WHAT IF Check report

This file was created 2012-01-31 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 pdb2vz9.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

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

Space group as read from CRYST card: P 1 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 1
Warning: one pair of SEQRES sequences is sneakingly different
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Polymer chain multiplicity and SEQRES multiplicity disagree 2 1
Z and NCS seem to support the 3D multiplicity

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.

4168 NAP   (3002-)  A  -
4169 NAP   (3001-)  B  -
4170 NAP   (3002-)  B  -
4171 NAP   (3001-)  A  -

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: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

1027 SER   (1027-)  A
3472 GLU   (1419-)  B

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 MET   (   1-)  A    High
   2 GLU   (   2-)  A    High
   3 GLU   (   3-)  A    High
   4 VAL   (   4-)  A    High
   5 VAL   (   5-)  A    High
   6 ILE   (   6-)  A    High
   7 ALA   (   7-)  A    High
   8 GLY   (   8-)  A    High
   9 MET   (   9-)  A    High
  10 SER   (  10-)  A    High
  11 GLY   (  11-)  A    High
  12 LYS   (  12-)  A    High
  13 LEU   (  13-)  A    High
  14 PRO   (  14-)  A    High
  15 GLU   (  15-)  A    High
  16 SER   (  16-)  A    High
  17 GLU   (  17-)  A    High
  18 ASN   (  18-)  A    High
  19 LEU   (  19-)  A    High
  20 GLU   (  20-)  A    High
  21 GLU   (  21-)  A    High
  22 PHE   (  22-)  A    High
  23 TRP   (  23-)  A    High
  24 ALA   (  24-)  A    High
  25 ASN   (  25-)  A    High
And so on for a total of 3896 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: 30

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

  45 TYR   (  45-)  A
 172 TYR   ( 172-)  A
 243 TYR   ( 243-)  A
 277 TYR   ( 277-)  A
 289 TYR   ( 289-)  A
 734 TYR   ( 734-)  A
 874 TYR   ( 874-)  A
 891 TYR   ( 891-)  A
1003 TYR   (1003-)  A
1223 TYR   (1255-)  A
1474 TYR   (1506-)  A
1521 TYR   (1553-)  A
1536 TYR   (1568-)  A
1620 TYR   (1652-)  A
1624 TYR   (1656-)  A
1810 TYR   (1842-)  A
1855 TYR   (1887-)  A
1964 TYR   (1996-)  A
1983 TYR   (2015-)  A
2126 TYR   (  45-)  B
2324 TYR   ( 243-)  B
2358 TYR   ( 277-)  B
2370 TYR   ( 289-)  B
2815 TYR   ( 734-)  B
2955 TYR   ( 874-)  B
2972 TYR   ( 891-)  B
3074 TYR   ( 993-)  B
3084 TYR   (1003-)  B
3308 TYR   (1255-)  B
3559 TYR   (1506-)  B
3606 TYR   (1553-)  B
3621 TYR   (1568-)  B
3705 TYR   (1652-)  B
3709 TYR   (1656-)  B
3895 TYR   (1842-)  B
3940 TYR   (1887-)  B
4049 TYR   (1996-)  B
4068 TYR   (2015-)  B

Warning: Phenylalanine convention problem

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

  64 PHE   (  64-)  A
  65 PHE   (  65-)  A
 147 PHE   ( 147-)  A
 200 PHE   ( 200-)  A
 215 PHE   ( 215-)  A
 263 PHE   ( 263-)  A
 395 PHE   ( 395-)  A
 450 PHE   ( 450-)  A
 661 PHE   ( 661-)  A
 686 PHE   ( 686-)  A
 730 PHE   ( 730-)  A
 821 PHE   ( 821-)  A
 850 PHE   ( 850-)  A
 864 PHE   ( 864-)  A
 985 PHE   ( 985-)  A
1007 PHE   (1007-)  A
1096 PHE   (1096-)  A
1311 PHE   (1343-)  A
1350 PHE   (1382-)  A
1364 PHE   (1396-)  A
1370 PHE   (1402-)  A
1383 PHE   (1415-)  A
1391 PHE   (1423-)  A
1482 PHE   (1514-)  A
1500 PHE   (1532-)  A
And so on for a total of 71 lines.

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.

  76 ASP   (  76-)  A
 849 ASP   ( 849-)  A
 971 ASP   ( 971-)  A
 995 ASP   ( 995-)  A
1468 ASP   (1500-)  A
2157 ASP   (  76-)  B
3076 ASP   ( 995-)  B
3553 ASP   (1500-)  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.

 218 GLU   ( 218-)  A
 543 GLU   ( 543-)  A
 660 GLU   ( 660-)  A
1697 GLU   (1729-)  A
1777 GLU   (1809-)  A
2693 GLU   ( 612-)  B
3782 GLU   (1729-)  B
3862 GLU   (1809-)  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.

  68 HIS   (  68-)  A      CG   ND1  CE1 109.68    4.1
 703 LEU   ( 703-)  A      N    CA   C    97.08   -5.0
1261 HIS   (1293-)  A      CG   ND1  CE1 109.61    4.0
1702 ARG   (1734-)  A      CB   CG   CD  105.56   -4.3
1895 ARG   (1927-)  A      CB   CG   CD  105.80   -4.2
2149 HIS   (  68-)  B      CG   ND1  CE1 109.66    4.1
2412 HIS   ( 331-)  B      CG   ND1  CE1 109.63    4.0
3574 GLN   (1521-)  B      N    CA   C   123.82    4.5
3787 ARG   (1734-)  B      CB   CG   CD  105.47   -4.3
3831 HIS   (1778-)  B      CG   ND1  CE1 109.71    4.1
3980 ARG   (1927-)  B      CB   CG   CD  104.72   -4.7

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.

  76 ASP   (  76-)  A
 218 GLU   ( 218-)  A
 543 GLU   ( 543-)  A
 660 GLU   ( 660-)  A
 849 ASP   ( 849-)  A
 971 ASP   ( 971-)  A
 995 ASP   ( 995-)  A
1468 ASP   (1500-)  A
1697 GLU   (1729-)  A
1777 GLU   (1809-)  A
2157 ASP   (  76-)  B
2693 GLU   ( 612-)  B
3076 ASP   ( 995-)  B
3553 ASP   (1500-)  B
3782 GLU   (1729-)  B
3862 GLU   (1809-)  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.

 703 LEU   ( 703-)  A    5.75
3574 GLN   (1521-)  B    4.89
3701 VAL   (1648-)  B    4.46
   5 VAL   (   5-)  A    4.38
1155 LEU   (1183-)  A    4.37
2086 VAL   (   5-)  B    4.30
1718 GLU   (1750-)  A    4.29
3183 SER   (1102-)  B    4.23
 901 ARG   ( 901-)  A    4.09
1102 SER   (1102-)  A    4.09
3311 ILE   (1258-)  B    4.04

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 : -5.039

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.

1768 PHE   (1800-)  A    -3.5
 985 PHE   ( 985-)  A    -3.4
 413 PRO   ( 413-)  A    -3.1
2494 PRO   ( 413-)  B    -3.1
3277 PRO   (1224-)  B    -3.1
3066 PHE   ( 985-)  B    -3.1
1617 PRO   (1649-)  A    -3.1
3407 PRO   (1354-)  B    -3.0
1838 PRO   (1870-)  A    -3.0
3155 THR   (1074-)  B    -3.0
1074 THR   (1074-)  A    -3.0
1069 TYR   (1069-)  A    -2.9
3517 PRO   (1464-)  B    -2.9
3493 PRO   (1440-)  B    -2.9
1408 PRO   (1440-)  A    -2.9
3150 TYR   (1069-)  B    -2.9
1432 PRO   (1464-)  A    -2.9
2717 PRO   ( 636-)  B    -2.9
3237 PRO   (1181-)  B    -2.8
2491 PRO   ( 410-)  B    -2.8
 410 PRO   ( 410-)  A    -2.8
2932 PRO   ( 851-)  B    -2.8
 982 THR   ( 982-)  A    -2.7
 617 PRO   ( 617-)  A    -2.7
2445 PRO   ( 364-)  B    -2.7
And so on for a total of 263 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.

  40 TRP   (  40-)  A  Poor phi/psi
  42 ALA   (  42-)  A  Poor phi/psi
  45 TYR   (  45-)  A  Poor phi/psi
  57 LEU   (  57-)  A  Poor phi/psi
  60 PHE   (  60-)  A  Poor phi/psi
  61 ASP   (  61-)  A  omega poor
 103 THR   ( 103-)  A  omega poor
 127 LEU   ( 127-)  A  omega poor
 149 ASP   ( 149-)  A  Poor phi/psi
 154 SER   ( 154-)  A  omega poor
 160 ALA   ( 160-)  A  Poor phi/psi
 163 SER   ( 163-)  A  Poor phi/psi
 215 PHE   ( 215-)  A  Poor phi/psi
 227 ALA   ( 227-)  A  Poor phi/psi
 237 SER   ( 237-)  A  Poor phi/psi
 238 LEU   ( 238-)  A  Poor phi/psi
 248 ASN   ( 248-)  A  Poor phi/psi
 255 GLY   ( 255-)  A  Poor phi/psi
 277 TYR   ( 277-)  A  Poor phi/psi
 278 ALA   ( 278-)  A  Poor phi/psi
 296 GLY   ( 296-)  A  Poor phi/psi
 311 ALA   ( 311-)  A  Poor phi/psi
 313 CYS   ( 313-)  A  omega poor
 317 ARG   ( 317-)  A  Poor phi/psi
 320 LEU   ( 320-)  A  omega poor
And so on for a total of 300 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 : -5.324

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.

4007 SER   (1954-)  B    0.35
 558 SER   ( 558-)  A    0.36
2251 SER   ( 170-)  B    0.36
2639 SER   ( 558-)  B    0.36
1922 SER   (1954-)  A    0.37
 170 SER   ( 170-)  A    0.37
 231 VAL   ( 231-)  A    0.38
1039 SER   (1039-)  A    0.38
2312 VAL   ( 231-)  B    0.38
2636 SER   ( 555-)  B    0.39
1186 SER   (1218-)  A    0.39
2816 SER   ( 735-)  B    0.39
 584 GLU   ( 584-)  A    0.40

Warning: Unusual backbone conformations

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

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

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

   9 MET   (   9-)  A      0
  10 SER   (  10-)  A      0
  13 LEU   (  13-)  A      0
  14 PRO   (  14-)  A      0
  15 GLU   (  15-)  A      0
  32 MET   (  32-)  A      0
  39 ARG   (  39-)  A      0
  40 TRP   (  40-)  A      0
  41 LYS   (  41-)  A      0
  42 ALA   (  42-)  A      0
  45 TYR   (  45-)  A      0
  47 LEU   (  47-)  A      0
  50 ARG   (  50-)  A      0
  51 MET   (  51-)  A      0
  57 LEU   (  57-)  A      0
  59 ARG   (  59-)  A      0
  62 ALA   (  62-)  A      0
  65 PHE   (  65-)  A      0
  68 HIS   (  68-)  A      0
  74 THR   (  74-)  A      0
 101 ARG   ( 101-)  A      0
 103 THR   ( 103-)  A      0
 104 SER   ( 104-)  A      0
 113 SER   ( 113-)  A      0
 120 LEU   ( 120-)  A      0
And so on for a total of 1667 lines.

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!

1843 GLY   (1875-)  A   1.63   11
3928 GLY   (1875-)  B   1.61   12
3226 GLY   (1145-)  B   1.52   80

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...

1717 ALA   (1749-)  A   1.52
3802 ALA   (1749-)  B   1.57

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].

  14 PRO   (  14-)  A   115.9 envelop C-beta (108 degrees)
 153 PRO   ( 153-)  A   112.1 envelop C-beta (108 degrees)
 334 PRO   ( 334-)  A    43.7 envelop C-delta (36 degrees)
 364 PRO   ( 364-)  A    49.4 half-chair C-delta/C-gamma (54 degrees)
 367 PRO   ( 367-)  A    51.7 half-chair C-delta/C-gamma (54 degrees)
 410 PRO   ( 410-)  A    35.3 envelop C-delta (36 degrees)
 413 PRO   ( 413-)  A    28.0 envelop C-delta (36 degrees)
 486 PRO   ( 486-)  A    99.8 envelop C-beta (108 degrees)
 574 PRO   ( 574-)  A    35.9 envelop C-delta (36 degrees)
 617 PRO   ( 617-)  A   112.6 envelop C-beta (108 degrees)
 635 PRO   ( 635-)  A   108.2 envelop C-beta (108 degrees)
 640 PRO   ( 640-)  A    50.4 half-chair C-delta/C-gamma (54 degrees)
 654 PRO   ( 654-)  A    99.0 envelop C-beta (108 degrees)
 705 PRO   ( 705-)  A    11.7 half-chair N/C-delta (18 degrees)
 742 PRO   ( 742-)  A    51.6 half-chair C-delta/C-gamma (54 degrees)
 828 PRO   ( 828-)  A   104.5 envelop C-beta (108 degrees)
 845 PRO   ( 845-)  A   127.8 half-chair C-beta/C-alpha (126 degrees)
 965 PRO   ( 965-)  A    51.8 half-chair C-delta/C-gamma (54 degrees)
1005 PRO   (1005-)  A   100.3 envelop C-beta (108 degrees)
1043 PRO   (1043-)  A    48.2 half-chair C-delta/C-gamma (54 degrees)
1061 PRO   (1061-)  A  -116.7 envelop C-gamma (-108 degrees)
1105 PRO   (1105-)  A    21.7 half-chair N/C-delta (18 degrees)
1192 PRO   (1224-)  A   142.8 envelop C-alpha (144 degrees)
1247 PRO   (1279-)  A    52.2 half-chair C-delta/C-gamma (54 degrees)
1274 PRO   (1306-)  A  -115.0 envelop C-gamma (-108 degrees)
And so on for a total of 81 lines.

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.

 856 CYS   ( 856-)  A      CB  <-> 2937 CYS   ( 856-)  B      SG     0.63    2.77  INTRA BL
2580 MET   ( 499-)  B      SD  <-> 2583 GLN   ( 502-)  B      NE2    0.62    2.68  INTRA BF
 671 PHE   ( 671-)  A      CE2 <->  773 ARG   ( 773-)  A      NH2    0.59    2.51  INTRA BL
 499 MET   ( 499-)  A      SD  <->  502 GLN   ( 502-)  A      NE2    0.59    2.71  INTRA BF
3084 TYR   (1003-)  B      CZ  <-> 3118 HIS   (1037-)  B      CE1    0.51    2.69  INTRA BL
2032 GLY   (2064-)  A      O   <-> 2034 VAL   (2066-)  A      N      0.48    2.22  INTRA BL
2104 TRP   (  23-)  B      CE2 <-> 2431 HIS   ( 350-)  B      CD2    0.47    2.73  INTRA BF
1003 TYR   (1003-)  A      CZ  <-> 1037 HIS   (1037-)  A      CE1    0.47    2.73  INTRA BL
  23 TRP   (  23-)  A      CE2 <->  350 HIS   ( 350-)  A      CD2    0.46    2.74  INTRA BL
4117 GLY   (2064-)  B      O   <-> 4119 VAL   (2066-)  B      N      0.46    2.24  INTRA BL
1003 TYR   (1003-)  A      CE1 <-> 1037 HIS   (1037-)  A      CE1    0.42    2.78  INTRA BL
3084 TYR   (1003-)  B      CE1 <-> 3118 HIS   (1037-)  B      CE1    0.42    2.78  INTRA BL
2290 ASP   ( 209-)  B      CG  <-> 2294 ARG   ( 213-)  B      NH2    0.40    2.70  INTRA BF
1692 ARG   (1724-)  A      NH1 <-> 4171 NAP   (3001-)  A      C8A    0.40    2.70  INTRA BL
3356 ASN   (1303-)  B      N   <-> 3357 PRO   (1304-)  B      CD     0.39    2.61  INTRA BF
3461 THR   (1408-)  B      N   <-> 3462 PRO   (1409-)  B      CD     0.39    2.61  INTRA BF
3852 LEU   (1799-)  B      O   <-> 3855 GLU   (1802-)  B      N      0.39    2.31  INTRA BF
3573 GLU   (1520-)  B      O   <-> 3575 ASP   (1522-)  B      N      0.38    2.32  INTRA BF
 642 CYS   ( 642-)  A      SG  <->  743 VAL   ( 743-)  A      CG2    0.38    3.02  INTRA BL
1693 ASP   (1725-)  A      OD1 <-> 1694 THR   (1726-)  A      N      0.38    2.22  INTRA BL
1137 GLN   (1137-)  A      NE2 <-> 1364 PHE   (1396-)  A      CE2    0.38    2.72  INTRA BF
1648 VAL   (1680-)  A      N   <-> 4171 NAP   (3001-)  A      O1N    0.38    2.32  INTRA BL
3579 LYS   (1526-)  B      NZ  <-> 3605 HIS   (1552-)  B      NE2    0.37    2.63  INTRA BF
1444 ASN   (1476-)  A      CB  <-> 1454 MET   (1486-)  A      SD     0.37    3.03  INTRA BF
3063 THR   ( 982-)  B      O   <-> 3065 GLU   ( 984-)  B      N      0.36    2.34  INTRA BF
And so on for a total of 1279 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.

1834 ARG   (1866-)  A      -8.48
3919 ARG   (1866-)  B      -8.21
 384 ARG   ( 384-)  A      -8.18
2465 ARG   ( 384-)  B      -8.13
2397 ARG   ( 316-)  B      -7.98
 316 ARG   ( 316-)  A      -7.92
 317 ARG   ( 317-)  A      -7.78
2398 ARG   ( 317-)  B      -7.78
3777 ARG   (1724-)  B      -7.70
1692 ARG   (1724-)  A      -7.66
 973 ARG   ( 973-)  A      -7.59
1885 ARG   (1917-)  A      -7.53
3921 LEU   (1868-)  B      -7.44
2757 ARG   ( 676-)  B      -7.44
3463 GLN   (1410-)  B      -7.41
3970 ARG   (1917-)  B      -7.36
1829 GLN   (1861-)  A      -7.35
1836 LEU   (1868-)  A      -7.35
3054 ARG   ( 973-)  B      -7.24
3423 ARG   (1370-)  B      -7.16
1335 GLN   (1367-)  A      -7.08
3591 ARG   (1538-)  B      -6.95
 790 ARG   ( 790-)  A      -6.94
2871 ARG   ( 790-)  B      -6.90
1889 ARG   (1921-)  A      -6.88
And so on for a total of 153 lines.

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.

1453 GLU   (1485-)  A      1455 - HIS   1487- ( A)         -5.08
1489 GLN   (1521-)  A      1491 - ARG   1523- ( A)         -4.73
1834 ARG   (1866-)  A      1836 - LEU   1868- ( A)         -6.79
2900 VAL   ( 819-)  B      2902 - PHE    821- ( B)         -4.60
3192 HIS   (1111-)  B      3194 - LYS   1113- ( B)         -4.40
3418 PRO   (1365-)  B      3421 - GLY   1368- ( B)         -5.02
3574 GLN   (1521-)  B      3576 - ARG   1523- ( B)         -4.62
3919 ARG   (1866-)  B      3921 - LEU   1868- ( B)         -6.69
4124 GLU   (2071-)  B      4126 - MET   2073- ( B)         -4.51

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.

1842 THR   (1874-)  A   -3.25
3253 LEU   (1200-)  B   -2.86
2219 ALA   ( 138-)  B   -2.72
 138 ALA   ( 138-)  A   -2.68
3441 HIS   (1388-)  B   -2.65
1356 HIS   (1388-)  A   -2.62
1667 VAL   (1699-)  A   -2.59
3752 VAL   (1699-)  B   -2.59
3927 THR   (1874-)  B   -2.55
 686 PHE   ( 686-)  A   -2.52
2125 LEU   (  44-)  B   -2.52

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.

 136 GLN   ( 136-)  A     -  139 MET   ( 139-)  A        -1.84
1493 GLU   (1525-)  A     - 1496 THR   (1528-)  A        -1.33
4025 ALA   (1972-)  B     - 4028 LEU   (1975-)  B        -1.66

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.

  25 ASN   (  25-)  A
 136 GLN   ( 136-)  A
 199 GLN   ( 199-)  A
 248 ASN   ( 248-)  A
 271 GLN   ( 271-)  A
 358 HIS   ( 358-)  A
 387 ASN   ( 387-)  A
 425 GLN   ( 425-)  A
 440 GLN   ( 440-)  A
 444 HIS   ( 444-)  A
 560 GLN   ( 560-)  A
 746 GLN   ( 746-)  A
1204 ASN   (1236-)  A
1233 GLN   (1265-)  A
1375 GLN   (1407-)  A
1444 ASN   (1476-)  A
1745 ASN   (1777-)  A
1792 GLN   (1824-)  A
1816 HIS   (1848-)  A
1996 ASN   (2028-)  A
2006 ASN   (2038-)  A
2069 GLN   (2101-)  A
2106 ASN   (  25-)  B
2217 GLN   ( 136-)  B
2280 GLN   ( 199-)  B
And so on for a total of 51 lines.

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.

  18 ASN   (  18-)  A      N
  19 LEU   (  19-)  A      N
  33 VAL   (  33-)  A      N
  38 ARG   (  38-)  A      N
  39 ARG   (  39-)  A      N
  39 ARG   (  39-)  A      NH1
  41 LYS   (  41-)  A      N
  50 ARG   (  50-)  A      N
  53 LYS   (  53-)  A      N
  53 LYS   (  53-)  A      NZ
  56 ASP   (  56-)  A      N
  59 ARG   (  59-)  A      NE
  60 PHE   (  60-)  A      N
  80 ARG   (  80-)  A      NH1
  86 THR   (  86-)  A      OG1
  87 TYR   (  87-)  A      OH
  92 ASP   (  92-)  A      N
 105 THR   ( 105-)  A      N
 112 SER   ( 112-)  A      N
 113 SER   ( 113-)  A      N
 122 ARG   ( 122-)  A      N
 123 ASP   ( 123-)  A      N
 130 TYR   ( 130-)  A      N
 133 ILE   ( 133-)  A      N
 142 ASN   ( 142-)  A      ND2
And so on for a total of 632 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.

  76 ASP   (  76-)  A      OD2
  78 GLN   (  78-)  A      OE1
  84 GLU   (  84-)  A      OE1
 291 GLU   ( 291-)  A      OE1
 328 ASN   ( 328-)  A      OD1
 356 ASN   ( 356-)  A      OD1
 417 HIS   ( 417-)  A      ND1
 425 GLN   ( 425-)  A      OE1
 502 GLN   ( 502-)  A      OE1
 751 HIS   ( 751-)  A      ND1
 804 HIS   ( 804-)  A      ND1
 878 HIS   ( 878-)  A      NE2
 945 GLU   ( 945-)  A      OE1
 991 ASP   ( 991-)  A      OD2
1037 HIS   (1037-)  A      ND1
1060 ASP   (1060-)  A      OD1
1175 GLU   (1207-)  A      OE1
1175 GLU   (1207-)  A      OE2
1264 GLN   (1296-)  A      OE1
1301 ASN   (1333-)  A      OD1
1650 GLN   (1682-)  A      OE1
1816 HIS   (1848-)  A      NE2
1951 GLN   (1983-)  A      OE1
2010 GLU   (2042-)  A      OE1
2112 ASP   (  31-)  B      OD1
And so on for a total of 52 lines.

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

  31 ASP   (  31-)  A   H-bonding suggests Asn; but Alt-Rotamer
 216 ASP   ( 216-)  A   H-bonding suggests Asn; but Alt-Rotamer
 291 GLU   ( 291-)  A   H-bonding suggests Gln; but Alt-Rotamer
 980 ASP   ( 980-)  A   H-bonding suggests Asn; but Alt-Rotamer
1175 GLU   (1207-)  A   H-bonding suggests Gln
1182 ASP   (1214-)  A   H-bonding suggests Asn
1214 GLU   (1246-)  A   H-bonding suggests Gln
1244 ASP   (1276-)  A   H-bonding suggests Asn; but Alt-Rotamer
1294 ASP   (1326-)  A   H-bonding suggests Asn; but Alt-Rotamer
1399 ASP   (1431-)  A   H-bonding suggests Asn; but Alt-Rotamer
1736 GLU   (1768-)  A   H-bonding suggests Gln
1770 GLU   (1802-)  A   H-bonding suggests Gln; but Alt-Rotamer
2081 GLU   (2113-)  A   H-bonding suggests Gln
2112 ASP   (  31-)  B   H-bonding suggests Asn; but Alt-Rotamer
2204 ASP   ( 123-)  B   H-bonding suggests Asn
2372 GLU   ( 291-)  B   H-bonding suggests Gln; but Alt-Rotamer
2382 ASP   ( 301-)  B   H-bonding suggests Asn
2513 GLU   ( 432-)  B   H-bonding suggests Gln
2628 ASP   ( 547-)  B   H-bonding suggests Asn
2930 ASP   ( 849-)  B   H-bonding suggests Asn
3061 ASP   ( 980-)  B   H-bonding suggests Asn
3065 GLU   ( 984-)  B   H-bonding suggests Gln
3299 GLU   (1246-)  B   H-bonding suggests Gln
3464 ASP   (1411-)  B   H-bonding suggests Asn; but Alt-Rotamer
3484 ASP   (1431-)  B   H-bonding suggests Asn; but Alt-Rotamer
3614 ASP   (1561-)  B   H-bonding suggests Asn
3660 ASP   (1607-)  B   H-bonding suggests Asn; but Alt-Rotamer
3821 GLU   (1768-)  B   H-bonding suggests Gln
3855 GLU   (1802-)  B   H-bonding suggests Gln; but Alt-Rotamer
4043 ASP   (1990-)  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 :  -1.725
  2nd generation packing quality :  -2.645
  Ramachandran plot appearance   :  -5.039 (bad)
  chi-1/chi-2 rotamer normality  :  -5.324 (bad)
  Backbone conformation          :  -0.568

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.381 (tight)
  Bond angles                    :   0.641 (tight)
  Omega angle restraints         :   1.075
  Side chain planarity           :   0.294 (tight)
  Improper dihedral distribution :   0.648
  B-factor distribution          :   0.630
  Inside/Outside distribution    :   0.995

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 : 3.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :  -2.0
  chi-1/chi-2 rotamer normality  :  -2.8
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.381 (tight)
  Bond angles                    :   0.641 (tight)
  Omega angle restraints         :   1.075
  Side chain planarity           :   0.294 (tight)
  Improper dihedral distribution :   0.648
  B-factor distribution          :   0.630
  Inside/Outside distribution    :   0.995
==============

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.