WHAT IF Check report

This file was created 2012-01-29 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 pdb3ag4.ent

Checks that need to be done early-on in validation

Warning: Unconventional orthorhombic cell

The primitive P 2 2 2 or P 21 21 21 cell specified does not conform to the convention that the axes should be given in order of increasing length.

The CRYST1 cell dimensions

    A    = 183.364  B   = 206.648  C    = 178.137
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    = 183.364  B   = 206.648  C    = 178.137
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 178.137  B   = 183.364  C    = 206.648
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 178.137  B   = 183.364  C    = 206.648
    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|

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 N

All-atom RMS fit for the two chains : 0.197
CA-only RMS fit for the two chains : 0.134

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: B and O

All-atom RMS fit for the two chains : 0.488
CA-only RMS fit for the two chains : 0.360

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: B and O

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: C and P

All-atom RMS fit for the two chains : 0.184
CA-only RMS fit for the two chains : 0.118

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: C and P

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: D and Q

All-atom RMS fit for the two chains : 0.540
CA-only RMS fit for the two chains : 0.394

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: D and Q

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: E and R

All-atom RMS fit for the two chains : 0.384
CA-only RMS fit for the two chains : 0.169

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: E and R

Warning: Problem detected upon counting molecules and matrices

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

Space group as read from CRYST card: P 21 21 21
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 4
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
There is also strong SEQRES evidence for a multiplicity of: 2
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 2 4
Z and NCS seem to support the 3D multiplicity
There is strong evidence, though, for multiplicity and Z: 2 8

Error: Matthews Coefficient (Vm) very high

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

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 434381.906
Volume of the Unit Cell V= 6749271.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 7.769
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.110 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
There is strong evidence, though, for multiplicity and Z: 2 8
which would result in the much more normal Vm= 3.884
and which also agrees with the number of NCS matrices (labeled `don't use')
that the user provided in the MTRIX records 1

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.

3553 FME   (   1-)  A  -         OK
3555 FME   (   1-)  B  -         OK
3562 SAC   (   1-)  I  -         OK
3565 FME   (   1-)  N  -         OK
3575 HEA   ( 515-)  A  -         Atom types
3576 HEA   ( 516-)  A  -         Atom types
3577 CYN   ( 520-)  A  -         Size
3581 TGL   ( 521-)  A  -
3582 PGV   ( 524-)  A  -         OK
3583 PGV   ( 522-)  C  -         OK
3584 CUA   ( 228-)  B  -         Atom types
3585 CHD   (1085-)  T  -         OK
3587 CHD   ( 525-)  C  -         OK
3588 PEK   ( 264-)  C  -         OK
3589 PGV   ( 267-)  C  -         OK
3590 PGV   ( 268-)  C  -         OK
3591 CDL   ( 270-)  C  -
3592 CHD   ( 271-)  C  -         OK
3593 TGL   ( 523-)  A  -
3594 PSC   ( 229-)  B  -         OK
3596 PEK   ( 265-)  G  -         OK
3597 CDL   ( 269-)  G  -
3598 DMU   ( 272-)  C  -         OK
3599 PEK   (1263-)  P  -         OK
3600 CHD   (  60-)  J  -         OK
And so on for a total of 52 lines.

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.

   1 PHE   (   2-)  A  -   N   bound to 3553 FME   (   1-)  A  -   C
 514 ALA   (   2-)  B  -   N   bound to 3555 FME   (   1-)  B  -   C
1509 THR   (   2-)  I  -   N   bound to 3562 SAC   (   1-)  I  -   C
1777 PHE   (   2-)  N  -   N   bound to 3565 FME   (   1-)  N  -   C
2290 ALA   (   2-)  O  -   N   bound to 3632 FME   (   1-)  O  -   C
3285 THR   (   2-)  V  -   N   bound to 3631 SAC   (   1-)  V  -   C

Non-validating, descriptive output paragraph

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

3579  MG   ( 518-)  B  -
3607  MG   ( 518-)  O  -

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

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: Z

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.

1356 TPO   (  11-)  G
2945 LYS   (  31-)  R
2956 VAL   (  42-)  R
3132 TPO   (  11-)  T

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.

1143 HIS   (   5-)  E    High
1342 GLN   (  95-)  F    High
1343 LEU   (  96-)  F    High
1344 ALA   (  97-)  F    High
1345 HIS   (  98-)  F    High
1346 ALA   (   1-)  G    High
1347 SER   (   2-)  G    High
1348 ALA   (   3-)  G    High
1349 ALA   (   4-)  G    High
1350 LYS   (   5-)  G    High
1351 GLY   (   6-)  G    High
1352 ASP   (   7-)  G    High
1353 HIS   (   8-)  G    High
1354 GLY   (   9-)  G    High
1356 TPO   (  11-)  G    High
1383 HIS   (  38-)  G    High
1384 SER   (  39-)  G    High
1385 GLY   (  40-)  G    High
1386 HIS   (  41-)  G    High
1387 ARG   (  42-)  G    High
1388 GLU   (  43-)  G    High
1430 LYS   (   7-)  H    High
1431 ILE   (   8-)  H    High
1432 LYS   (   9-)  H    High
1469 LYS   (  46-)  H    High
And so on for a total of 60 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

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

Note: B-factor plot

Chain identifier: X

Note: B-factor plot

Chain identifier: Y

Note: B-factor plot

Chain identifier: Z

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.

1014 ARG   (  19-)  D
1687 ARG   (  54-)  K
2790 ARG   (  19-)  Q
3463 ARG   (  54-)  X

Warning: Tyrosine convention problem

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

  53 TYR   (  54-)  A
 128 TYR   ( 129-)  A
 259 TYR   ( 260-)  A
 269 TYR   ( 270-)  A
 371 TYR   ( 372-)  A
 439 TYR   ( 440-)  A
 501 TYR   ( 502-)  A
 597 TYR   (  85-)  B
 622 TYR   ( 110-)  B
 633 TYR   ( 121-)  B
 704 TYR   ( 192-)  B
 705 TYR   ( 193-)  B
 730 TYR   ( 218-)  B
 839 TYR   ( 102-)  C
 919 TYR   ( 182-)  C
 930 TYR   ( 193-)  C
 994 TYR   ( 257-)  C
1099 TYR   ( 104-)  D
1156 TYR   (  18-)  E
1220 TYR   (  82-)  E
1278 TYR   (  31-)  F
1336 TYR   (  89-)  F
1434 TYR   (  11-)  H
1479 TYR   (  56-)  H
1558 TYR   (  51-)  I
And so on for a total of 52 lines.

Warning: Phenylalanine convention problem

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

  21 PHE   (  22-)  A
  77 PHE   (  78-)  A
 108 PHE   ( 109-)  A
 163 PHE   ( 164-)  A
 218 PHE   ( 219-)  A
 234 PHE   ( 235-)  A
 250 PHE   ( 251-)  A
 320 PHE   ( 321-)  A
 347 PHE   ( 348-)  A
 376 PHE   ( 377-)  A
 386 PHE   ( 387-)  A
 396 PHE   ( 397-)  A
 424 PHE   ( 425-)  A
 458 PHE   ( 459-)  A
 475 PHE   ( 476-)  A
 521 PHE   (   9-)  B
 535 PHE   (  23-)  B
 544 PHE   (  32-)  B
 630 PHE   ( 118-)  B
 718 PHE   ( 206-)  B
 804 PHE   (  67-)  C
 831 PHE   (  94-)  C
 910 PHE   ( 173-)  C
 935 PHE   ( 198-)  C
 970 PHE   ( 233-)  C
And so on for a total of 97 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.

  13 ASP   (  14-)  A
  50 ASP   (  51-)  A
 143 ASP   ( 144-)  A
 211 ASP   ( 212-)  A
 226 ASP   ( 227-)  A
 363 ASP   ( 364-)  A
 368 ASP   ( 369-)  A
 406 ASP   ( 407-)  A
 441 ASP   ( 442-)  A
 444 ASP   ( 445-)  A
 523 ASP   (  11-)  B
 569 ASP   (  57-)  B
 600 ASP   (  88-)  B
 627 ASP   ( 115-)  B
 651 ASP   ( 139-)  B
1013 ASP   (  18-)  D
1049 ASP   (  54-)  D
1120 ASP   ( 125-)  D
1136 ASP   ( 141-)  D
1150 ASP   (  12-)  E
1161 ASP   (  23-)  E
1178 ASP   (  40-)  E
1187 ASP   (  49-)  E
1198 ASP   (  60-)  E
1245 ASP   ( 107-)  E
And so on for a total of 70 lines.

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.

  39 GLU   (  40-)  A
 118 GLU   ( 119-)  A
 241 GLU   ( 242-)  A
 473 GLU   ( 474-)  A
 480 GLU   ( 481-)  A
 506 GLU   ( 507-)  A
 530 GLU   (  18-)  B
 531 GLU   (  19-)  B
 572 GLU   (  60-)  B
 574 GLU   (  62-)  B
 621 GLU   ( 109-)  B
 626 GLU   ( 114-)  B
 639 GLU   ( 127-)  B
 644 GLU   ( 132-)  B
 649 GLU   ( 137-)  B
 659 GLU   ( 147-)  B
 669 GLU   ( 157-)  B
 732 GLU   ( 220-)  B
 801 GLU   (  64-)  C
 865 GLU   ( 128-)  C
 890 GLU   ( 153-)  C
 920 GLU   ( 183-)  C
 973 GLU   ( 236-)  C
1004 GLU   (   9-)  D
1037 GLU   (  42-)  D
And so on for a total of 105 lines.

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.

  14 ILE   (  15-)  A      CG1  CD1   1.67    4.1
  36 ILE   (  37-)  A      CG1  CD1   1.70    4.9
  37 ARG   (  38-)  A      CD   NE    1.55    4.8
  52 ILE   (  53-)  A      CG1  CD1   1.71    5.0
  67 PHE   (  68-)  A      CD2  CE2   1.54    5.3
  69 VAL   (  70-)  A      C    O     1.31    4.0
  72 ILE   (  73-)  A      CG1  CD1   1.68    4.2
  73 MET   (  74-)  A      CB   CG    1.73    7.0
  74 ILE   (  75-)  A      CG1  CD1   1.72    5.4
  78 GLY   (  79-)  A      N    CA    1.52    4.3
  80 TRP   (  81-)  A      CE2  CZ2   1.48    4.0
  80 TRP   (  81-)  A      CE3  CZ3   1.52    4.7
  94 PRO   (  95-)  A      N    CA    1.54    4.8
  99 MET   ( 100-)  A      CB   CG    1.64    4.0
 111 LEU   ( 112-)  A      CG   CD1   1.73    6.4
 112 LEU   ( 113-)  A      CB   CG    1.69    7.8
 112 LEU   ( 113-)  A      CG   CD1   1.73    6.2
 127 VAL   ( 128-)  A      CA   CB    1.62    4.3
 138 ALA   ( 139-)  A      C    O     1.32    4.4
 192 VAL   ( 193-)  A      CB   CG2   1.66    4.1
 194 LEU   ( 195-)  A      CB   CG    1.61    4.1
 225 GLY   ( 226-)  A      N    CA    1.53    5.0
 227 PRO   ( 228-)  A      N    CA    1.40   -4.4
 247 LEU   ( 248-)  A      CA   C     1.62    4.4
 250 PHE   ( 251-)  A      CA   C     1.62    4.5
And so on for a total of 147 lines.

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.992069 -0.000643 -0.000270|
 | -0.000643  0.994972 -0.000611|
 | -0.000270 -0.000611  0.991058|
Proposed new scale matrix

 |  0.005498  0.000004  0.000001|
 |  0.000003  0.004863  0.000003|
 |  0.000002  0.000003  0.005665|
With corresponding cell

    A    = 181.898  B   = 205.615  C    = 176.533
    Alpha=  90.071  Beta=  90.031  Gamma=  90.074

The CRYST1 cell dimensions

    A    = 183.364  B   = 206.648  C    = 178.137
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 6727.511
(Under-)estimated Z-score: 60.450

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.

  37 ARG   (  38-)  A      CG   CD   NE  117.55    4.1
  60 HIS   (  61-)  A      CG   ND1  CE1 109.66    4.1
  73 MET   (  74-)  A      CB   CG   SD   94.50   -6.1
  86 ILE   (  87-)  A     -C    N    CA  113.07   -4.8
 137 HIS   ( 138-)  A      CG   ND1  CE1 109.98    4.4
 150 HIS   ( 151-)  A      CG   ND1  CE1 109.74    4.1
 168 ILE   ( 169-)  A      C    CA   CB  101.88   -4.3
 188 MET   ( 189-)  A      CG   SD   CE   87.22   -6.2
 193 LEU   ( 194-)  A      CB   CG   CD2 123.63    4.3
 194 LEU   ( 195-)  A      CA   CB   CG  102.10   -4.1
 235 TRP   ( 236-)  A      CA   CB   CG  105.50   -4.3
 239 HIS   ( 240-)  A      N    CA   CB  118.46    4.7
 239 HIS   ( 240-)  A      CA   CB   CG  106.81   -7.0
 250 PHE   ( 251-)  A      C    CA   CB  102.31   -4.1
 277 MET   ( 278-)  A      CA   CB   CG  102.73   -5.7
 277 MET   ( 278-)  A      CG   SD   CE   77.80  -10.5
 289 HIS   ( 290-)  A      CG   ND1  CE1 110.38    4.8
 290 HIS   ( 291-)  A      CA   CB   CG  109.15   -4.7
 294 VAL   ( 295-)  A      N    CA   CB  118.01    4.4
 296 MET   ( 297-)  A      CG   SD   CE   85.98   -6.8
 306 SER   ( 307-)  A      CA   CB   OG  102.59   -4.3
 309 MET   ( 310-)  A      CG   SD   CE   76.53  -11.1
 313 ILE   ( 314-)  A     -C    N    CA  113.41   -4.6
 365 VAL   ( 366-)  A     -C    N    CA  114.41   -4.1
 376 PHE   ( 377-)  A     -C    N    CA  114.25   -4.1
And so on for a total of 179 lines.

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.

  13 ASP   (  14-)  A
  39 GLU   (  40-)  A
  50 ASP   (  51-)  A
 118 GLU   ( 119-)  A
 143 ASP   ( 144-)  A
 211 ASP   ( 212-)  A
 226 ASP   ( 227-)  A
 241 GLU   ( 242-)  A
 363 ASP   ( 364-)  A
 368 ASP   ( 369-)  A
 406 ASP   ( 407-)  A
 441 ASP   ( 442-)  A
 444 ASP   ( 445-)  A
 473 GLU   ( 474-)  A
 480 GLU   ( 481-)  A
 506 GLU   ( 507-)  A
 523 ASP   (  11-)  B
 530 GLU   (  18-)  B
 531 GLU   (  19-)  B
 569 ASP   (  57-)  B
 572 GLU   (  60-)  B
 574 GLU   (  62-)  B
 600 ASP   (  88-)  B
 621 GLU   ( 109-)  B
 626 GLU   ( 114-)  B
And so on for a total of 179 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 193 LEU   ( 194-)  A      CG    13.6    -9.11   -33.01
 379 VAL   ( 380-)  A      CB    20.3    -6.38   -32.96
 554 ILE   (  42-)  B      CB     6.6    40.83    32.31
1575 ILE   (  68-)  I      CB    -7.4    22.65    32.31
1752 LEU   (  19-)  M      CG    -6.1   -43.72   -33.01
1767 LEU   (  34-)  M      CG     8.3   -18.33   -33.01
1969 LEU   ( 194-)  N      CG     9.0   -17.19   -33.01
2155 VAL   ( 380-)  N      CB     6.6   -24.34   -32.96
2380 ASN   (  92-)  O      CA    -7.8    18.68    33.59
3076 THR   (  53-)  S      CB    -6.1    20.37    34.09
3077 ASN   (  54-)  S      CA     6.7    46.39    33.59
3414 LYS   (  58-)  W      CA    -6.2    23.68    33.92
3456 ARG   (  47-)  X      CA    -6.7    22.97    33.91
The average deviation= 1.742

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.

1520 LEU   (  13-)  I    5.49
  27 MET   (  28-)  A    5.32
  60 HIS   (  61-)  A    5.32
3117 HIS   (  94-)  S    5.18
2651 LEU   ( 138-)  P    4.98
1975 PRO   ( 200-)  N    4.90
3491 PHE   (  29-)  Y    4.87
 318 LYS   ( 319-)  A    4.84
3128 ASP   (   7-)  T    4.82
2253 SER   ( 478-)  N    4.77
2074 VAL   ( 299-)  N    4.77
2182 ASP   ( 407-)  N    4.68
 251 GLY   ( 252-)  A    4.66
2398 TYR   ( 110-)  O    4.63
3482 ARG   (  20-)  Y    4.59
1164 ALA   (  26-)  E    4.59
1258 GLU   (  11-)  F    4.59
2542 SER   (  29-)  P    4.57
1469 LYS   (  46-)  H    4.55
1805 GLY   (  30-)  N    4.53
 842 SER   ( 105-)  C    4.52
 309 MET   ( 310-)  A    4.52
3414 LYS   (  58-)  W    4.50
 551 LEU   (  39-)  B    4.49
 317 VAL   ( 318-)  A    4.47
2353 TRP   (  65-)  O    4.46
1984 LEU   ( 209-)  N    4.44
 364 ILE   ( 365-)  A    4.37
2127 GLY   ( 352-)  N    4.36
3272 ASP   (  73-)  U    4.34
1342 GLN   (  95-)  F    4.33
2132 VAL   ( 357-)  N    4.32
2664 LEU   ( 151-)  P    4.30
 992 SER   ( 255-)  C    4.25
2025 GLY   ( 250-)  N    4.24
 477 SER   ( 478-)  A    4.17
2696 GLU   ( 183-)  P    4.17
2779 SER   (   8-)  Q    4.14
  34 LEU   (  35-)  A    4.12
  78 GLY   (  79-)  A    4.10
2730 VAL   ( 217-)  P    4.10
1340 PRO   (  93-)  F    4.09
 471 ILE   ( 472-)  A    4.09
1733 LYS   (  47-)  L    4.08
1539 ALA   (  32-)  I    4.05
2861 GLY   (  90-)  Q    4.02
1306 GLY   (  59-)  F    4.01
  51 GLN   (  52-)  A    4.00
2653 SER   ( 140-)  P    4.00

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.511

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

  60 HIS   (  61-)  A    7.56
2717 HIS   ( 204-)  P    6.62
  90 ASP   (  91-)  A    5.85
 746 HIS   (   9-)  C    5.55
1294 ASN   (  47-)  F    5.53
 421 ASN   ( 422-)  A    5.45
 968 HIS   ( 231-)  C    5.38
2153 HIS   ( 378-)  N    5.37
2890 GLN   ( 119-)  Q    5.35
2492 HIS   ( 204-)  O    5.22
3089 ASN   (  66-)  S    5.19
 215 ASN   ( 216-)  A    4.96
2469 GLN   ( 181-)  O    4.86
2008 HIS   ( 233-)  N    4.80
 693 GLN   ( 181-)  B    4.66
2449 HIS   ( 161-)  O    4.56
 370 TYR   ( 371-)  A    4.49
  39 GLU   (  40-)  A    4.46
 377 HIS   ( 378-)  A    4.43
2271 ASN   ( 496-)  N    4.39
 773 HIS   (  36-)  C    4.27
2584 HIS   (  71-)  P    4.22
1728 HIS   (  42-)  L    4.20
 963 HIS   ( 226-)  C    4.16
1866 ASP   (  91-)  N    4.16
1335 HIS   (  88-)  F    4.14
 226 ASP   ( 227-)  A    4.12
2139 ASP   ( 364-)  N    4.10
2154 TYR   ( 379-)  N    4.09

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

2015 HIS   ( 240-)  N      CB   5.49
 239 HIS   ( 240-)  A      CB   4.89
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -0.947

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.

3117 HIS   (  94-)  S    -3.3
1431 ILE   (   8-)  H    -2.9
3207 ILE   (   8-)  U    -2.9
2745 HIS   ( 232-)  P    -2.8
2321 LEU   (  33-)  O    -2.8
 545 LEU   (  33-)  B    -2.8
 572 GLU   (  60-)  B    -2.7
1903 VAL   ( 128-)  N    -2.7
1353 HIS   (   8-)  G    -2.6
3076 THR   (  53-)  S    -2.6
1179 LEU   (  41-)  E    -2.6
2348 GLU   (  60-)  O    -2.6
 217 THR   ( 218-)  A    -2.6
3037 THR   (  14-)  S    -2.5
2955 LEU   (  41-)  R    -2.5
 127 VAL   ( 128-)  A    -2.5
1775 LYS   (  42-)  M    -2.5
 969 HIS   ( 232-)  C    -2.5
1432 LYS   (   9-)  H    -2.4
3119 LEU   (  96-)  S    -2.4
3290 PRO   (   7-)  V    -2.4
3360 ARG   (   4-)  W    -2.4
1434 TYR   (  11-)  H    -2.4
1385 GLY   (  40-)  G    -2.4
3129 HIS   (   8-)  T    -2.3
And so on for a total of 66 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.

  80 TRP   (  81-)  A  omega poor
 118 GLU   ( 119-)  A  Poor phi/psi
 122 GLY   ( 123-)  A  omega poor
 123 THR   ( 124-)  A  omega poor
 129 PRO   ( 130-)  A  PRO omega poor
 139 GLY   ( 140-)  A  omega poor
 168 ILE   ( 169-)  A  omega poor
 215 ASN   ( 216-)  A  Poor phi/psi
 286 VAL   ( 287-)  A  omega poor
 288 ALA   ( 289-)  A  omega poor
 316 GLY   ( 317-)  A  omega poor
 330 ASN   ( 331-)  A  omega poor
 368 ASP   ( 369-)  A  Poor phi/psi
 378 TYR   ( 379-)  A  omega poor
 438 ARG   ( 439-)  A  Poor phi/psi
 486 LEU   ( 487-)  A  Poor phi/psi
 493 TRP   ( 494-)  A  omega poor
 497 CYS   ( 498-)  A  PRO omega poor
 504 PHE   ( 505-)  A  Poor phi/psi
 505 GLU   ( 506-)  A  omega poor
 517 MET   (   5-)  B  Poor phi/psi
 528 ILE   (  16-)  B  omega poor
 530 GLU   (  18-)  B  omega poor
 544 PHE   (  32-)  B  omega poor
 548 SER   (  36-)  B  omega poor
And so on for a total of 173 lines.

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

1924 SER   ( 149-)  N    0.35
2368 SER   (  80-)  O    0.35
1372 SER   (  27-)  G    0.35
2054 SER   ( 279-)  N    0.35
 592 SER   (  80-)  B    0.36
 932 SER   ( 195-)  C    0.36
1876 SER   ( 101-)  N    0.36
1809 SER   (  34-)  N    0.36
 100 SER   ( 101-)  A    0.36
 306 SER   ( 307-)  A    0.36
2030 SER   ( 255-)  N    0.36
 278 SER   ( 279-)  A    0.36
 841 SER   ( 104-)  C    0.36
2017 GLU   ( 242-)  N    0.36
2617 SER   ( 104-)  P    0.36
 155 SER   ( 156-)  A    0.37
 361 SER   ( 362-)  A    0.37
3269 SER   (  70-)  U    0.38
 548 SER   (  36-)  B    0.39
3311 SER   (  28-)  V    0.40
 254 SER   ( 255-)  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!

   8 SER   (   9-)  A      0
   9 THR   (  10-)  A      0
  11 HIS   (  12-)  A      0
  40 LEU   (  41-)  A      0
  42 GLN   (  43-)  A      0
  43 PRO   (  44-)  A      0
  45 THR   (  46-)  A      0
  46 LEU   (  47-)  A      0
  47 LEU   (  48-)  A      0
  50 ASP   (  51-)  A      0
  66 PHE   (  67-)  A      0
  67 PHE   (  68-)  A      0
  68 MET   (  69-)  A      0
  73 MET   (  74-)  A      0
  77 PHE   (  78-)  A      0
  81 LEU   (  82-)  A      0
  82 VAL   (  83-)  A      0
  89 PRO   (  90-)  A      0
  91 MET   (  92-)  A      0
  93 PHE   (  94-)  A      0
 116 MET   ( 117-)  A      0
 117 VAL   ( 118-)  A      0
 118 GLU   ( 119-)  A      0
 119 ALA   ( 120-)  A      0
 121 ALA   ( 122-)  A      0
And so on for a total of 1097 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!

1470 GLY   (  47-)  H   2.10   80
3161 GLY   (  40-)  T   2.04   17
3246 GLY   (  47-)  U   1.82   80
1468 ALA   (  45-)  H   1.69   50

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...

1341 HIS   (  94-)  F   1.97

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. 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]

  43 PRO   (  44-)  A    0.19 LOW
 105 PRO   ( 106-)  A    0.49 HIGH
 106 PRO   ( 107-)  A    0.14 LOW
 172 PRO   ( 173-)  A    0.45 HIGH
 221 PRO   ( 222-)  A    0.02 LOW
 335 PRO   ( 336-)  A    0.03 LOW
 436 PRO   ( 437-)  A    0.52 HIGH
 678 PRO   ( 166-)  B    0.46 HIGH
 688 PRO   ( 176-)  B    0.46 HIGH
 727 PRO   ( 215-)  B    0.49 HIGH
 754 PRO   (  17-)  C    0.49 HIGH
 810 PRO   (  73-)  C    0.53 HIGH
 847 PRO   ( 110-)  C    0.46 HIGH
 854 PRO   ( 117-)  C    0.03 LOW
 860 PRO   ( 123-)  C    0.45 HIGH
 863 PRO   ( 126-)  C    0.12 LOW
 867 PRO   ( 130-)  C    0.50 HIGH
1020 PRO   (  25-)  D    0.15 LOW
1181 PRO   (  43-)  E    0.46 HIGH
1183 PRO   (  45-)  E    0.46 HIGH
1254 PRO   (   7-)  F    0.19 LOW
1297 PRO   (  50-)  F    0.03 LOW
1330 PRO   (  83-)  F    0.20 LOW
1340 PRO   (  93-)  F    0.19 LOW
1394 PRO   (  49-)  G    0.16 LOW
1438 PRO   (  15-)  H    0.48 HIGH
1677 PRO   (  44-)  K    0.11 LOW
1683 PRO   (  50-)  K    0.49 HIGH
1819 PRO   (  44-)  N    0.13 LOW
1870 PRO   (  95-)  N    0.17 LOW
1881 PRO   ( 106-)  N    0.52 HIGH
1949 PRO   ( 174-)  N    0.06 LOW
1997 PRO   ( 222-)  N    0.20 LOW
2042 PRO   ( 267-)  N    0.46 HIGH
2283 PRO   ( 508-)  N    0.11 LOW
2357 PRO   (  69-)  O    0.47 HIGH
2623 PRO   ( 110-)  P    0.52 HIGH
2630 PRO   ( 117-)  P    0.06 LOW
2631 PRO   ( 118-)  P    0.48 HIGH
2636 PRO   ( 123-)  P    0.48 HIGH
2785 PRO   (  14-)  Q    0.52 HIGH
3059 PRO   (  36-)  S    0.18 LOW
3073 PRO   (  50-)  S    0.11 LOW
3106 PRO   (  83-)  S    0.09 LOW
3147 PRO   (  26-)  T    0.51 HIGH
3214 PRO   (  15-)  U    0.14 LOW
3469 PRO   (   7-)  Y    0.45 HIGH
3498 PRO   (  36-)  Y    0.46 HIGH

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].

 173 PRO   ( 174-)  A   103.7 envelop C-beta (108 degrees)
1018 PRO   (  23-)  D  -115.1 envelop C-gamma (-108 degrees)
1101 PRO   ( 106-)  D  -113.4 envelop C-gamma (-108 degrees)
1698 PRO   (  12-)  L   -64.4 envelop C-beta (-72 degrees)
2016 PRO   ( 241-)  N   101.5 envelop C-beta (108 degrees)
2111 PRO   ( 336-)  N  -120.6 half-chair C-delta/C-gamma (-126 degrees)
2621 PRO   ( 108-)  P  -112.7 envelop C-gamma (-108 degrees)
2794 PRO   (  23-)  Q  -116.2 envelop C-gamma (-108 degrees)
2877 PRO   ( 106-)  Q   -60.1 half-chair C-beta/C-alpha (-54 degrees)
2901 PRO   ( 130-)  Q   -25.7 half-chair C-alpha/N (-18 degrees)
2959 PRO   (  45-)  R   100.8 envelop C-beta (108 degrees)
3220 PRO   (  21-)  U   -61.5 half-chair C-beta/C-alpha (-54 degrees)
3290 PRO   (   7-)  V    -6.3 envelop N (0 degrees)
3453 PRO   (  44-)  X    -2.1 envelop N (0 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

2015 HIS   ( 240-)  N      NE2  <->  2019 TYR   ( 244-)  N      CE2  1.77    1.33  INTRA BL
 239 HIS   ( 240-)  A      NE2  <->   243 TYR   ( 244-)  A      CE2  1.73    1.37  INTRA BL
2290 ALA   (   2-)  O      N    <->  3632 FME   (   1-)  O      C    1.38    1.32  INTRA BL
3285 THR   (   2-)  V      N    <->  3631 SAC   (   1-)  V      C    1.36    1.34  INTRA BF
 885 HIS   ( 148-)  C      NE2  <->  3586 UNX   ( 262-)  C     UNK   0.99    2.11  INTRA BF
2661 HIS   ( 148-)  P      NE2  <->  3615 UNX   ( 262-)  P     UNK   0.97    2.13  INTRA BF
2745 HIS   ( 232-)  P      NE2  <->  3615 UNX   ( 262-)  P     UNK   0.93    2.17  INTRA BF
2015 HIS   ( 240-)  N      CE1  <->  2019 TYR   ( 244-)  N      CE2  0.91    2.29  INTRA BL
 969 HIS   ( 232-)  C      NE2  <->  3586 UNX   ( 262-)  C     UNK   0.90    2.20  INTRA BF
 239 HIS   ( 240-)  A      CE1  <->   243 TYR   ( 244-)  A      CE2  0.87    2.33  INTRA BL
2290 ALA   (   2-)  O      CA   <->  3632 FME   (   1-)  O      C    0.79    2.41  INTRA BL
2015 HIS   ( 240-)  N      CD2  <->  2019 TYR   ( 244-)  N      CE2  0.78    2.42  INTRA BL
 239 HIS   ( 240-)  A      CD2  <->   243 TYR   ( 244-)  A      CE2  0.78    2.42  INTRA BL
2015 HIS   ( 240-)  N      NE2  <->  2019 TYR   ( 244-)  N      CD2  0.75    2.35  INTRA BL
3075 ILE   (  52-)  S      O    <->  3117 HIS   (  94-)  S      CE1  0.73    2.07  INTRA BF
3285 THR   (   2-)  V      CA   <->  3631 SAC   (   1-)  V      C    0.73    2.47  INTRA BF
3615 UNX   ( 262-)  P     UNK   <->  3648 HOH   (3259 )  P      O    0.72    2.08  INTRA BF
2015 HIS   ( 240-)  N      NE2  <->  2019 TYR   ( 244-)  N      CZ   0.66    2.44  INTRA BL
2749 GLU   ( 236-)  P      OE2  <->  3615 UNX   ( 262-)  P     UNK   0.65    2.15  INTRA BF
 239 HIS   ( 240-)  A      NE2  <->   243 TYR   ( 244-)  A      CD2  0.65    2.45  INTRA BL
1517 ARG   (  10-)  I      NH2  <->  3594 PSC   ( 229-)  B      C07  0.65    2.45  INTRA BF
 973 GLU   ( 236-)  C      OE2  <->  3586 UNX   ( 262-)  C     UNK   0.63    2.17  INTRA BF
1706 ARG   (  20-)  L      NH2  <->  3601 TGL   ( 522-)  L      CC3  0.63    2.47  INTRA BF
 239 HIS   ( 240-)  A      NE2  <->   243 TYR   ( 244-)  A      CZ   0.62    2.48  INTRA BL
3152 CYS   (  31-)  T      SG   <->  3625 CDL   (1269-)  T      C55  0.61    2.79  INTRA BF
And so on for a total of 496 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

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.

 625 TYR   ( 113-)  B      -6.69
3283 LYS   (  84-)  U      -6.47
1507 LYS   (  84-)  H      -6.38
3551 LYS   (  42-)  Z      -6.14
1342 GLN   (  95-)  F      -6.14
1353 HIS   (   8-)  G      -6.05
 571 GLN   (  59-)  B      -6.04
1383 HIS   (  38-)  G      -6.04
 859 HIS   ( 122-)  C      -6.01
3129 HIS   (   8-)  T      -5.97
2347 GLN   (  59-)  O      -5.94
1389 ARG   (  44-)  G      -5.90
2401 TYR   ( 113-)  O      -5.87
1099 TYR   ( 104-)  D      -5.85
2635 HIS   ( 122-)  P      -5.85
3051 GLN   (  28-)  S      -5.84
3118 GLN   (  95-)  S      -5.83
3168 PHE   (  47-)  T      -5.82
1096 HIS   ( 101-)  D      -5.70
1818 GLN   (  43-)  N      -5.70
1515 GLN   (   8-)  I      -5.65
2875 TYR   ( 104-)  Q      -5.64
1275 GLN   (  28-)  F      -5.59
1272 ARG   (  25-)  F      -5.58
3291 GLN   (   8-)  V      -5.58
And so on for a total of 87 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.

1386 HIS   (  41-)  G      1389 - ARG     44- ( G)         -5.42
1689 TYR   (   3-)  L      1691 - GLU      5- ( L)         -4.88
3162 HIS   (  41-)  T      3165 - ARG     44- ( T)         -5.27
3465 TYR   (   3-)  Y      3467 - GLU      5- ( Y)         -4.68

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

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: C

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: D

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: E

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: F

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: G

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: H

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: I

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: J

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: K

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: L

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: M

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: N

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: O

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: P

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: Q

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: R

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: S

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: T

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: U

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: V

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: W

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: X

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: Y

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: Z

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.

3208 LYS   (   9-)  U   -2.72
3475 PHE   (  13-)  Y   -2.69
  90 ASP   (  91-)  A   -2.58
1475 VAL   (  52-)  H   -2.55
 849 LEU   ( 112-)  C   -2.54
 290 HIS   ( 291-)  A   -2.54
2625 LEU   ( 112-)  P   -2.52
1012 VAL   (  17-)  D   -2.51
2066 HIS   ( 291-)  N   -2.51

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.

 285 ILE   ( 286-)  A     -  288 ALA   ( 289-)  A        -1.58
1397 HIS   (  52-)  G     - 1400 ILE   (  55-)  G        -1.66
2061 ILE   ( 286-)  N     - 2064 ALA   ( 289-)  N        -1.57

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: Z

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.

3633 HOH   (2458 )  A      O
3633 HOH   (4001 )  A      O
3633 HOH   (4275 )  A      O
3633 HOH   (4341 )  A      O
3633 HOH   (4545 )  A      O
3633 HOH   (4691 )  A      O
3633 HOH   (4723 )  A      O
3634 HOH   (4570 )  B      O
3635 HOH   (4316 )  C      O
3635 HOH   (4624 )  C      O
3635 HOH   (4671 )  C      O
3635 HOH   (4710 )  C      O
3635 HOH   (4791 )  C      O
3636 HOH   (4517 )  D      O
3636 HOH   (4662 )  D      O
3638 HOH   (4397 )  F      O
3638 HOH   (4699 )  F      O
3639 HOH   (4415 )  G      O
3639 HOH   (4519 )  G      O
3639 HOH   (4580 )  G      O
3639 HOH   (4637 )  G      O
3640 HOH   (2170 )  H      O
3641 HOH   (4746 )  I      O
3642 HOH   (4651 )  J      O
3642 HOH   (4799 )  J      O
And so on for a total of 52 lines.

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.

 177 GLN   ( 178-)  A
 179 GLN   ( 180-)  A
 522 GLN   (  10-)  B
 693 GLN   ( 181-)  B
 787 ASN   (  50-)  C
 805 GLN   (  68-)  C
 967 ASN   ( 230-)  C
1027 ASN   (  32-)  D
1032 GLN   (  37-)  D
1232 ASN   (  94-)  E
1379 ASN   (  34-)  G
1421 ASN   (  76-)  G
1446 GLN   (  23-)  H
1454 GLN   (  31-)  H
1515 GLN   (   8-)  I
1668 GLN   (  35-)  K
1953 GLN   ( 178-)  N
1955 GLN   ( 180-)  N
2298 GLN   (  10-)  O
2516 HIS   (   3-)  P
2563 ASN   (  50-)  P
2581 GLN   (  68-)  P
2589 GLN   (  76-)  P
2635 HIS   ( 122-)  P
2800 HIS   (  29-)  Q
2808 GLN   (  37-)  Q
2880 HIS   ( 109-)  Q
3103 GLN   (  80-)  S
3117 HIS   (  94-)  S
3197 ASN   (  76-)  T
3230 GLN   (  31-)  U
3291 GLN   (   8-)  V
3353 GLN   (  70-)  V
3444 GLN   (  35-)  X

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.

   3 ASN   (   4-)  A      N
   4 ARG   (   5-)  A      N
  37 ARG   (  38-)  A      NH1
  42 GLN   (  43-)  A      N
  84 LEU   (  85-)  A      N
  95 ARG   (  96-)  A      N
  95 ARG   (  96-)  A      NE
  95 ARG   (  96-)  A      NH2
  96 MET   (  97-)  A      N
 125 TRP   ( 126-)  A      N
 125 TRP   ( 126-)  A      NE1
 213 ASN   ( 214-)  A      ND2
 215 ASN   ( 216-)  A      ND2
 239 HIS   ( 240-)  A      NE2
 265 GLU   ( 266-)  A      N
 288 ALA   ( 289-)  A      N
 300 THR   ( 301-)  A      N
 334 SER   ( 335-)  A      OG
 367 HIS   ( 368-)  A      ND1
 370 TYR   ( 371-)  A      OH
 381 SER   ( 382-)  A      OG
 404 LEU   ( 405-)  A      N
 421 ASN   ( 422-)  A      ND2
 427 GLN   ( 428-)  A      NE2
 437 ARG   ( 438-)  A      NH2
And so on for a total of 225 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.

 150 HIS   ( 151-)  A      ND1
 241 GLU   ( 242-)  A      OE1
 241 GLU   ( 242-)  A      OE2
 363 ASP   ( 364-)  A      OD1
 427 GLN   ( 428-)  A      OE1
 522 GLN   (  10-)  B      OE1
 574 GLU   (  62-)  B      OE1
 746 HIS   (   9-)  C      ND1
 827 GLU   (  90-)  C      OE1
 840 HIS   ( 103-)  C      ND1
 865 GLU   ( 128-)  C      OE2
 870 ASN   ( 133-)  C      OD1
 944 HIS   ( 207-)  C      NE2
1352 ASP   (   7-)  G      OD2
1353 HIS   (   8-)  G      ND1
1926 HIS   ( 151-)  N      ND1
2017 GLU   ( 242-)  N      OE1
2017 GLU   ( 242-)  N      OE2
2139 ASP   ( 364-)  N      OD1
2203 GLN   ( 428-)  N      OE1
2298 GLN   (  10-)  O      OE1
2350 GLU   (  62-)  O      OE1
2584 HIS   (  71-)  P      NE2
2603 GLU   (  90-)  P      OE1
2616 HIS   ( 103-)  P      ND1
2646 ASN   ( 133-)  P      OD1
2674 GLN   ( 161-)  P      OE1
2693 GLU   ( 180-)  P      OE2
2720 HIS   ( 207-)  P      NE2
2883 GLU   ( 112-)  Q      OE1
2992 HIS   (  78-)  R      ND1
2994 GLU   (  80-)  R      OE2
3128 ASP   (   7-)  T      OD2
3129 HIS   (   8-)  T      ND1

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: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

3579  MG   ( 518-)  B     0.81   1.39 Scores about as good as CA
3580  NA   ( 519-)  A     1.21   0.99 Scores about as good as CA
3607  MG   ( 518-)  O     0.75   1.27 Scores about as good as CA
3608  NA   ( 519-)  N     1.27   1.05 Scores about as good as CA

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

3633 HOH   (4105 )  A      O  0.97  K  4 NCS 1/1
3641 HOH   (2418 )  I      O  1.08  K  4 NCS 1/1
3650 HOH   (4293 )  R      O  1.00  K  4 NCS 1/1

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.

  49 ASP   (  50-)  A   H-bonding suggests Asn; but Alt-Rotamer
 211 ASP   ( 212-)  A   H-bonding suggests Asn; but Alt-Rotamer
 523 ASP   (  11-)  B   H-bonding suggests Asn
 572 GLU   (  60-)  B   H-bonding suggests Gln; but Alt-Rotamer
1107 GLU   ( 112-)  D   H-bonding suggests Gln
1352 ASP   (   7-)  G   H-bonding suggests Asn
1458 ASP   (  35-)  H   H-bonding suggests Asn; but Alt-Rotamer
1497 ASP   (  74-)  H   H-bonding suggests Asn; but Alt-Rotamer
1987 ASP   ( 212-)  N   H-bonding suggests Asn; but Alt-Rotamer
2348 GLU   (  60-)  O   H-bonding suggests Gln; but Alt-Rotamer
2624 GLU   ( 111-)  P   H-bonding suggests Gln
3128 ASP   (   7-)  T   H-bonding suggests Asn
3164 GLU   (  43-)  T   H-bonding suggests Gln
3234 ASP   (  35-)  U   H-bonding suggests Asn; but Alt-Rotamer
3272 ASP   (  73-)  U   H-bonding suggests Asn; but Alt-Rotamer
3273 ASP   (  74-)  U   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.613
  2nd generation packing quality :  -1.253
  Ramachandran plot appearance   :  -0.947
  chi-1/chi-2 rotamer normality  :  -1.742
  Backbone conformation          :   0.229

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.302
  Bond angles                    :   1.107
  Omega angle restraints         :   1.225
  Side chain planarity           :   1.702
  Improper dihedral distribution :   1.486
  B-factor distribution          :   0.634
  Inside/Outside distribution    :   1.137

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 : 2.05


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.302
  Bond angles                    :   1.107
  Omega angle restraints         :   1.225
  Side chain planarity           :   1.702
  Improper dihedral distribution :   1.486
  B-factor distribution          :   0.634
  Inside/Outside distribution    :   1.137
==============

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.