WHAT IF Check report

This file was created 2011-12-16 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 pdb1lf9.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.197
CA-only RMS fit for the two chains : 0.155

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 21 21 21
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 2
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Z, symmetry, and molecular multiplicity disagree
Could it be that Z must be: 8

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 152382.750
Volume of the Unit Cell V= 1364470.1
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.477
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.230 Or should we use the previously suggested Z = 8
which would result in Vm= 2.239
And remember, a matrix counting problem has been reported earlier already

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

1351 ACR   ( 700-)  A  -
1354 ACR   ( 701-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Coordinate problems, unexpected atoms, B-factor and occupancy checks

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

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.

   6 ARG   (  16-)  A
 109 ARG   ( 119-)  A
 120 ARG   ( 130-)  A
 173 ARG   ( 183-)  A
 426 ARG   ( 436-)  A
 494 ARG   ( 504-)  A
 531 ARG   ( 541-)  A
 565 ARG   ( 575-)  A
 596 ARG   ( 606-)  A
 671 ARG   ( 681-)  A
 680 ARG   (  16-)  B
 783 ARG   ( 119-)  B
 794 ARG   ( 130-)  B
 847 ARG   ( 183-)  B
1074 ARG   ( 410-)  B
1100 ARG   ( 436-)  B
1168 ARG   ( 504-)  B
1205 ARG   ( 541-)  B
1239 ARG   ( 575-)  B
1270 ARG   ( 606-)  B
1345 ARG   ( 681-)  B

Warning: Tyrosine convention problem

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

  36 TYR   (  46-)  A
  53 TYR   (  63-)  A
  97 TYR   ( 107-)  A
 159 TYR   ( 169-)  A
 177 TYR   ( 187-)  A
 273 TYR   ( 283-)  A
 379 TYR   ( 389-)  A
 396 TYR   ( 406-)  A
 433 TYR   ( 443-)  A
 464 TYR   ( 474-)  A
 480 TYR   ( 490-)  A
 491 TYR   ( 501-)  A
 492 TYR   ( 502-)  A
 571 TYR   ( 581-)  A
 599 TYR   ( 609-)  A
 649 TYR   ( 659-)  A
 710 TYR   (  46-)  B
 727 TYR   (  63-)  B
 771 TYR   ( 107-)  B
 833 TYR   ( 169-)  B
 851 TYR   ( 187-)  B
 947 TYR   ( 283-)  B
1053 TYR   ( 389-)  B
1070 TYR   ( 406-)  B
1107 TYR   ( 443-)  B
1138 TYR   ( 474-)  B
1154 TYR   ( 490-)  B
1165 TYR   ( 501-)  B
1166 TYR   ( 502-)  B
1245 TYR   ( 581-)  B
1273 TYR   ( 609-)  B
1323 TYR   ( 659-)  B

Warning: Phenylalanine convention problem

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

  90 PHE   ( 100-)  A
 115 PHE   ( 125-)  A
 240 PHE   ( 250-)  A
 414 PHE   ( 424-)  A
 617 PHE   ( 627-)  A
 764 PHE   ( 100-)  B
 789 PHE   ( 125-)  B
 914 PHE   ( 250-)  B
1088 PHE   ( 424-)  B
1291 PHE   ( 627-)  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.

  61 ASP   (  71-)  A
  71 ASP   (  81-)  A
  78 ASP   (  88-)  A
  92 ASP   ( 102-)  A
 117 ASP   ( 127-)  A
 146 ASP   ( 156-)  A
 198 ASP   ( 208-)  A
 202 ASP   ( 212-)  A
 204 ASP   ( 214-)  A
 214 ASP   ( 224-)  A
 244 ASP   ( 254-)  A
 334 ASP   ( 344-)  A
 347 ASP   ( 357-)  A
 349 ASP   ( 359-)  A
 356 ASP   ( 366-)  A
 402 ASP   ( 412-)  A
 469 ASP   ( 479-)  A
 476 ASP   ( 486-)  A
 504 ASP   ( 514-)  A
 517 ASP   ( 527-)  A
 539 ASP   ( 549-)  A
 606 ASP   ( 616-)  A
 666 ASP   ( 676-)  A
 679 ASP   (  15-)  B
 735 ASP   (  71-)  B
 745 ASP   (  81-)  B
 752 ASP   (  88-)  B
 766 ASP   ( 102-)  B
 791 ASP   ( 127-)  B
 820 ASP   ( 156-)  B
 872 ASP   ( 208-)  B
 876 ASP   ( 212-)  B
 878 ASP   ( 214-)  B
 888 ASP   ( 224-)  B
 918 ASP   ( 254-)  B
1008 ASP   ( 344-)  B
1021 ASP   ( 357-)  B
1023 ASP   ( 359-)  B
1030 ASP   ( 366-)  B
1076 ASP   ( 412-)  B
1143 ASP   ( 479-)  B
1150 ASP   ( 486-)  B
1178 ASP   ( 514-)  B
1191 ASP   ( 527-)  B
1213 ASP   ( 549-)  B
1280 ASP   ( 616-)  B
1340 ASP   ( 676-)  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.

  19 GLU   (  29-)  A
  88 GLU   (  98-)  A
 133 GLU   ( 143-)  A
 167 GLU   ( 177-)  A
 205 GLU   ( 215-)  A
 222 GLU   ( 232-)  A
 233 GLU   ( 243-)  A
 253 GLU   ( 263-)  A
 257 GLU   ( 267-)  A
 269 GLU   ( 279-)  A
 425 GLU   ( 435-)  A
 441 GLU   ( 451-)  A
 453 GLU   ( 463-)  A
 459 GLU   ( 469-)  A
 482 GLU   ( 492-)  A
 595 GLU   ( 605-)  A
 615 GLU   ( 625-)  A
 626 GLU   ( 636-)  A
 630 GLU   ( 640-)  A
 693 GLU   (  29-)  B
 762 GLU   (  98-)  B
 807 GLU   ( 143-)  B
 841 GLU   ( 177-)  B
 879 GLU   ( 215-)  B
 896 GLU   ( 232-)  B
 907 GLU   ( 243-)  B
 927 GLU   ( 263-)  B
 931 GLU   ( 267-)  B
 943 GLU   ( 279-)  B
1099 GLU   ( 435-)  B
1115 GLU   ( 451-)  B
1127 GLU   ( 463-)  B
1133 GLU   ( 469-)  B
1156 GLU   ( 492-)  B
1269 GLU   ( 605-)  B
1289 GLU   ( 625-)  B
1294 GLU   ( 630-)  B
1304 GLU   ( 640-)  B

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.999271  0.000072 -0.000035|
 |  0.000072  0.999405  0.000173|
 | -0.000035  0.000173  0.998478|
Proposed new scale matrix

 |  0.012433  0.000000  0.000000|
 |  0.000000  0.009721 -0.000002|
 |  0.000000 -0.000001  0.006081|
With corresponding cell

    A    =  80.431  B   = 102.872  C    = 164.440
    Alpha=  89.980  Beta=  90.001  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  80.491  B   = 102.931  C    = 164.686
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 43.508
(Under-)estimated Z-score: 4.861

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.

 738 GLU   (  74-)  B      C    CA   CB  101.58   -4.5

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.

   6 ARG   (  16-)  A
  19 GLU   (  29-)  A
  61 ASP   (  71-)  A
  71 ASP   (  81-)  A
  78 ASP   (  88-)  A
  88 GLU   (  98-)  A
  92 ASP   ( 102-)  A
 109 ARG   ( 119-)  A
 117 ASP   ( 127-)  A
 120 ARG   ( 130-)  A
 133 GLU   ( 143-)  A
 146 ASP   ( 156-)  A
 167 GLU   ( 177-)  A
 173 ARG   ( 183-)  A
 198 ASP   ( 208-)  A
 202 ASP   ( 212-)  A
 204 ASP   ( 214-)  A
 205 GLU   ( 215-)  A
 214 ASP   ( 224-)  A
 222 GLU   ( 232-)  A
 233 GLU   ( 243-)  A
 244 ASP   ( 254-)  A
 253 GLU   ( 263-)  A
 257 GLU   ( 267-)  A
 269 GLU   ( 279-)  A
And so on for a total of 106 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.

 408 VAL   ( 418-)  A    4.46
 479 THR   ( 489-)  A    4.38
 552 THR   ( 562-)  A    4.28
1226 THR   ( 562-)  B    4.23
1047 TRP   ( 383-)  B    4.10
1153 THR   ( 489-)  B    4.08
 770 GLY   ( 106-)  B    4.04

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.

  16 PRO   (  26-)  A    -2.8
 690 PRO   (  26-)  B    -2.7
  55 PRO   (  65-)  A    -2.7
 329 LEU   ( 339-)  A    -2.5
1003 LEU   ( 339-)  B    -2.5
 155 TYR   ( 165-)  A    -2.5
 729 PRO   (  65-)  B    -2.5
 173 ARG   ( 183-)  A    -2.5
 829 TYR   ( 165-)  B    -2.5
 847 ARG   ( 183-)  B    -2.4
 367 MET   ( 377-)  A    -2.3
1001 TYR   ( 337-)  B    -2.3
 327 TYR   ( 337-)  A    -2.3
 706 THR   (  42-)  B    -2.3
  32 THR   (  42-)  A    -2.3
1041 MET   ( 377-)  B    -2.3
 425 GLU   ( 435-)  A    -2.2
1099 GLU   ( 435-)  B    -2.1
 106 GLY   ( 116-)  A    -2.1
 491 TYR   ( 501-)  A    -2.1
1172 LEU   ( 508-)  B    -2.1
 498 LEU   ( 508-)  A    -2.1
 908 PHE   ( 244-)  B    -2.1
 744 THR   (  80-)  B    -2.1
1161 GLY   ( 497-)  B    -2.1
 989 TRP   ( 325-)  B    -2.1
 428 GLU   ( 438-)  A    -2.1
 115 PHE   ( 125-)  A    -2.1
 487 GLY   ( 497-)  A    -2.0
 381 THR   ( 391-)  A    -2.0
 789 PHE   ( 125-)  B    -2.0
  70 THR   (  80-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  14 ASN   (  24-)  A  Poor phi/psi
  15 GLY   (  25-)  A  PRO omega poor
  32 THR   (  42-)  A  Poor phi/psi
  50 SER   (  60-)  A  Poor phi/psi
  54 TYR   (  64-)  A  Poor phi/psi, PRO omega poor
  81 LYS   (  91-)  A  Poor phi/psi
 106 GLY   ( 116-)  A  Poor phi/psi
 150 LYS   ( 160-)  A  Poor phi/psi
 151 ASN   ( 161-)  A  Poor phi/psi
 165 ASN   ( 175-)  A  Poor phi/psi
 174 ASP   ( 184-)  A  Poor phi/psi
 195 LYS   ( 205-)  A  Poor phi/psi
 207 LYS   ( 217-)  A  Poor phi/psi
 208 GLN   ( 218-)  A  Poor phi/psi
 231 ASN   ( 241-)  A  Poor phi/psi
 321 ASP   ( 331-)  A  Poor phi/psi
 419 GLY   ( 429-)  A  PRO omega poor
 428 GLU   ( 438-)  A  Poor phi/psi
 429 GLU   ( 439-)  A  Poor phi/psi
 487 GLY   ( 497-)  A  Poor phi/psi
 491 TYR   ( 501-)  A  Poor phi/psi
 499 SER   ( 509-)  A  Poor phi/psi
 566 TYR   ( 576-)  A  Poor phi/psi
 568 HIS   ( 578-)  A  Poor phi/psi
 640 SER   ( 650-)  A  PRO omega poor
And so on for a total of 54 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.

 965 SER   ( 301-)  B    0.36
1229 VAL   ( 565-)  B    0.36
 460 SER   ( 470-)  A    0.39

Warning: Unusual backbone conformations

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

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

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

   9 ASN   (  19-)  A      0
  13 VAL   (  23-)  A      0
  14 ASN   (  24-)  A      0
  16 PRO   (  26-)  A      0
  20 ASP   (  30-)  A      0
  22 TRP   (  32-)  A      0
  25 ALA   (  35-)  A      0
  27 LYS   (  37-)  A      0
  28 GLN   (  38-)  A      0
  30 VAL   (  40-)  A      0
  32 THR   (  42-)  A      0
  34 ASN   (  44-)  A      0
  35 ASN   (  45-)  A      0
  38 SER   (  48-)  A      0
  39 LYS   (  49-)  A      0
  41 TRP   (  51-)  A      0
  45 ALA   (  55-)  A      0
  50 SER   (  60-)  A      0
  51 GLU   (  61-)  A      0
  54 TYR   (  64-)  A      0
  55 PRO   (  65-)  A      0
  61 ASP   (  71-)  A      0
  63 LYS   (  73-)  A      0
  64 GLU   (  74-)  A      0
  65 ILE   (  75-)  A      0
And so on for a total of 534 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 : 1.216

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!

 770 GLY   ( 106-)  B   1.56   16
  96 GLY   ( 106-)  A   1.52   16

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].

 391 PRO   ( 401-)  A  -112.1 envelop C-gamma (-108 degrees)
 435 PRO   ( 445-)  A  -114.0 envelop C-gamma (-108 degrees)
 590 PRO   ( 600-)  A  -134.7 half-chair C-delta/C-gamma (-126 degrees)
1065 PRO   ( 401-)  B  -117.5 half-chair C-delta/C-gamma (-126 degrees)
1264 PRO   ( 600-)  B  -132.7 half-chair C-delta/C-gamma (-126 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.

 550 ASP   ( 560-)  A      OD1 <->  596 ARG   ( 606-)  A      NH2    0.30    2.40  INTRA BL
  66 LYS   (  76-)  A      NZ  <->   78 ASP   (  88-)  A      OD2    0.28    2.42  INTRA
 353 ARG   ( 363-)  A      NH2 <-> 1355 HOH   ( 842 )  A      O      0.27    2.43  INTRA BL
1224 ASP   ( 560-)  B      OD1 <-> 1270 ARG   ( 606-)  B      NH2    0.27    2.43  INTRA
 740 LYS   (  76-)  B      NZ  <->  752 ASP   (  88-)  B      OD2    0.27    2.43  INTRA BL
1239 ARG   ( 575-)  B      NH2 <-> 1354 ACR   ( 701-)  B      O3B    0.25    2.45  INTRA BL
 970 LYS   ( 306-)  B      NZ  <-> 1356 HOH   ( 940 )  B      O      0.25    2.45  INTRA BL
 550 ASP   ( 560-)  A      CG  <->  596 ARG   ( 606-)  A      NH2    0.21    2.89  INTRA BL
 977 ASN   ( 313-)  B      ND2 <-> 1356 HOH   ( 853 )  B      O      0.21    2.49  INTRA BL
 713 LYS   (  49-)  B      NZ  <-> 1356 HOH   (1100 )  B      O      0.20    2.50  INTRA
  94 SER   ( 104-)  A      CA  <->  293 MET   ( 303-)  A      CE     0.17    3.03  INTRA
 624 ILE   ( 634-)  A      N   <->  646 HIS   ( 656-)  A      NE2    0.17    2.83  INTRA BL
 428 GLU   ( 438-)  A      OE1 <-> 1351 ACR   ( 700-)  A      N4B    0.17    2.53  INTRA BL
  95 LEU   ( 105-)  A      N   <->  293 MET   ( 303-)  A      CE     0.15    2.95  INTRA
 809 SER   ( 145-)  B      N   <->  812 ASP   ( 148-)  B      OD2    0.15    2.55  INTRA BF
1182 ASN   ( 518-)  B      ND2 <-> 1356 HOH   ( 860 )  B      O      0.15    2.55  INTRA BL
   8 ASN   (  18-)  A      ND2 <-> 1355 HOH   (1058 )  A      O      0.15    2.55  INTRA BF
 876 ASP   ( 212-)  B      OD2 <->  884 THR   ( 220-)  B      N      0.14    2.56  INTRA BF
 701 LYS   (  37-)  B      NZ  <->  725 GLU   (  61-)  B      OE1    0.14    2.56  INTRA BL
1188 GLY   ( 524-)  B      N   <-> 1356 HOH   ( 919 )  B      O      0.14    2.56  INTRA
 265 ASN   ( 275-)  A      ND2 <-> 1355 HOH   ( 917 )  A      O      0.14    2.56  INTRA BF
 901 ASP   ( 237-)  B      N   <-> 1356 HOH   ( 946 )  B      O      0.14    2.56  INTRA
 278 ASN   ( 288-)  A      CB  <-> 1355 HOH   ( 973 )  A      O      0.14    2.66  INTRA BF
 857 ASN   ( 193-)  B      OD1 <->  909 GLU   ( 245-)  B      N      0.14    2.56  INTRA BL
 953 ASN   ( 289-)  B      N   <-> 1356 HOH   (1114 )  B      O      0.13    2.57  INTRA BF
And so on for a total of 225 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.

 571 TYR   ( 581-)  A      -6.74
1245 TYR   ( 581-)  B      -6.71
1039 ASN   ( 375-)  B      -5.40
 365 ASN   ( 375-)  A      -5.39
 680 ARG   (  16-)  B      -5.38
1255 HIS   ( 591-)  B      -5.27
 421 LYS   ( 431-)  A      -5.27
 581 HIS   ( 591-)  A      -5.27
 916 GLN   ( 252-)  B      -5.24
 206 ASN   ( 216-)  A      -5.19
 880 ASN   ( 216-)  B      -5.19
 242 GLN   ( 252-)  A      -5.18
1095 LYS   ( 431-)  B      -5.17
 620 GLU   ( 630-)  A      -5.16
 671 ARG   ( 681-)  A      -5.13
1345 ARG   ( 681-)  B      -5.09
  14 ASN   (  24-)  A      -5.08
1294 GLU   ( 630-)  B      -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.

  13 VAL   (  23-)  A        15 - GLY     25- ( A)         -4.60
 687 VAL   (  23-)  B       689 - GLY     25- ( B)         -4.62

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

1227 ILE   ( 563-)  B   -2.57

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1356 HOH   (1059 )  B      O     53.64   16.58   19.41

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.

1355 HOH   (1031 )  A      O
1355 HOH   (1060 )  A      O
1356 HOH   ( 914 )  B      O
1356 HOH   (1157 )  B      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.

   8 ASN   (  18-)  A
  35 ASN   (  45-)  A
  46 ASN   (  56-)  A
 285 ASN   ( 295-)  A
 290 ASN   ( 300-)  A
 371 ASN   ( 381-)  A
 483 ASN   ( 493-)  A
 490 GLN   ( 500-)  A
 508 ASN   ( 518-)  A
 544 ASN   ( 554-)  A
 656 ASN   ( 666-)  A
 709 ASN   (  45-)  B
 720 ASN   (  56-)  B
 916 GLN   ( 252-)  B
 959 ASN   ( 295-)  B
 964 ASN   ( 300-)  B
 977 ASN   ( 313-)  B
1045 ASN   ( 381-)  B
1164 GLN   ( 500-)  B
1182 ASN   ( 518-)  B
1218 ASN   ( 554-)  B
1330 ASN   ( 666-)  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 ILE   (  12-)  A      N
  13 VAL   (  23-)  A      N
  56 THR   (  66-)  A      N
  94 SER   ( 104-)  A      OG
  95 LEU   ( 105-)  A      N
  96 GLY   ( 106-)  A      N
 105 LYS   ( 115-)  A      N
 108 TYR   ( 118-)  A      N
 108 TYR   ( 118-)  A      OH
 166 ASN   ( 176-)  A      N
 182 SER   ( 192-)  A      N
 188 GLY   ( 198-)  A      N
 189 TYR   ( 199-)  A      OH
 208 GLN   ( 218-)  A      N
 215 SER   ( 225-)  A      N
 227 ASP   ( 237-)  A      N
 239 SER   ( 249-)  A      OG
 243 SER   ( 253-)  A      N
 315 TRP   ( 325-)  A      NE1
 324 THR   ( 334-)  A      N
 333 ARG   ( 343-)  A      NE
 333 ARG   ( 343-)  A      NH2
 340 ASN   ( 350-)  A      ND2
 367 MET   ( 377-)  A      N
 370 GLN   ( 380-)  A      NE2
And so on for a total of 78 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.

 148 HIS   ( 158-)  A      ND1
 222 GLU   ( 232-)  A      OE2
 387 GLU   ( 397-)  A      OE1
 428 GLU   ( 438-)  A      OE1
 441 GLU   ( 451-)  A      OE2
 637 ASP   ( 647-)  A      OD2
 822 HIS   ( 158-)  B      ND1
 896 GLU   ( 232-)  B      OE2
1061 GLU   ( 397-)  B      OE1
1102 GLU   ( 438-)  B      OE1
1115 GLU   ( 451-)  B      OE2
1311 ASP   ( 647-)  B      OD2

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.

  61 ASP   (  71-)  A   H-bonding suggests Asn
  82 ASP   (  92-)  A   H-bonding suggests Asn
 113 ASP   ( 123-)  A   H-bonding suggests Asn; but Alt-Rotamer
 138 ASP   ( 148-)  A   H-bonding suggests Asn
 214 ASP   ( 224-)  A   H-bonding suggests Asn
 222 GLU   ( 232-)  A   H-bonding suggests Gln; but Alt-Rotamer
 268 ASP   ( 278-)  A   H-bonding suggests Asn; but Alt-Rotamer
 387 GLU   ( 397-)  A   H-bonding suggests Gln
 413 ASP   ( 423-)  A   H-bonding suggests Asn
 441 GLU   ( 451-)  A   H-bonding suggests Gln; but Alt-Rotamer
 523 ASP   ( 533-)  A   H-bonding suggests Asn
 735 ASP   (  71-)  B   H-bonding suggests Asn
 756 ASP   (  92-)  B   H-bonding suggests Asn
 787 ASP   ( 123-)  B   H-bonding suggests Asn; but Alt-Rotamer
 812 ASP   ( 148-)  B   H-bonding suggests Asn
 888 ASP   ( 224-)  B   H-bonding suggests Asn
 896 GLU   ( 232-)  B   H-bonding suggests Gln; but Alt-Rotamer
 942 ASP   ( 278-)  B   H-bonding suggests Asn; but Alt-Rotamer
 995 ASP   ( 331-)  B   H-bonding suggests Asn
1061 GLU   ( 397-)  B   H-bonding suggests Gln
1087 ASP   ( 423-)  B   H-bonding suggests Asn
1115 GLU   ( 451-)  B   H-bonding suggests Gln; but Alt-Rotamer
1197 ASP   ( 533-)  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 :   0.161
  2nd generation packing quality :  -0.467
  Ramachandran plot appearance   :  -1.252
  chi-1/chi-2 rotamer normality  :  -1.268
  Backbone conformation          :  -0.303

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.275 (tight)
  Bond angles                    :   0.544 (tight)
  Omega angle restraints         :   0.221 (tight)
  Side chain planarity           :   0.263 (tight)
  Improper dihedral distribution :   0.566
  B-factor distribution          :   0.491
  Inside/Outside distribution    :   1.003

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -0.0
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.275 (tight)
  Bond angles                    :   0.544 (tight)
  Omega angle restraints         :   0.221 (tight)
  Side chain planarity           :   0.263 (tight)
  Improper dihedral distribution :   0.566
  B-factor distribution          :   0.491
  Inside/Outside distribution    :   1.003
==============

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.