WHAT IF Check report

This file was created 2011-12-29 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 pdb1jqn.ent

Checks that need to be done early-on in validation

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    = 117.950  B   = 249.060  C    =  83.120
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 117.950  B   = 143.920  C    = 143.920
    Alpha=  33.569  Beta= 114.191  Gamma= 114.191

Dimensions of the conventional cell

    A    =  83.120  B   = 117.950  C    = 249.060
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000  0.000000 -1.000000|
 |  1.000000  0.000000  0.000000|
 |  0.000000 -1.000000  0.000000|

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 878 DCO   ( 901-)  A  -         Fragmented

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

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 187 GLU   ( 190-)  A      CG
 187 GLU   ( 190-)  A      CD
 187 GLU   ( 190-)  A      OE1
 187 GLU   ( 190-)  A      OE2
 440 ARG   ( 443-)  A      CG
 440 ARG   ( 443-)  A      CD
 440 ARG   ( 443-)  A      NE
 440 ARG   ( 443-)  A      CZ
 440 ARG   ( 443-)  A      NH1
 440 ARG   ( 443-)  A      NH2

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

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.

 189 ARG   ( 192-)  A
 269 ARG   ( 272-)  A
 578 ARG   ( 581-)  A

Warning: Tyrosine convention problem

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

 166 TYR   ( 169-)  A
 217 TYR   ( 220-)  A
 309 TYR   ( 312-)  A
 311 TYR   ( 314-)  A
 469 TYR   ( 472-)  A
 524 TYR   ( 527-)  A
 555 TYR   ( 558-)  A
 618 TYR   ( 621-)  A
 631 TYR   ( 634-)  A
 668 TYR   ( 671-)  A

Warning: Phenylalanine convention problem

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

  72 PHE   (  75-)  A
  75 PHE   (  78-)  A
 203 PHE   ( 206-)  A
 276 PHE   ( 279-)  A
 502 PHE   ( 505-)  A
 616 PHE   ( 619-)  A

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.

  22 ASP   (  25-)  A
 249 ASP   ( 252-)  A
 540 ASP   ( 543-)  A
 812 ASP   ( 821-)  A
 852 ASP   ( 861-)  A

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.

  83 GLU   (  86-)  A
  99 GLU   ( 102-)  A
 124 GLU   ( 127-)  A
 129 GLU   ( 132-)  A
 167 GLU   ( 170-)  A
 207 GLU   ( 210-)  A
 226 GLU   ( 229-)  A
 307 GLU   ( 310-)  A
 347 GLU   ( 350-)  A
 348 GLU   ( 351-)  A
 622 GLU   ( 625-)  A
 637 GLU   ( 640-)  A
 648 GLU   ( 651-)  A
 656 GLU   ( 659-)  A
 794 GLU   ( 803-)  A
 856 GLU   ( 865-)  A

Geometric checks

Warning: Unusual bond lengths

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

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

 302 GLU   ( 305-)  A      CD   OE1   1.35    5.5
 302 GLU   ( 305-)  A      CD   OE2   1.36    5.8
 303 GLU   ( 306-)  A      CD   OE1   1.33    4.3

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.

  86 HIS   (  89-)  A      CG   ND1  CE1 109.67    4.1
 263 HIS   ( 266-)  A      CG   ND1  CE1 109.62    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.

  22 ASP   (  25-)  A
  83 GLU   (  86-)  A
  99 GLU   ( 102-)  A
 124 GLU   ( 127-)  A
 129 GLU   ( 132-)  A
 167 GLU   ( 170-)  A
 189 ARG   ( 192-)  A
 207 GLU   ( 210-)  A
 226 GLU   ( 229-)  A
 249 ASP   ( 252-)  A
 269 ARG   ( 272-)  A
 307 GLU   ( 310-)  A
 347 GLU   ( 350-)  A
 348 GLU   ( 351-)  A
 540 ASP   ( 543-)  A
 578 ARG   ( 581-)  A
 622 GLU   ( 625-)  A
 637 GLU   ( 640-)  A
 648 GLU   ( 651-)  A
 656 GLU   ( 659-)  A
 794 GLU   ( 803-)  A
 812 ASP   ( 821-)  A
 852 ASP   ( 861-)  A
 856 GLU   ( 865-)  A

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.

 721 ALA   ( 730-)  A    4.84
 747 ASP   ( 756-)  A    4.75
 719 LEU   ( 728-)  A    4.50
 545 ALA   ( 548-)  A    4.30
 723 LEU   ( 732-)  A    4.15

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.

 684 PRO   ( 687-)  A    -2.4
 250 ARG   ( 253-)  A    -2.4
  24 LEU   (  27-)  A    -2.3
 504 THR   ( 507-)  A    -2.3
 160 ASN   ( 163-)  A    -2.2
 529 GLN   ( 532-)  A    -2.2
 718 MET   ( 727-)  A    -2.1
 351 GLU   ( 354-)  A    -2.1
 435 ARG   ( 438-)  A    -2.0
 608 THR   ( 611-)  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.

  23 ALA   (  26-)  A  Poor phi/psi
 159 ASP   ( 162-)  A  Poor phi/psi
 162 ASP   ( 165-)  A  Poor phi/psi
 231 TYR   ( 234-)  A  Poor phi/psi
 303 GLU   ( 306-)  A  Poor phi/psi
 341 GLY   ( 344-)  A  Poor phi/psi
 344 THR   ( 347-)  A  Poor phi/psi
 363 CYS   ( 366-)  A  Poor phi/psi
 387 LEU   ( 390-)  A  Poor phi/psi
 692 PRO   ( 695-)  A  Poor phi/psi
 716 ARG   ( 725-)  A  Poor phi/psi
 718 MET   ( 727-)  A  Poor phi/psi
 722 TRP   ( 731-)  A  Poor phi/psi
 723 LEU   ( 732-)  A  Poor phi/psi
 777 LEU   ( 786-)  A  Poor phi/psi
 871 ARG   ( 880-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.796

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.

 841 SER   ( 850-)  A    0.37
  39 SER   (  42-)  A    0.37
 819 SER   ( 828-)  A    0.37
 551 SER   ( 554-)  A    0.38
 629 SER   ( 632-)  A    0.38
 658 SER   ( 661-)  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!

  24 LEU   (  27-)  A      0
  46 ASN   (  49-)  A      0
  47 ASP   (  50-)  A      0
  88 ILE   (  91-)  A      0
  93 GLU   (  96-)  A      0
  97 ASN   ( 100-)  A      0
 126 LEU   ( 129-)  A      0
 141 ARG   ( 144-)  A      0
 142 ARG   ( 145-)  A      0
 144 LEU   ( 147-)  A      0
 159 ASP   ( 162-)  A      0
 160 ASN   ( 163-)  A      0
 161 LYS   ( 164-)  A      0
 185 THR   ( 188-)  A      0
 189 ARG   ( 192-)  A      0
 208 ASN   ( 211-)  A      0
 209 SER   ( 212-)  A      0
 231 TYR   ( 234-)  A      0
 239 PRO   ( 242-)  A      0
 240 VAL   ( 243-)  A      0
 245 TRP   ( 248-)  A      0
 246 MET   ( 249-)  A      0
 250 ARG   ( 253-)  A      0
 251 ASP   ( 254-)  A      0
 288 SER   ( 291-)  A      0
And so on for a total of 195 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 : 0.856

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.

 608 THR   ( 611-)  A      CB  <->  880 HOH   (1065 )  A      O      0.46    2.34  INTRA BL
 807 SER   ( 816-)  A      N   <->  880 HOH   (1033 )  A      O      0.28    2.42  INTRA BF
 535 MET   ( 538-)  A      CE  <->  878 DCO   ( 901-)  A     CL1     0.27    2.93  INTRA BF
 323 THR   ( 326-)  A      CG2 <->  343 LEU   ( 346-)  A      N      0.27    2.83  INTRA BF
 745 CYS   ( 754-)  A      SG  <->  880 HOH   (1027 )  A      O      0.26    2.74  INTRA BL
 391 ASP   ( 394-)  A      OD2 <->  606 ARG   ( 609-)  A      NH2    0.23    2.47  INTRA BL
 790 ARG   ( 799-)  A      NH2 <->  880 HOH   (1032 )  A      O      0.23    2.47  INTRA BL
 346 ASN   ( 349-)  A      ND2 <->  385 VAL   ( 388-)  A      N      0.22    2.63  INTRA BL
  70 ARG   (  73-)  A      NH2 <->  186 ASP   ( 189-)  A      CB     0.21    2.89  INTRA BF
 694 GLY   ( 697-)  A      N   <->  880 HOH   ( 945 )  A      O      0.21    2.49  INTRA BF
 378 ARG   ( 381-)  A      NH1 <->  880 HOH   ( 991 )  A      O      0.17    2.53  INTRA BL
 696 ARG   ( 699-)  A      NH2 <->  878 DCO   ( 901-)  A      O5     0.16    2.54  INTRA BF
 584 ARG   ( 587-)  A      NH2 <->  875 ASP   ( 884-)  A      O      0.16    2.54  INTRA BL
 578 ARG   ( 581-)  A      NH2 <->  612 GLU   ( 615-)  A      OE2    0.15    2.55  INTRA BF
 578 ARG   ( 581-)  A      N   <->  880 HOH   (1065 )  A      O      0.15    2.55  INTRA BL
 783 TRP   ( 792-)  A      N   <->  784 PRO   ( 793-)  A      CD     0.15    2.85  INTRA BL
 393 ARG   ( 396-)  A      NH2 <->  880 HOH   (1096 )  A      O      0.14    2.56  INTRA BF
  99 GLU   ( 102-)  A      OE2 <->  106 ARG   ( 109-)  A      NH2    0.14    2.56  INTRA BF
 774 ASP   ( 783-)  A      OD2 <->  790 ARG   ( 799-)  A      NH2    0.14    2.56  INTRA BL
 319 ARG   ( 322-)  A      NE  <->  341 GLY   ( 344-)  A      CA     0.13    2.97  INTRA BF
 288 SER   ( 291-)  A      CB  <->  310 ARG   ( 313-)  A      NH2    0.13    2.97  INTRA BF
 129 GLU   ( 132-)  A      CD  <->  606 ARG   ( 609-)  A      NH1    0.13    2.97  INTRA BL
  36 ARG   (  39-)  A      NH2 <->  880 HOH   ( 983 )  A      O      0.13    2.57  INTRA BF
 161 LYS   ( 164-)  A      C   <->  163 ILE   ( 166-)  A      N      0.13    2.77  INTRA BF
 219 ARG   ( 222-)  A      NH1 <->  370 ASN   ( 373-)  A      O      0.13    2.57  INTRA BL
And so on for a total of 91 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

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.

 696 ARG   ( 699-)  A      -8.05
 578 ARG   ( 581-)  A      -6.92
 141 ARG   ( 144-)  A      -6.79
 435 ARG   ( 438-)  A      -6.64
 191 LEU   ( 194-)  A      -5.99
 602 LYS   ( 605-)  A      -5.99
 584 ARG   ( 587-)  A      -5.97
 434 LYS   ( 437-)  A      -5.93
 443 GLN   ( 446-)  A      -5.89
  91 LYS   (  94-)  A      -5.88
 335 GLU   ( 338-)  A      -5.77
 849 GLN   ( 858-)  A      -5.70
 302 GLU   ( 305-)  A      -5.64
 190 LYS   ( 193-)  A      -5.36
  43 ARG   (  46-)  A      -5.32
 463 GLN   ( 466-)  A      -5.29
 432 ASN   ( 435-)  A      -5.19
 208 ASN   ( 211-)  A      -5.18
 232 LYS   ( 235-)  A      -5.14
 441 ASN   ( 444-)  A      -5.11
 189 ARG   ( 192-)  A      -5.10
 161 LYS   ( 164-)  A      -5.08
 231 TYR   ( 234-)  A      -5.05
 228 ASN   ( 231-)  A      -5.05
 776 ARG   ( 785-)  A      -5.04
 142 ARG   ( 145-)  A      -5.04
 460 GLU   ( 463-)  A      -5.04
 291 GLU   ( 294-)  A      -5.01
 847 GLU   ( 856-)  A      -5.00

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.

 189 ARG   ( 192-)  A       192 - ARG    195- ( A)         -5.27

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

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.

 804 ALA   ( 813-)  A   -2.60
 721 ALA   ( 730-)  A   -2.52
 440 ARG   ( 443-)  A   -2.50

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

 600 SER   ( 603-)  A     -  603 GLY   ( 606-)  A        -1.99

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

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 880 HOH   (1043 )  A      O
 880 HOH   (1045 )  A      O
Marked this atom as acceptor  878 DCO  ( 901-) A     CL1
Marked this atom as acceptor  878 DCO  ( 901-) A     CL2

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.

 169 ASN   ( 172-)  A
 212 GLN   ( 215-)  A
 228 ASN   ( 231-)  A
 253 ASN   ( 256-)  A
 345 GLN   ( 348-)  A
 346 ASN   ( 349-)  A
 443 GLN   ( 446-)  A
 510 ASN   ( 513-)  A
 517 GLN   ( 520-)  A
 730 GLN   ( 739-)  A
 791 ASN   ( 800-)  A
 808 HIS   ( 817-)  A
 824 ASN   ( 833-)  A

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.

   5 LEU   (   8-)  A      N
  29 LEU   (  32-)  A      N
  66 LEU   (  69-)  A      N
  70 ARG   (  73-)  A      NH2
 127 SER   ( 130-)  A      N
 137 THR   ( 140-)  A      OG1
 138 GLU   ( 141-)  A      N
 166 TYR   ( 169-)  A      OH
 167 GLU   ( 170-)  A      N
 233 LEU   ( 236-)  A      N
 240 VAL   ( 243-)  A      N
 309 TYR   ( 312-)  A      N
 342 LEU   ( 345-)  A      N
 343 LEU   ( 346-)  A      N
 393 ARG   ( 396-)  A      NE
 393 ARG   ( 396-)  A      NH1
 393 ARG   ( 396-)  A      NH2
 504 THR   ( 507-)  A      N
 507 ASP   ( 510-)  A      N
 512 ASN   ( 515-)  A      ND2
 529 GLN   ( 532-)  A      N
 539 SER   ( 542-)  A      N
 540 ASP   ( 543-)  A      N
 558 GLN   ( 561-)  A      NE2
 578 ARG   ( 581-)  A      NH2
 582 ILE   ( 585-)  A      N
 606 ARG   ( 609-)  A      NE
 610 GLN   ( 613-)  A      N
 612 GLU   ( 615-)  A      N
 620 LEU   ( 623-)  A      N
 622 GLU   ( 625-)  A      N
 647 LYS   ( 650-)  A      N
 673 LYS   ( 676-)  A      N
 696 ARG   ( 699-)  A      N
 704 ARG   ( 713-)  A      N
 704 ARG   ( 713-)  A      NH2
 705 ALA   ( 714-)  A      N
 712 TRP   ( 721-)  A      NE1
 716 ARG   ( 725-)  A      N
 719 LEU   ( 728-)  A      N
 735 ASP   ( 744-)  A      N
 738 GLN   ( 747-)  A      N
 746 ARG   ( 755-)  A      NH1
 754 ARG   ( 763-)  A      NE
 776 ARG   ( 785-)  A      NH1
 776 ARG   ( 785-)  A      NH2
 793 GLN   ( 802-)  A      NE2
 813 LEU   ( 822-)  A      N
 871 ARG   ( 880-)  A      NE
Only metal coordination for  503 GLU  ( 506-) A      OE1

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.

 558 GLN   ( 561-)  A      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.

 796 ASP   ( 805-)  A   H-bonding suggests Asn
 806 ASP   ( 815-)  A   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 :   0.208
  2nd generation packing quality :  -0.849
  Ramachandran plot appearance   :  -1.201
  chi-1/chi-2 rotamer normality  :  -1.796
  Backbone conformation          :   0.502

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.320 (tight)
  Bond angles                    :   0.530 (tight)
  Omega angle restraints         :   0.156 (tight)
  Side chain planarity           :   0.250 (tight)
  Improper dihedral distribution :   0.543
  B-factor distribution          :   0.375
  Inside/Outside distribution    :   0.974

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 : 2.35


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.4
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.320 (tight)
  Bond angles                    :   0.530 (tight)
  Omega angle restraints         :   0.156 (tight)
  Side chain planarity           :   0.250 (tight)
  Improper dihedral distribution :   0.543
  B-factor distribution          :   0.375
  Inside/Outside distribution    :   0.974
==============

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.