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 pdb1jqo.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 : 1.309
CA-only RMS fit for the two chains : 1.027

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: 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: 204957.578
Volume of the Unit Cell V= 7033668.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.290
Vm by authors and this calculated Vm agree reasonably well
Matthews coefficient read from REMARK 280 Vm= 4.020

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.

1811 SO4   ( 971-)  A  -
1812 SO4   (1071-)  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: 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.

   1 ILE   (  35-)  A    High
   2 GLU   (  36-)  A    High
   3 TYR   (  37-)  A    High
  85 HIS   ( 119-)  A    High
  86 ARG   ( 120-)  A    High
  87 ARG   ( 121-)  A    High
  88 ARG   ( 122-)  A    High
  89 ASN   ( 123-)  A    High
 283 ARG   ( 334-)  A    High
 289 ARG   ( 340-)  A    High
 293 GLU   ( 344-)  A    High
 294 GLU   ( 345-)  A    High
 296 HIS   ( 347-)  A    High
 297 SER   ( 348-)  A    High
 298 SER   ( 349-)  A    High
 299 SER   ( 350-)  A    High
 300 GLY   ( 351-)  A    High
 301 SER   ( 352-)  A    High
 302 LYS   ( 353-)  A    High
 303 VAL   ( 354-)  A    High
 304 THR   ( 355-)  A    High
 313 GLN   ( 364-)  A    High
 710 ILE   ( 769-)  A    High
 711 THR   ( 770-)  A    High
 712 THR   ( 771-)  A    High
And so on for a total of 98 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) :293.000

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: Tyrosine convention problem

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

 268 TYR   ( 319-)  A
 306 TYR   ( 357-)  A
 481 TYR   ( 532-)  A
 567 TYR   ( 618-)  A
 677 TYR   ( 728-)  A
 805 TYR   ( 864-)  A
 838 TYR   ( 897-)  A
1172 TYR   ( 319-)  B
1224 TYR   ( 371-)  B
1236 TYR   ( 383-)  B
1471 TYR   ( 618-)  B
1709 TYR   ( 864-)  B
1742 TYR   ( 897-)  B
1785 TYR   ( 947-)  B

Warning: Phenylalanine convention problem

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

 277 PHE   ( 328-)  A
 310 PHE   ( 361-)  A
 355 PHE   ( 406-)  A
 467 PHE   ( 518-)  A
 478 PHE   ( 529-)  A
 514 PHE   ( 565-)  A
 628 PHE   ( 679-)  A
 637 PHE   ( 688-)  A
 643 PHE   ( 694-)  A
 691 PHE   ( 742-)  A
 727 PHE   ( 786-)  A
 750 PHE   ( 809-)  A
 763 PHE   ( 822-)  A
 845 PHE   ( 904-)  A
1181 PHE   ( 328-)  B
1259 PHE   ( 406-)  B
1382 PHE   ( 529-)  B
1418 PHE   ( 565-)  B
1435 PHE   ( 582-)  B
1532 PHE   ( 679-)  B
1595 PHE   ( 742-)  B
1631 PHE   ( 786-)  B
1749 PHE   ( 904-)  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.

  17 ASP   (  51-)  A
  60 ASP   (  94-)  A
  91 ASP   ( 142-)  A
 241 ASP   ( 292-)  A
 243 ASP   ( 294-)  A
 374 ASP   ( 425-)  A
 377 ASP   ( 428-)  A
 387 ASP   ( 438-)  A
 476 ASP   ( 527-)  A
 491 ASP   ( 542-)  A
 556 ASP   ( 607-)  A
 611 ASP   ( 662-)  A
 778 ASP   ( 837-)  A
 803 ASP   ( 862-)  A
 820 ASP   ( 879-)  A
 825 ASP   ( 884-)  A
 908 ASP   (  38-)  B
 995 ASP   ( 142-)  B
1081 ASP   ( 228-)  B
1145 ASP   ( 292-)  B
1147 ASP   ( 294-)  B
1278 ASP   ( 425-)  B
1281 ASP   ( 428-)  B
1291 ASP   ( 438-)  B
1380 ASP   ( 527-)  B
1395 ASP   ( 542-)  B
1456 ASP   ( 603-)  B
1460 ASP   ( 607-)  B
1515 ASP   ( 662-)  B
1571 ASP   ( 718-)  B
1682 ASP   ( 837-)  B
1707 ASP   ( 862-)  B
1724 ASP   ( 879-)  B
1729 ASP   ( 884-)  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.

  29 GLU   (  63-)  A
  48 GLU   (  82-)  A
  94 GLU   ( 145-)  A
 112 GLU   ( 163-)  A
 164 GLU   ( 215-)  A
 169 GLU   ( 220-)  A
 178 GLU   ( 229-)  A
 223 GLU   ( 274-)  A
 274 GLU   ( 325-)  A
 294 GLU   ( 345-)  A
 336 GLU   ( 387-)  A
 360 GLU   ( 411-)  A
 407 GLU   ( 458-)  A
 429 GLU   ( 480-)  A
 432 GLU   ( 483-)  A
 442 GLU   ( 493-)  A
 501 GLU   ( 552-)  A
 632 GLU   ( 683-)  A
 676 GLU   ( 727-)  A
 684 GLU   ( 735-)  A
 697 GLU   ( 748-)  A
 793 GLU   ( 852-)  A
 823 GLU   ( 882-)  A
 880 GLU   ( 946-)  A
 886 GLU   ( 952-)  A
 933 GLU   (  63-)  B
 983 GLU   ( 113-)  B
1012 GLU   ( 159-)  B
1016 GLU   ( 163-)  B
1073 GLU   ( 220-)  B
1082 GLU   ( 229-)  B
1127 GLU   ( 274-)  B
1178 GLU   ( 325-)  B
1198 GLU   ( 345-)  B
1264 GLU   ( 411-)  B
1311 GLU   ( 458-)  B
1336 GLU   ( 483-)  B
1363 GLU   ( 510-)  B
1405 GLU   ( 552-)  B
1601 GLU   ( 748-)  B
1675 GLU   ( 830-)  B
1711 GLU   ( 866-)  B
1727 GLU   ( 882-)  B
1790 GLU   ( 952-)  B

Geometric checks

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.

 714 ARG   ( 773-)  A     -C    N    CA  130.42    4.8
 923 HIS   (  53-)  B      CG   ND1  CE1 109.64    4.0
1315 HIS   ( 462-)  B      CG   ND1  CE1 109.85    4.3
1329 GLY   ( 476-)  B      N    CA   C   124.11    4.0

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.

  17 ASP   (  51-)  A
  29 GLU   (  63-)  A
  48 GLU   (  82-)  A
  60 ASP   (  94-)  A
  91 ASP   ( 142-)  A
  94 GLU   ( 145-)  A
 112 GLU   ( 163-)  A
 164 GLU   ( 215-)  A
 169 GLU   ( 220-)  A
 178 GLU   ( 229-)  A
 223 GLU   ( 274-)  A
 241 ASP   ( 292-)  A
 243 ASP   ( 294-)  A
 274 GLU   ( 325-)  A
 294 GLU   ( 345-)  A
 336 GLU   ( 387-)  A
 360 GLU   ( 411-)  A
 374 ASP   ( 425-)  A
 377 ASP   ( 428-)  A
 387 ASP   ( 438-)  A
 407 GLU   ( 458-)  A
 429 GLU   ( 480-)  A
 432 GLU   ( 483-)  A
 442 GLU   ( 493-)  A
 476 ASP   ( 527-)  A
And so on for a total of 78 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.

1663 GLU   ( 818-)  B    5.71
 629 CYS   ( 680-)  A    5.24
1190 ASP   ( 337-)  B    5.22
1639 VAL   ( 794-)  B    4.88
  53 LEU   (  87-)  A    4.85
  87 ARG   ( 121-)  A    4.76
 735 VAL   ( 794-)  A    4.71
  19 HIS   (  53-)  A    4.26
1598 ALA   ( 745-)  B    4.21
1323 THR   ( 470-)  B    4.19
1533 CYS   ( 680-)  B    4.17
 408 SER   ( 459-)  A    4.11
1362 ASP   ( 509-)  B    4.05
1105 VAL   ( 252-)  B    4.02

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 : -4.667

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.

 883 PRO   ( 949-)  A    -3.1
1787 PRO   ( 949-)  B    -3.1
  58 PRO   (  92-)  A    -3.0
 319 PRO   ( 370-)  A    -2.9
1123 ILE   ( 270-)  B    -2.9
1384 PRO   ( 531-)  B    -2.9
  21 PRO   (  55-)  A    -2.8
1505 THR   ( 652-)  B    -2.8
 505 ARG   ( 556-)  A    -2.7
 696 PRO   ( 747-)  A    -2.7
1322 ILE   ( 469-)  B    -2.6
 761 PRO   ( 820-)  A    -2.6
1637 LEU   ( 792-)  B    -2.6
1328 ILE   ( 475-)  B    -2.6
 877 PRO   ( 943-)  A    -2.5
1632 HIS   ( 787-)  B    -2.5
1665 PRO   ( 820-)  B    -2.5
 623 GLY   ( 674-)  A    -2.5
1527 GLY   ( 674-)  B    -2.5
1059 THR   ( 206-)  B    -2.4
1557 HIS   ( 704-)  B    -2.4
1211 TYR   ( 358-)  B    -2.4
 901 GLN   ( 967-)  A    -2.4
1125 ILE   ( 272-)  B    -2.3
 446 LYS   ( 497-)  A    -2.3
And so on for a total of 63 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.

  86 ARG   ( 120-)  A  Poor phi/psi
 101 SER   ( 152-)  A  Poor phi/psi
 127 PRO   ( 178-)  A  Poor phi/psi
 199 GLU   ( 250-)  A  Poor phi/psi
 222 ASN   ( 273-)  A  Poor phi/psi
 279 LEU   ( 330-)  A  Poor phi/psi
 303 VAL   ( 354-)  A  Poor phi/psi
 310 PHE   ( 361-)  A  Poor phi/psi
 344 SER   ( 395-)  A  Poor phi/psi
 377 ASP   ( 428-)  A  Poor phi/psi
 399 LEU   ( 450-)  A  Poor phi/psi
 445 GLY   ( 496-)  A  Poor phi/psi
 446 LYS   ( 497-)  A  Poor phi/psi
 477 SER   ( 528-)  A  Poor phi/psi
 487 THR   ( 538-)  A  Poor phi/psi
 505 ARG   ( 556-)  A  Poor phi/psi
 522 SER   ( 573-)  A  Poor phi/psi
 541 LYS   ( 592-)  A  Poor phi/psi
 542 GLY   ( 593-)  A  Poor phi/psi
 611 ASP   ( 662-)  A  Poor phi/psi
 623 GLY   ( 674-)  A  Poor phi/psi
 633 GLU   ( 684-)  A  Poor phi/psi
 704 ASN   ( 755-)  A  Poor phi/psi
 714 ARG   ( 773-)  A  Poor phi/psi
 726 ARG   ( 785-)  A  Poor phi/psi
And so on for a total of 74 lines.

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 : -4.418

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.

 526 SER   ( 577-)  A    0.36
1345 SER   ( 492-)  B    0.38
1529 VAL   ( 676-)  B    0.38

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!

  19 HIS   (  53-)  A      0
  40 LYS   (  74-)  A      0
  88 ARG   ( 122-)  A      0
  89 ASN   ( 123-)  A      0
  90 SER   ( 141-)  A      0
  91 ASP   ( 142-)  A      0
 102 GLU   ( 153-)  A      0
 103 VAL   ( 154-)  A      0
 125 ALA   ( 176-)  A      0
 126 HIS   ( 177-)  A      0
 127 PRO   ( 178-)  A      0
 128 THR   ( 179-)  A      0
 130 SER   ( 181-)  A      0
 151 ALA   ( 202-)  A      0
 152 LYS   ( 203-)  A      0
 153 ASP   ( 204-)  A      0
 178 GLU   ( 229-)  A      0
 198 HIS   ( 249-)  A      0
 199 GLU   ( 250-)  A      0
 200 THR   ( 251-)  A      0
 222 ASN   ( 273-)  A      0
 229 VAL   ( 280-)  A      0
 237 TRP   ( 288-)  A      0
 238 MET   ( 289-)  A      0
 242 ARG   ( 293-)  A      0
And so on for a total of 446 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 0.928

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!

 503 GLY   ( 554-)  A   1.81   18
1407 GLY   ( 554-)  B   1.80   10
 692 ARG   ( 743-)  A   1.59   10
 220 GLY   ( 271-)  A   1.58   63
 734 GLY   ( 793-)  A   1.53   21

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...

 713 LEU   ( 772-)  A   2.19

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].

 226 PRO   ( 277-)  A  -112.6 envelop C-gamma (-108 degrees)
 512 PRO   ( 563-)  A    48.8 half-chair C-delta/C-gamma (54 degrees)
 609 PRO   ( 660-)  A  -118.1 half-chair C-delta/C-gamma (-126 degrees)
 862 PRO   ( 921-)  A    52.8 half-chair C-delta/C-gamma (54 degrees)
 883 PRO   ( 949-)  A   113.8 envelop C-beta (108 degrees)
1130 PRO   ( 277-)  B  -113.1 envelop C-gamma (-108 degrees)
1564 PRO   ( 711-)  B  -116.2 envelop C-gamma (-108 degrees)
1741 PRO   ( 896-)  B  -112.4 envelop C-gamma (-108 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.

   1 ILE   (  35-)  A      N   <->   82 GLN   ( 116-)  A      OE1    0.44    2.26  INTRA BF
1241 ARG   ( 388-)  B      NH2 <-> 1255 ALA   ( 402-)  B      CA     0.39    2.71  INTRA BF
1306 LEU   ( 453-)  B      O   <-> 1383 GLY   ( 530-)  B      N      0.39    2.31  INTRA BL
   1 ILE   (  35-)  A      N   <->   82 GLN   ( 116-)  A      CD     0.35    2.75  INTRA BF
1165 ARG   ( 312-)  B      NH2 <-> 1380 ASP   ( 527-)  B      OD1    0.33    2.37  INTRA BF
1420 ARG   ( 567-)  B      NH2 <-> 1423 ASP   ( 570-)  B      OD1    0.32    2.38  INTRA BF
 126 HIS   ( 177-)  A      O   <->  128 THR   ( 179-)  A      N      0.32    2.38  INTRA BL
 128 THR   ( 179-)  A      CG2 <->  624 GLU   ( 675-)  A      N      0.31    2.79  INTRA BL
1699 LYS   ( 854-)  B      N   <-> 1700 PRO   ( 855-)  B      CD     0.31    2.69  INTRA BF
 746 ASP   ( 805-)  A      OD1 <->  748 ARG   ( 807-)  A      N      0.31    2.39  INTRA BL
 432 GLU   ( 483-)  A      OE2 <->  436 GLN   ( 487-)  A      NE2    0.29    2.41  INTRA BF
  94 GLU   ( 145-)  A      CG  <->   95 THR   ( 146-)  A      N      0.28    2.72  INTRA BF
   1 ILE   (  35-)  A      N   <->   82 GLN   ( 116-)  A      NE2    0.27    2.58  INTRA BF
1563 LYS   ( 710-)  B      N   <-> 1566 TRP   ( 713-)  B      CE3    0.27    2.83  INTRA BF
1650 ASP   ( 805-)  B      OD1 <-> 1651 VAL   ( 806-)  B      N      0.26    2.34  INTRA BF
 692 ARG   ( 743-)  A      NH1 <->  697 GLU   ( 748-)  A      OE1    0.26    2.44  INTRA BF
  35 ALA   (  69-)  A      O   <->   39 GLY   (  73-)  A      N      0.26    2.44  INTRA BL
1041 GLN   ( 188-)  B      NE2 <-> 1042 LYS   ( 189-)  B      NZ     0.26    2.59  INTRA BF
1622 TRP   ( 777-)  B      CZ3 <-> 1626 TRP   ( 781-)  B      NE1    0.26    2.84  INTRA BF
 283 ARG   ( 334-)  A      NH1 <-> 1079 ARG   ( 226-)  B      NH2    0.25    2.60  INTRA BF
1420 ARG   ( 567-)  B      CZ  <-> 1423 ASP   ( 570-)  B      OD2    0.25    2.55  INTRA BF
 376 GLY   ( 427-)  A      O   <->  378 LYS   ( 429-)  A      N      0.25    2.45  INTRA BF
 832 LEU   ( 891-)  A      C   <->  836 ASN   ( 895-)  A      ND2    0.25    2.85  INTRA BL
1331 TYR   ( 478-)  B      O   <-> 1334 TRP   ( 481-)  B      N      0.25    2.45  INTRA BF
 632 GLU   ( 683-)  A      CG  <->  634 HIS   ( 685-)  A      NE2    0.24    2.86  INTRA BF
And so on for a total of 475 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.

 708 ARG   ( 759-)  A      -8.07
1612 ARG   ( 759-)  B      -7.82
 505 ARG   ( 556-)  A      -7.68
1351 ARG   ( 498-)  B      -7.50
1409 ARG   ( 556-)  B      -7.34
1187 ARG   ( 334-)  B      -6.97
1767 GLN   ( 922-)  B      -6.83
 446 LYS   ( 497-)  A      -6.44
1350 LYS   ( 497-)  B      -6.29
 863 GLN   ( 922-)  A      -6.29
 181 ARG   ( 232-)  A      -6.24
1217 GLN   ( 364-)  B      -6.17
  88 ARG   ( 122-)  A      -5.80
 283 ARG   ( 334-)  A      -5.80
 313 GLN   ( 364-)  A      -5.79
1348 ARG   ( 495-)  B      -5.68
 444 ARG   ( 495-)  A      -5.68
 421 HIS   ( 472-)  A      -5.67
 714 ARG   ( 773-)  A      -5.61
1785 TYR   ( 947-)  B      -5.57
 447 ARG   ( 498-)  A      -5.57
1772 LYS   ( 927-)  B      -5.54
1483 ARG   ( 630-)  B      -5.48
 819 LYS   ( 878-)  A      -5.47
 923 HIS   (  53-)  B      -5.47
 868 LYS   ( 927-)  A      -5.46
1494 ARG   ( 641-)  B      -5.43
1758 ARG   ( 913-)  B      -5.41
 854 ARG   ( 913-)  A      -5.40
 859 LYS   ( 918-)  A      -5.40
 590 ARG   ( 641-)  A      -5.35
 992 ARG   ( 122-)  B      -5.34
 656 VAL   ( 707-)  A      -5.20
 880 GLU   ( 946-)  A      -5.17
 175 ARG   ( 226-)  A      -5.16
 485 MET   ( 536-)  A      -5.15
1500 ARG   ( 647-)  B      -5.13
 596 ARG   ( 647-)  A      -5.12
1662 ASN   ( 817-)  B      -5.10
 152 LYS   ( 203-)  A      -5.08
 456 GLN   ( 507-)  A      -5.07
1805 GLN   ( 967-)  B      -5.06
1376 GLU   ( 523-)  B      -5.04
 472 GLU   ( 523-)  A      -5.01

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

  38 GLU   (  72-)  A        40 - LYS     74- ( A)         -4.36

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.

 613 ILE   ( 664-)  A   -2.92
1637 LEU   ( 792-)  B   -2.61

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.

 139 ASN   ( 190-)  A
 183 GLN   ( 234-)  A
 650 HIS   ( 701-)  A
 724 GLN   ( 783-)  A
 814 GLN   ( 873-)  A
 846 GLN   ( 905-)  A
 863 GLN   ( 922-)  A
 917 ASN   (  47-)  B
 923 HIS   (  53-)  B
1041 GLN   ( 188-)  B
1043 ASN   ( 190-)  B
1054 ASN   ( 201-)  B
1091 GLN   ( 238-)  B
1126 ASN   ( 273-)  B
1200 HIS   ( 347-)  B
1217 GLN   ( 364-)  B
1734 GLN   ( 889-)  B
1740 ASN   ( 895-)  B
1750 GLN   ( 905-)  B
1806 ASN   ( 968-)  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.

   1 ILE   (  35-)  A      N
   3 TYR   (  37-)  A      N
   4 ASP   (  38-)  A      N
  91 ASP   ( 142-)  A      N
  98 ARG   ( 149-)  A      NE
 117 GLN   ( 168-)  A      NE2
 129 GLN   ( 180-)  A      N
 132 ARG   ( 183-)  A      N
 134 SER   ( 185-)  A      N
 155 THR   ( 206-)  A      N
 179 ILE   ( 230-)  A      N
 185 THR   ( 236-)  A      OG1
 187 GLN   ( 238-)  A      N
 223 GLU   ( 274-)  A      N
 224 ARG   ( 275-)  A      NE
 232 ILE   ( 283-)  A      N
 242 ARG   ( 293-)  A      NH1
 281 MET   ( 332-)  A      N
 282 TRP   ( 333-)  A      N
 283 ARG   ( 334-)  A      N
 288 LEU   ( 339-)  A      N
 306 TYR   ( 357-)  A      N
 309 GLU   ( 360-)  A      N
 312 LYS   ( 363-)  A      N
 320 TYR   ( 371-)  A      N
And so on for a total of 178 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.

 120 ASP   ( 171-)  A      OD1
 137 GLN   ( 188-)  A      OE1
 169 GLU   ( 220-)  A      OE2
 285 ASN   ( 336-)  A      OD1
 391 GLN   ( 442-)  A      OE1
 411 HIS   ( 462-)  A      ND1
 456 GLN   ( 507-)  A      OE1
 545 GLN   ( 596-)  A      OE1
 570 GLN   ( 621-)  A      OE1
 993 ASN   ( 123-)  B      OD1
1067 ASP   ( 214-)  B      OD1
1073 GLU   ( 220-)  B      OE2
1081 ASP   ( 228-)  B      OD2
1189 ASN   ( 336-)  B      OD1
1400 GLU   ( 547-)  B      OE2
1474 GLN   ( 621-)  B      OE1
1536 GLU   ( 683-)  B      OE2
1557 HIS   ( 704-)  B      ND1
1601 GLU   ( 748-)  B      OE1
1628 GLN   ( 783-)  B      OE1
1790 GLU   ( 952-)  B      OE1

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.

 178 GLU   ( 229-)  A   H-bonding suggests Gln
 270 ASP   ( 321-)  A   H-bonding suggests Asn
 329 ASP   ( 380-)  A   H-bonding suggests Asn; but Alt-Rotamer
 556 ASP   ( 607-)  A   H-bonding suggests Asn
 624 GLU   ( 675-)  A   H-bonding suggests Gln
 667 ASP   ( 718-)  A   H-bonding suggests Asn
 869 GLU   ( 928-)  A   H-bonding suggests Gln
 929 GLU   (  59-)  B   H-bonding suggests Gln
1093 GLU   ( 240-)  B   H-bonding suggests Gln; but Alt-Rotamer
1278 ASP   ( 425-)  B   H-bonding suggests Asn; but Alt-Rotamer
1442 ASP   ( 589-)  B   H-bonding suggests Asn
1460 ASP   ( 607-)  B   H-bonding suggests Asn; but Alt-Rotamer
1476 GLU   ( 623-)  B   H-bonding suggests Gln; but Alt-Rotamer
1528 GLU   ( 675-)  B   H-bonding suggests Gln
1603 GLU   ( 750-)  B   H-bonding suggests Gln
1648 ASP   ( 803-)  B   H-bonding suggests Asn
1724 ASP   ( 879-)  B   H-bonding suggests Asn
1773 GLU   ( 928-)  B   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.758
  2nd generation packing quality :  -1.648
  Ramachandran plot appearance   :  -4.667 (bad)
  chi-1/chi-2 rotamer normality  :  -4.418 (bad)
  Backbone conformation          :   0.567

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.349 (tight)
  Bond angles                    :   0.604 (tight)
  Omega angle restraints         :   0.169 (tight)
  Side chain planarity           :   0.219 (tight)
  Improper dihedral distribution :   0.624
  B-factor distribution          :   0.418
  Inside/Outside distribution    :   0.997

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 : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :  -2.0
  chi-1/chi-2 rotamer normality  :  -2.0
  Backbone conformation          :   1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.349 (tight)
  Bond angles                    :   0.604 (tight)
  Omega angle restraints         :   0.169 (tight)
  Side chain planarity           :   0.219 (tight)
  Improper dihedral distribution :   0.624
  B-factor distribution          :   0.418
  Inside/Outside distribution    :   0.997
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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Bond lengths and angles, DNA/RNA
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DSSP
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      Dictionary of protein secondary structure: pattern
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Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
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Puckering parameters
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      A general definition of ring puckering coordinates
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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
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      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.