
 339 ARG   ( 166-)  B      -6.05
1120 ARG   ( 154-)  H      -6.05
 474 ARG   ( 100-)  D      -5.98
1458 GLN   (  57-)  K      -5.93
 739 ARG   ( 189-)  E      -5.92
1205 TYR   (  26-)  I      -5.71
 716 ARG   ( 166-)  E      -5.70
 362 ARG   ( 189-)  B      -5.64
1220 GLN   (  41-)  I      -5.50
 755 LYS   (   2-)  G      -5.26
 968 LYS   (   2-)  H      -5.21
  48 ARG   (  50-)  A      -5.14
 453 TYR   (  79-)  D      -5.12
1518 ARG   (   9-)  L      -5.11
1442 GLN   (  41-)  K      -5.07
 660 LYS   ( 105-)  E      -5.05
1594 GLN   (  85-)  L      -5.03
  77 TYR   (  79-)  A      -5.01

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

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

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: D

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: E

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: F

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: G

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: H

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: I

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: J

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: K

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: L

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.

1036 LEU   (  70-)  H   -3.05
 823 LEU   (  70-)  G   -2.63

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

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

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.

1634 HOH   ( 208 )  B      O     23.38  -38.07   -0.10

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.

1633 HOH   ( 182 )  A      O
1634 HOH   ( 210 )  B      O
1636 HOH   ( 187 )  D      O
1636 HOH   ( 192 )  D      O
1637 HOH   ( 213 )  E      O
1639 HOH   ( 232 )  G      O
1640 HOH   ( 241 )  H      O

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.

 241 ASN   (  62-)  B
 617 ASN   (  62-)  E
 625 GLN   (  70-)  E
 830 ASN   (  77-)  G
 843 GLN   (  90-)  G
 852 GLN   (  99-)  G
 973 ASN   (   7-)  H
 986 ASN   (  20-)  H
1043 ASN   (  77-)  H
1056 GLN   (  90-)  H
1065 GLN   (  99-)  H
1090 GLN   ( 124-)  H
1313 ASN   (  24-)  J
1314 GLN   (  25-)  J
1362 ASN   (  73-)  J
1374 GLN   (  85-)  J
1461 ASN   (  60-)  K
1533 ASN   (  24-)  L
1534 GLN   (  25-)  L
1582 ASN   (  73-)  L
1594 GLN   (  85-)  L

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.

  36 LYS   (  38-)  A      N
  38 GLU   (  40-)  A      N
  43 LEU   (  45-)  A      N
  45 GLU   (  47-)  A      N
  98 ARG   ( 100-)  A      NH1
 111 THR   ( 113-)  A      OG1
 146 PHE   ( 148-)  A      N
 157 ASP   ( 159-)  A      N
 159 TYR   ( 161-)  A      OH
 170 GLU   ( 172-)  A      N
 218 ARG   (  39-)  B      NE
 220 ASP   (  41-)  B      N
 225 GLU   (  46-)  B      N
 227 ARG   (  48-)  B      NE
 228 ALA   (  49-)  B      N
 254 VAL   (  75-)  B      N
 261 ASN   (  82-)  B      ND2
 272 ARG   (  93-)  B      NH1
 306 ARG   ( 133-)  B      NE
 315 VAL   ( 142-)  B      N
 323 ASN   ( 150-)  B      ND2
 352 SER   ( 179-)  B      OG
 362 ARG   ( 189-)  B      NE
 365 LYS   ( 307-)  C      N
 412 LYS   (  38-)  D      N
And so on for a total of 127 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.

  64 ASP   (  66-)  A      OD2
 195 HIS   (  16-)  B      ND1
 222 ASP   (  43-)  B      OD2
 311 GLU   ( 138-)  B      OE1
 311 GLU   ( 138-)  B      OE2
 440 ASP   (  66-)  D      OD2
 523 HIS   ( 149-)  D      ND1
 684 ASN   ( 134-)  E      OD1
 793 GLU   (  40-)  G      OE1
 870 ASP   ( 117-)  G      OD2
1043 ASN   (  77-)  H      OD1
1163 ASP   ( 197-)  H      OD1
1316 ASN   (  27-)  J      OD1
1336 HIS   (  47-)  J      ND1
1536 ASN   (  27-)  L      OD1
1556 HIS   (  47-)  L      NE2

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  19 GLU   (  21-)  A   H-bonding suggests Gln
  64 ASP   (  66-)  A   H-bonding suggests Asn; but Alt-Rotamer
 395 GLU   (  21-)  D   H-bonding suggests Gln
 399 ASP   (  25-)  D   H-bonding suggests Asn; but Alt-Rotamer
 440 ASP   (  66-)  D   H-bonding suggests Asn; but Alt-Rotamer
 475 GLU   ( 101-)  D   H-bonding suggests Gln
 784 ASP   (  31-)  G   H-bonding suggests Asn
 886 ASP   ( 133-)  G   H-bonding suggests Asn
 928 GLU   ( 175-)  G   H-bonding suggests Gln
 950 ASP   ( 197-)  G   H-bonding suggests Asn; but Alt-Rotamer
1099 ASP   ( 133-)  H   H-bonding suggests Asn; but Alt-Rotamer
1141 GLU   ( 175-)  H   H-bonding suggests Gln
1163 ASP   ( 197-)  H   H-bonding suggests Asn
1263 ASP   (  84-)  I   H-bonding suggests Asn
1485 ASP   (  84-)  K   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 :   0.030
  2nd generation packing quality :  -1.111
  Ramachandran plot appearance   :  -2.286
  chi-1/chi-2 rotamer normality  :  -2.962
  Backbone conformation          :   0.048

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.329 (tight)
  Bond angles                    :   0.613 (tight)
  Omega angle restraints         :   0.226 (tight)
  Side chain planarity           :   0.248 (tight)
  Improper dihedral distribution :   0.605
  B-factor distribution          :   0.479
  Inside/Outside distribution    :   1.017

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 : 2.41


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.0
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.329 (tight)
  Bond angles                    :   0.613 (tight)
  Omega angle restraints         :   0.226 (tight)
  Side chain planarity           :   0.248 (tight)
  Improper dihedral distribution :   0.605
  B-factor distribution          :   0.479
  Inside/Outside distribution    :   1.017
==============

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.