WHAT IF Check report

This file was created 2012-01-25 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb2j25.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 : 1.000
CA-only RMS fit for the two chains : 0.737

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: Topology could not be determined for some ligands

Some 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 two or less which PRODRUG also cannot cope with), 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.

1015 BMA   (1500-)  B  -         OK
1016 A10   (1502-)  B  -         Fragmented
1025 BMA   (1505-)  B  -         OK
1026 MAN   (1501-)  B  -         OK

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 995 NAG   (1498-)  A  -   O4  bound to  996 NAG   (1499-)  A  -   C1
 998 NAG   (1498-)  B  -   O4  bound to  999 NAG   (1499-)  B  -   C1
 999 NAG   (1499-)  B  -   O4  bound to 1015 BMA   (1500-)  B  -   C1
1000 NAG   (1503-)  B  -   O4  bound to 1001 NAG   (1504-)  B  -   C1
1001 NAG   (1504-)  B  -   O4  bound to 1025 BMA   (1505-)  B  -   C1
1002 NAG   (1506-)  B  -   O4  bound to 1003 NAG   (1507-)  B  -   C1

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: Missing atoms

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

  59 ASN   (  59-)  A      CG
  59 ASN   (  59-)  A      OD1
  59 ASN   (  59-)  A      ND2
  61 THR   (  61-)  A      CB
  61 THR   (  61-)  A      OG1
  61 THR   (  61-)  A      CG2
 242 SER   ( 242-)  A      CB
 242 SER   ( 242-)  A      OG
 300 GLU   ( 300-)  A      CG
 300 GLU   ( 300-)  A      CD
 300 GLU   ( 300-)  A      OE1
 300 GLU   ( 300-)  A      OE2
 347 PHE   ( 347-)  A      CG
 347 PHE   ( 347-)  A      CD1
 347 PHE   ( 347-)  A      CD2
 347 PHE   ( 347-)  A      CE1
 347 PHE   ( 347-)  A      CE2
 347 PHE   ( 347-)  A      CZ
 397 PHE   ( 397-)  A      CD1
 397 PHE   ( 397-)  A      CD2
 397 PHE   ( 397-)  A      CE1
 397 PHE   ( 397-)  A      CE2
 397 PHE   ( 397-)  A      CZ
 466 LYS   ( 466-)  A      CG
 466 LYS   ( 466-)  A      CD
And so on for a total of 59 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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

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: Tyrosine convention problem

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

  11 TYR   (  11-)  A
  22 TYR   (  22-)  A
 108 TYR   ( 108-)  A
 116 TYR   ( 116-)  A
 133 TYR   ( 133-)  A
 135 TYR   ( 135-)  A
 205 TYR   ( 205-)  A
 212 TYR   ( 212-)  A
 304 TYR   ( 304-)  A
 313 TYR   ( 313-)  A
 373 TYR   ( 373-)  A
 412 TYR   ( 412-)  A
 418 TYR   ( 418-)  A
 487 TYR   ( 487-)  A
 492 TYR   ( 492-)  A
 508 TYR   (  11-)  B
 519 TYR   (  22-)  B
 605 TYR   ( 108-)  B
 613 TYR   ( 116-)  B
 632 TYR   ( 135-)  B
 702 TYR   ( 205-)  B
 709 TYR   ( 212-)  B
 801 TYR   ( 304-)  B
 870 TYR   ( 373-)  B
 909 TYR   ( 412-)  B
 915 TYR   ( 418-)  B
 984 TYR   ( 487-)  B
 989 TYR   ( 492-)  B

Warning: Phenylalanine convention problem

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

  26 PHE   (  26-)  A
  75 PHE   (  75-)  A
 109 PHE   ( 109-)  A
 142 PHE   ( 142-)  A
 147 PHE   ( 147-)  A
 246 PHE   ( 246-)  A
 331 PHE   ( 331-)  A
 337 PHE   ( 337-)  A
 411 PHE   ( 411-)  A
 417 PHE   ( 417-)  A
 426 PHE   ( 426-)  A
 523 PHE   (  26-)  B
 572 PHE   (  75-)  B
 606 PHE   ( 109-)  B
 639 PHE   ( 142-)  B
 644 PHE   ( 147-)  B
 743 PHE   ( 246-)  B
 813 PHE   ( 316-)  B
 828 PHE   ( 331-)  B
 834 PHE   ( 337-)  B
 908 PHE   ( 411-)  B
 914 PHE   ( 417-)  B
 923 PHE   ( 426-)  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.

 153 ASP   ( 153-)  A
 650 ASP   ( 153-)  B
 812 ASP   ( 315-)  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.

  72 GLU   (  72-)  A
 151 GLU   ( 151-)  A
 569 GLU   (  72-)  B
 648 GLU   ( 151-)  B

Geometric checks

Warning: Unusual bond lengths

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

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

 378 TRP   ( 378-)  A      CB   CG    1.37   -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.

 274 HIS   ( 274-)  A      CG   ND1  CE1 109.64    4.0
 422 HIS   ( 422-)  A      CG   ND1  CE1 109.68    4.1
 628 ARG   ( 131-)  B      CB   CG   CD  105.34   -4.4
 659 HIS   ( 162-)  B      CG   ND1  CE1 109.64    4.0
 891 VAL   ( 394-)  B      C    CA   CB  117.91    4.1

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.

  72 GLU   (  72-)  A
 151 GLU   ( 151-)  A
 153 ASP   ( 153-)  A
 569 GLU   (  72-)  B
 648 GLU   ( 151-)  B
 650 ASP   ( 153-)  B
 812 ASP   ( 315-)  B

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.

 873 VAL   ( 376-)  B    4.17

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.

 313 TYR   ( 313-)  A    -3.6
 826 ARG   ( 329-)  B    -3.0
 778 LEU   ( 281-)  B    -2.8
 281 LEU   ( 281-)  A    -2.8
 343 VAL   ( 343-)  A    -2.7
 329 ARG   ( 329-)  A    -2.5
 482 THR   ( 482-)  A    -2.5
 895 VAL   ( 398-)  B    -2.5
 979 THR   ( 482-)  B    -2.5
 912 PRO   ( 415-)  B    -2.4
 130 ILE   ( 130-)  A    -2.3
 595 PRO   (  98-)  B    -2.3
 627 ILE   ( 130-)  B    -2.3
   2 ARG   (   2-)  A    -2.2
 697 GLN   ( 200-)  B    -2.2
 235 GLU   ( 235-)  A    -2.2
 850 ARG   ( 353-)  B    -2.2
 732 GLU   ( 235-)  B    -2.2
 814 LEU   ( 317-)  B    -2.2
 200 GLN   ( 200-)  A    -2.2
 415 PRO   ( 415-)  A    -2.1
 289 PRO   ( 289-)  A    -2.1
 499 ARG   (   2-)  B    -2.1
 370 ASN   ( 370-)  A    -2.1
  98 PRO   (  98-)  A    -2.1
 483 ILE   ( 483-)  A    -2.0
 489 ILE   ( 489-)  A    -2.0
  73 GLN   (  73-)  A    -2.0
 345 SER   ( 345-)  A    -2.0
 116 TYR   ( 116-)  A    -2.0
 947 MET   ( 450-)  B    -2.0
 560 THR   (  63-)  B    -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.

  19 ASN   (  19-)  A  Poor phi/psi
  32 PRO   (  32-)  A  omega poor
  46 GLY   (  46-)  A  Poor phi/psi
  75 PHE   (  75-)  A  Poor phi/psi
 108 TYR   ( 108-)  A  omega poor
 124 ALA   ( 124-)  A  Poor phi/psi
 140 ASP   ( 140-)  A  Poor phi/psi
 144 LEU   ( 144-)  A  Poor phi/psi
 192 ASN   ( 192-)  A  Poor phi/psi
 233 GLU   ( 233-)  A  Poor phi/psi
 235 GLU   ( 235-)  A  Poor phi/psi
 251 PHE   ( 251-)  A  omega poor
 281 LEU   ( 281-)  A  Poor phi/psi
 288 LEU   ( 288-)  A  PRO omega poor
 323 THR   ( 323-)  A  Poor phi/psi
 341 ALA   ( 341-)  A  Poor phi/psi
 343 VAL   ( 343-)  A  Poor phi/psi
 345 SER   ( 345-)  A  omega poor
 346 LYS   ( 346-)  A  Poor phi/psi
 347 PHE   ( 347-)  A  omega poor
 373 TYR   ( 373-)  A  omega poor
 374 HIS   ( 374-)  A  Poor phi/psi
 381 TRP   ( 381-)  A  Poor phi/psi
 390 GLY   ( 390-)  A  PRO omega poor
 469 PRO   ( 469-)  A  omega poor
And so on for a total of 62 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 : -4.035

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 PHE   (   9-)  A      0
  11 TYR   (  11-)  A      0
  12 SER   (  12-)  A      0
  18 CYS   (  18-)  A      0
  19 ASN   (  19-)  A      0
  20 ALA   (  20-)  A      0
  22 TYR   (  22-)  A      0
  23 CYS   (  23-)  A      0
  24 ASP   (  24-)  A      0
  32 PRO   (  32-)  A      0
  34 LEU   (  34-)  A      0
  45 SER   (  45-)  A      0
  48 ARG   (  48-)  A      0
  49 MET   (  49-)  A      0
  57 GLN   (  57-)  A      0
  59 ASN   (  59-)  A      0
  60 HIS   (  60-)  A      0
  61 THR   (  61-)  A      0
  65 LEU   (  65-)  A      0
  73 GLN   (  73-)  A      0
  75 PHE   (  75-)  A      0
  79 LYS   (  79-)  A      0
  81 PHE   (  81-)  A      0
  85 MET   (  85-)  A      0
 108 TYR   ( 108-)  A      0
And so on for a total of 428 lines.

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].

  55 PRO   (  55-)  A   -29.2 envelop C-alpha (-36 degrees)
  71 PRO   (  71-)  A  -117.7 half-chair C-delta/C-gamma (-126 degrees)
 139 PRO   ( 139-)  A    47.0 half-chair C-delta/C-gamma (54 degrees)
 182 PRO   ( 182-)  A   125.2 half-chair C-beta/C-alpha (126 degrees)
 201 PRO   ( 201-)  A   100.1 envelop C-beta (108 degrees)
 236 PRO   ( 236-)  A  -113.2 envelop C-gamma (-108 degrees)
 245 PRO   ( 245-)  A   -55.1 half-chair C-beta/C-alpha (-54 degrees)
 299 PRO   ( 299-)  A  -115.9 envelop C-gamma (-108 degrees)
 415 PRO   ( 415-)  A   131.8 half-chair C-beta/C-alpha (126 degrees)
 469 PRO   ( 469-)  A  -116.9 envelop C-gamma (-108 degrees)
 529 PRO   (  32-)  B   -47.1 half-chair C-beta/C-alpha (-54 degrees)
 552 PRO   (  55-)  B   -32.1 envelop C-alpha (-36 degrees)
 568 PRO   (  71-)  B  -126.6 half-chair C-delta/C-gamma (-126 degrees)
 595 PRO   (  98-)  B   103.6 envelop C-beta (108 degrees)
 679 PRO   ( 182-)  B   114.0 envelop C-beta (108 degrees)
 733 PRO   ( 236-)  B  -116.0 envelop C-gamma (-108 degrees)
 742 PRO   ( 245-)  B   -53.6 half-chair C-beta/C-alpha (-54 degrees)
 796 PRO   ( 299-)  B  -117.9 half-chair C-delta/C-gamma (-126 degrees)
 816 PRO   ( 319-)  B   -58.2 half-chair C-beta/C-alpha (-54 degrees)
 912 PRO   ( 415-)  B   125.6 half-chair C-beta/C-alpha (126 degrees)
 966 PRO   ( 469-)  B  -114.6 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.

1015 BMA   (1500-)  B      O3  <-> 1026 MAN   (1501-)  B      C1     0.93    1.47  INTRA BF
1001 NAG   (1504-)  B      O4  <-> 1025 BMA   (1505-)  B      C1     0.89    1.51  INTRA BF
1015 BMA   (1500-)  B      C3  <-> 1026 MAN   (1501-)  B      C1     0.77    2.43  INTRA BF
1001 NAG   (1504-)  B      C4  <-> 1025 BMA   (1505-)  B      C1     0.61    2.59  INTRA BF
 740 GLY   ( 243-)  B      N   <-> 1021 SO4   (1512-)  B      O3     0.47    2.23  INTRA
 243 GLY   ( 243-)  A      O   <->  845 TRP   ( 348-)  B      NE1    0.46    2.24  INTRA BF
 284 GLN   ( 284-)  A      NE2 <->  314 LEU   ( 314-)  A      N      0.42    2.43  INTRA BF
 274 HIS   ( 274-)  A      NE2 <-> 1027 HOH   (2020 )  A      O      0.41    2.29  INTRA
 257 ARG   ( 257-)  A      NH1 <-> 1013 SO4   (1508-)  A      O4     0.41    2.29  INTRA BF
 856 ARG   ( 359-)  B      NH1 <->  896 ASP   ( 399-)  B      OD2    0.37    2.33  INTRA
 142 PHE   ( 142-)  A      O   <->  211 ARG   ( 211-)  A      NH2    0.36    2.34  INTRA BF
 377 GLY   ( 377-)  A      C   <->  378 TRP   ( 378-)  A      CE3    0.36    2.74  INTRA
 532 GLY   (  35-)  B      O   <->  553 ILE   (  56-)  B      N      0.32    2.38  INTRA
 639 PHE   ( 142-)  B      O   <->  708 ARG   ( 211-)  B      NH2    0.32    2.38  INTRA BF
 576 LYS   (  79-)  B      N   <->  873 VAL   ( 376-)  B      O      0.31    2.39  INTRA BL
 342 CYS   ( 342-)  A      SG  <->  343 VAL   ( 343-)  A      N      0.30    2.90  INTRA BF
1015 BMA   (1500-)  B      C6  <-> 1016 A10   (1502-)  B      C1     0.28    2.82  INTRA BF
 371 LEU   ( 371-)  A      CD2 <->  378 TRP   ( 378-)  A      CH2    0.27    2.93  INTRA
  30 THR   (  30-)  A      O   <->   32 PRO   (  32-)  A      CD     0.26    2.54  INTRA BF
1001 NAG   (1504-)  B      C4  <-> 1025 BMA   (1505-)  B      O2     0.26    2.54  INTRA BF
 130 ILE   ( 130-)  A      N   <-> 1027 HOH   (2010 )  A      O      0.25    2.45  INTRA BL
 285 ARG   ( 285-)  A      NH1 <->  315 ASP   ( 315-)  A      OD2    0.25    2.45  INTRA BF
  35 GLY   (  35-)  A      O   <->   56 ILE   (  56-)  A      N      0.23    2.47  INTRA
 608 GLU   ( 111-)  B      CG  <->  666 GLN   ( 169-)  B      NE2    0.23    2.87  INTRA
 843 LYS   ( 346-)  B      O   <->  845 TRP   ( 348-)  B      N      0.23    2.47  INTRA BF
And so on for a total of 220 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.

 395 ARG   ( 395-)  A      -8.03
 938 LYS   ( 441-)  B      -6.79
 441 LYS   ( 441-)  A      -6.75
 169 GLN   ( 169-)  A      -6.64
 697 GLN   ( 200-)  B      -6.37
 200 GLN   ( 200-)  A      -6.37
 666 GLN   ( 169-)  B      -6.30
  31 PHE   (  31-)  A      -6.29
 814 LEU   ( 317-)  B      -5.80
  60 HIS   (  60-)  A      -5.49
 194 LYS   ( 194-)  A      -5.49
 262 ARG   ( 262-)  A      -5.48
 759 ARG   ( 262-)  B      -5.45
 557 HIS   (  60-)  B      -5.37
 130 ILE   ( 130-)  A      -5.27
 960 ARG   ( 463-)  B      -5.27
 993 ARG   ( 496-)  B      -5.24
  57 GLN   (  57-)  A      -5.24
 541 ARG   (  44-)  B      -5.21
  44 ARG   (  44-)  A      -5.18
 627 ILE   ( 130-)  B      -5.01
 691 LYS   ( 194-)  B      -5.01
 496 ARG   ( 496-)  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.

 557 HIS   (  60-)  B       560 - THR     63- ( B)         -4.71

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.

 783 LEU   ( 286-)  B   -3.06
  62 GLY   (  62-)  A   -3.01
 846 GLU   ( 349-)  B   -2.99
 667 ARG   ( 170-)  B   -2.86
 844 PHE   ( 347-)  B   -2.72
 170 ARG   ( 170-)  A   -2.60
 126 CYS   ( 126-)  A   -2.58

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: 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.

1027 HOH   (2002 )  A      O
1027 HOH   (2013 )  A      O
Bound group on Asn; dont flip   19 ASN  (  19-) A
Bound to:  995 NAG  (1498-) A
Bound group on Asn; dont flip  146 ASN  ( 146-) A
Bound to:  997 NAG  (1500-) A
Bound group on Asn; dont flip  516 ASN  (  19-) B
Bound to:  998 NAG  (1498-) B
Bound group on Asn; dont flip  556 ASN  (  59-) B
Bound to: 1000 NAG  (1503-) B
Bound group on Asn; dont flip  643 ASN  ( 146-) B
Bound to: 1002 NAG  (1506-) B

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.

  60 HIS   (  60-)  A
  70 GLN   (  70-)  A
 223 HIS   ( 223-)  A
 284 GLN   ( 284-)  A
 333 ASN   ( 333-)  A
 557 HIS   (  60-)  B
 720 HIS   ( 223-)  B
 771 HIS   ( 274-)  B
 781 GLN   ( 284-)  B
 859 GLN   ( 362-)  B
 893 ASN   ( 396-)  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.

   5 ILE   (   5-)  A      N
   9 PHE   (   9-)  A      N
  11 TYR   (  11-)  A      N
  20 ALA   (  20-)  A      N
  23 CYS   (  23-)  A      N
  35 GLY   (  35-)  A      N
  43 THR   (  43-)  A      OG1
  45 SER   (  45-)  A      N
  48 ARG   (  48-)  A      NE
  52 SER   (  52-)  A      OG
 101 GLN   ( 101-)  A      NE2
 116 TYR   ( 116-)  A      OH
 134 THR   ( 134-)  A      N
 140 ASP   ( 140-)  A      N
 141 ASP   ( 141-)  A      N
 147 PHE   ( 147-)  A      N
 179 TRP   ( 179-)  A      N
 180 THR   ( 180-)  A      N
 184 TRP   ( 184-)  A      N
 190 ALA   ( 190-)  A      N
 192 ASN   ( 192-)  A      ND2
 197 LEU   ( 197-)  A      N
 209 TRP   ( 209-)  A      NE1
 211 ARG   ( 211-)  A      NE
 212 TYR   ( 212-)  A      OH
And so on for a total of 102 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.

  24 ASP   (  24-)  A      OD1
 111 GLU   ( 111-)  A      OE1
 233 GLU   ( 233-)  A      OE1
 311 HIS   ( 311-)  A      ND1
 370 ASN   ( 370-)  A      OD1
 419 HIS   ( 419-)  A      NE2
 650 ASP   ( 153-)  B      OD1
 867 ASN   ( 370-)  B      OD1

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.

 203 ASP   ( 203-)  A   H-bonding suggests Asn
 218 ASP   ( 218-)  A   H-bonding suggests Asn
 233 GLU   ( 233-)  A   H-bonding suggests Gln; but Alt-Rotamer
 399 ASP   ( 399-)  A   H-bonding suggests Asn
 700 ASP   ( 203-)  B   H-bonding suggests Asn
 715 ASP   ( 218-)  B   H-bonding suggests Asn; but Alt-Rotamer
 730 GLU   ( 233-)  B   H-bonding suggests Gln; but Alt-Rotamer
 877 ASP   ( 380-)  B   H-bonding suggests Asn; but Alt-Rotamer
 896 ASP   ( 399-)  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 :  -0.320
  2nd generation packing quality :  -1.620
  Ramachandran plot appearance   :  -2.549
  chi-1/chi-2 rotamer normality  :  -4.035 (bad)
  Backbone conformation          :  -0.508

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.581 (tight)
  Bond angles                    :   0.748
  Omega angle restraints         :   1.196
  Side chain planarity           :   0.513 (tight)
  Improper dihedral distribution :   0.726
  B-factor distribution          :   0.333
  Inside/Outside distribution    :   1.037

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.581 (tight)
  Bond angles                    :   0.748
  Omega angle restraints         :   1.196
  Side chain planarity           :   0.513 (tight)
  Improper dihedral distribution :   0.726
  B-factor distribution          :   0.333
  Inside/Outside distribution    :   1.037
==============

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
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
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    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
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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
    R.W.W. Hooft, C. Sander and G. Vriend,
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Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
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Quality Control
    G.Vriend and C.Sander,
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      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.