WHAT IF Check report

This file was created 2011-12-18 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 pdb1v54.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    = 182.590  B   = 205.140  C    = 178.250
    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    = 182.590  B   = 205.140  C    = 178.250
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 178.250  B   = 182.590  C    = 205.140
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 178.250  B   = 182.590  C    = 205.140
    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 : 0.114
CA-only RMS fit for the two chains : 0.036

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 : 0.310
CA-only RMS fit for the two chains : 0.062

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 : 0.411
CA-only RMS fit for the two chains : 0.063

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 : 0.443
CA-only RMS fit for the two chains : 0.068

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: 433439.906
Volume of the Unit Cell V= 6676053.5
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 7.701
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.070 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= 3.851
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
3578 HEA   ( 515-)  A  -         Atom types
3579 HEA   ( 516-)  A  -         Atom types
3580 TGL   (3521-)  A  -
3581 PGV   (3266-)  C  -         OK
3582 PGV   (3524-)  A  -         OK
3583 CUA   ( 228-)  B  -         Atom types
3584 CHD   (4085-)  T  -         OK
3585 CHD   (3525-)  A  -         OK
3586 CHD   (3271-)  C  -         OK
3587 CDL   (3270-)  C  -
3588 PEK   (3264-)  C  -         OK
3589 PEK   (3265-)  C  -         OK
3590 PGV   (3267-)  C  -         OK
3591 PGV   (3268-)  C  -         OK
3593 TGL   (3523-)  A  -
3594 PSC   (3230-)  B  -         OK
3596 CDL   (3269-)  G  -
3597 PEK   (4263-)  P  -         OK
3598 CHD   (3060-)  J  -         OK
3599 TGL   (3522-)  L  -
3600 DMU   (3526-)  M  -         OK
3604 HEA   ( 515-)  N  -         Atom types
3605 HEA   ( 516-)  N  -         Atom types
3606 TGL   (4521-)  N  -
3607 TGL   (4522-)  Y  -
3608 PGV   (4266-)  P  -         OK
3609 PGV   (4524-)  N  -         OK
3610 CHD   (3085-)  G  -         OK
3611 CUA   ( 228-)  O  -         Atom types
3612 CHD   (4525-)  N  -         OK
3613 CHD   (4271-)  P  -         OK
3614 CDL   (4270-)  P  -
3615 PEK   (4264-)  P  -         OK
3616 PEK   (4265-)  T  -         OK
3617 PGV   (4267-)  P  -         OK
3619 TGL   (4523-)  N  -
3621 CDL   (4269-)  T  -
3622 DMU   (4526-)  Z  -         OK
3623 CHD   (4060-)  W  -         OK
3624 PEK   (3263-)  C  -         OK
3625 PGV   (4268-)  P  -         OK
3626 PSC   (4230-)  O  -         OK
3627 SAC   (   1-)  V  -         OK
3628 FME   (   1-)  O  -         OK

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

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

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

   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 3628 FME   (   1-)  O  -   C
3285 THR   (   2-)  V  -   N   bound to 3627 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.

3576  MG   (3518-)  B  -
3602  MG   (4518-)  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
3132 TPO   (  11-)  T

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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
 370 TYR   ( 371-)  A
 439 TYR   ( 440-)  A
 501 TYR   ( 502-)  A
 515 TYR   (   3-)  B
 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
1479 TYR   (  56-)  H
1542 TYR   (  35-)  I
And so on for a total of 55 lines.

Warning: Phenylalanine convention problem

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

  77 PHE   (  78-)  A
 108 PHE   ( 109-)  A
 163 PHE   ( 164-)  A
 218 PHE   ( 219-)  A
 236 PHE   ( 237-)  A
 250 PHE   ( 251-)  A
 267 PHE   ( 268-)  A
 320 PHE   ( 321-)  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
 718 PHE   ( 206-)  B
 804 PHE   (  67-)  C
 831 PHE   (  94-)  C
 910 PHE   ( 173-)  C
 934 PHE   ( 197-)  C
 935 PHE   ( 198-)  C
 970 PHE   ( 233-)  C
 981 PHE   ( 244-)  C
And so on for a total of 104 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
  49 ASP   (  50-)  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
 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 71 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
 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
 917 GLU   ( 180-)  C
 920 GLU   ( 183-)  C
1004 GLU   (   9-)  D
1037 GLU   (  42-)  D
1050 GLU   (  55-)  D
And so on for a total of 106 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.

  79 ASN   (  80-)  A      CG   OD1   1.33    5.0
  79 ASN   (  80-)  A      CG   ND2   1.23   -4.6
 375 HIS   ( 376-)  A      CG   CD2   1.40    4.2
 375 HIS   ( 376-)  A      ND1  CE1   1.37    4.3
1836 HIS   (  61-)  N      CG   CD2   1.40    4.1
1855 ASN   (  80-)  N      CG   OD1   1.33    4.8
1855 ASN   (  80-)  N      CG   ND2   1.22   -4.9

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.449
RMS-deviation in bond distances: 0.010

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

 |  0.998203 -0.000197 -0.000093|
 | -0.000197  0.998737 -0.000145|
 | -0.000093 -0.000145  0.998401|
Proposed new scale matrix

 |  0.005487  0.000001  0.000000|
 |  0.000000  0.004881  0.000000|
 |  0.000000  0.000000  0.005619|
With corresponding cell

    A    = 182.254  B   = 204.869  C    = 177.968
    Alpha=  90.002  Beta=  90.002  Gamma=  90.012

The CRYST1 cell dimensions

    A    = 182.590  B   = 205.140  C    = 178.250
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 298.657
(Under-)estimated Z-score: 12.737

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.

  60 HIS   (  61-)  A      CA   CB   CG  118.21    4.4
  60 HIS   (  61-)  A      CB   CG   ND1 131.02    6.3
  60 HIS   (  61-)  A      CB   CG   CD2 119.19   -7.6
 128 TYR   ( 129-)  A      C    CA   CB  102.44   -4.0
 330 ASN   ( 331-)  A      N    CA   C    99.64   -4.1
 377 HIS   ( 378-)  A      CA   CB   CG  107.20   -6.6
 377 HIS   ( 378-)  A      CB   CG   CD2 123.56   -4.3
 434 GLY   ( 435-)  A      N    CA   C   125.12    4.4
 506 GLU   ( 507-)  A      N    CA   C    99.68   -4.1
 564 HIS   (  52-)  B      CG   ND1  CE1 109.61    4.0
 616 TRP   ( 104-)  B     -CA  -C    N   103.55   -6.3
 616 TRP   ( 104-)  B     -C    N    CA  133.94    6.8
 616 TRP   ( 104-)  B      N    CA   C   125.78    5.2
 673 HIS   ( 161-)  B      N    CA   C    99.97   -4.0
1128 GLY   ( 133-)  D      N    CA   C   127.17    5.1
1180 VAL   (  42-)  E      N    CA   C    99.29   -4.3
1340 PRO   (  93-)  F      N    CA   C   126.90    6.0
1341 HIS   (  94-)  F     -C    N    CA  130.20    4.7
1341 HIS   (  94-)  F      N    CA   C   127.18    5.7
1341 HIS   (  94-)  F      CG   ND1  CE1 109.68    4.1
1342 GLN   (  95-)  F     -C    N    CA  130.72    5.0
1351 GLY   (   6-)  G      N    CA   C   124.32    4.1
1434 TYR   (  11-)  H     -C    N    CA  129.34    4.2
1836 HIS   (  61-)  N      CB   CG   ND1 127.72    4.1
1836 HIS   (  61-)  N      CD2  CG   ND1 111.67    5.6
1836 HIS   (  61-)  N      CB   CG   CD2 120.54   -6.6
1904 TYR   ( 129-)  N      C    CA   CB  102.35   -4.1
1905 PRO   ( 130-)  N      N    CA   C   101.06   -4.3
2106 ASN   ( 331-)  N      N    CA   C    99.11   -4.3
2153 HIS   ( 378-)  N      CA   CB   CG  105.44   -8.4
2153 HIS   ( 378-)  N      CD2  CG   ND1 110.34    4.2
2210 GLY   ( 435-)  N      N    CA   C   124.97    4.3
2392 TRP   ( 104-)  O     -CA  -C    N   104.40   -5.9
2392 TRP   ( 104-)  O     -C    N    CA  132.89    6.2
2392 TRP   ( 104-)  O      N    CA   C   125.23    5.0
2904 GLY   ( 133-)  Q      N    CA   C   126.68    4.9
2956 VAL   (  42-)  R      N    CA   C    97.68   -4.8
2992 HIS   (  78-)  R      CG   ND1  CE1 109.66    4.1
3116 PRO   (  93-)  S      N    CA   C   125.95    5.7
3117 HIS   (  94-)  S     -C    N    CA  134.09    6.9
3117 HIS   (  94-)  S      N    CA   C   127.89    6.0
3117 HIS   (  94-)  S      CG   ND1  CE1 110.52    4.9
3118 GLN   (  95-)  S     -C    N    CA  129.84    4.5
3138 ARG   (  17-)  T      CB   CG   CD  104.39   -4.9

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
  49 ASP   (  50-)  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
 572 GLU   (  60-)  B
 574 GLU   (  62-)  B
 600 ASP   (  88-)  B
 621 GLU   ( 109-)  B
 626 GLU   ( 114-)  B
 627 ASP   ( 115-)  B
And so on for a total of 181 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.

 615 GLN   ( 103-)  B      C     -8.4   -12.89     0.15
 616 TRP   ( 104-)  B      CA    -7.9    20.63    34.04
2391 GLN   ( 103-)  O      C     -8.1   -12.55     0.15
2392 TRP   ( 104-)  O      CA    -6.6    22.89    34.04
3117 HIS   (  94-)  S      CA    -6.2    22.71    34.11
The average deviation= 1.085

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.

1259 GLN   (  12-)  F    6.47
3035 GLN   (  12-)  S    6.22
  81 LEU   (  82-)  A    6.18
1857 LEU   (  82-)  N    5.92
 616 TRP   ( 104-)  B    5.52
1340 PRO   (  93-)  F    5.50
 424 PHE   ( 425-)  A    5.48
2200 PHE   ( 425-)  N    5.41
3117 HIS   (  94-)  S    5.40
3444 GLN   (  35-)  X    5.32
2392 TRP   ( 104-)  O    5.31
 169 ASN   ( 170-)  A    5.29
1341 HIS   (  94-)  F    5.17
3116 PRO   (  93-)  S    5.13
 213 ASN   ( 214-)  A    5.05
1831 VAL   (  56-)  N    4.97
1128 GLY   ( 133-)  D    4.88
1989 ASN   ( 214-)  N    4.86
2956 VAL   (  42-)  R    4.78
1668 GLN   (  35-)  K    4.74
3482 ARG   (  20-)  Y    4.71
2904 GLY   ( 133-)  Q    4.70
3262 LEU   (  63-)  U    4.66
2223 THR   ( 448-)  N    4.62
1905 PRO   ( 130-)  N    4.62
And so on for a total of 61 lines.

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.

2151 HIS   ( 376-)  N    4.24

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  12.10
 239 HIS   ( 240-)  A      CB  12.10
2153 HIS   ( 378-)  N      CB   4.11
1877 PHE   ( 102-)  N      CB   4.03
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -0.046

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    -3.2
1431 ILE   (   8-)  H    -2.9
3207 ILE   (   8-)  U    -2.9
 616 TRP   ( 104-)  B    -2.9
2392 TRP   ( 104-)  O    -2.8
1444 PRO   (  21-)  H    -2.8
2745 HIS   ( 232-)  P    -2.7
 969 HIS   ( 232-)  C    -2.7
3220 PRO   (  21-)  U    -2.6
2955 LEU   (  41-)  R    -2.5
1903 VAL   ( 128-)  N    -2.5
 127 VAL   ( 128-)  A    -2.5
2936 PRO   (  22-)  R    -2.5
1179 LEU   (  41-)  E    -2.5
3076 THR   (  53-)  S    -2.5
1993 THR   ( 218-)  N    -2.5
1436 THR   (  13-)  H    -2.5
3119 LEU   (  96-)  S    -2.4
1342 GLN   (  95-)  F    -2.4
1353 HIS   (   8-)  G    -2.4
1775 LYS   (  42-)  M    -2.3
 246 ILE   ( 247-)  A    -2.3
2022 ILE   ( 247-)  N    -2.3
1261 THR   (  14-)  F    -2.3
1343 LEU   (  96-)  F    -2.3
And so on for a total of 70 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.

  90 ASP   (  91-)  A  Poor phi/psi
 118 GLU   ( 119-)  A  Poor phi/psi
 129 PRO   ( 130-)  A  PRO omega poor
 213 ASN   ( 214-)  A  Poor phi/psi
 215 ASN   ( 216-)  A  Poor phi/psi
 333 TRP   ( 334-)  A  Poor phi/psi
 368 ASP   ( 369-)  A  Poor phi/psi
 438 ARG   ( 439-)  A  Poor phi/psi
 478 LYS   ( 479-)  A  Poor phi/psi
 482 LEU   ( 483-)  A  Poor phi/psi
 486 LEU   ( 487-)  A  Poor phi/psi
 497 CYS   ( 498-)  A  PRO omega poor
 504 PHE   ( 505-)  A  Poor phi/psi
 517 MET   (   5-)  B  Poor phi/psi
 571 GLN   (  59-)  B  Poor phi/psi
 603 ASN   (  91-)  B  Poor phi/psi
 604 ASN   (  92-)  B  Poor phi/psi
 616 TRP   ( 104-)  B  Poor phi/psi
 617 TYR   ( 105-)  B  Poor phi/psi
 647 LEU   ( 135-)  B  Poor phi/psi
 659 GLU   ( 147-)  B  Poor phi/psi
 670 ASP   ( 158-)  B  Poor phi/psi
 775 ASN   (  38-)  C  Poor phi/psi
 853 TRP   ( 116-)  C  PRO omega poor
 865 GLU   ( 128-)  C  Poor phi/psi
And so on for a total of 87 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.

1883 SER   ( 108-)  N    0.36
 841 SER   ( 104-)  C    0.36
2030 SER   ( 255-)  N    0.36
2617 SER   ( 104-)  P    0.36
2807 SER   (  36-)  Q    0.36
 100 SER   ( 101-)  A    0.37
 107 SER   ( 108-)  A    0.37
 254 SER   ( 255-)  A    0.37
1876 SER   ( 101-)  N    0.39
 155 SER   ( 156-)  A    0.40
1931 SER   ( 156-)  N    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 THR   (  10-)  A      0
  11 HIS   (  12-)  A      0
  43 PRO   (  44-)  A      0
  45 THR   (  46-)  A      0
  47 LEU   (  48-)  A      0
  49 ASP   (  50-)  A      0
  66 PHE   (  67-)  A      0
  67 PHE   (  68-)  A      0
  73 MET   (  74-)  A      0
  88 ALA   (  89-)  A      0
  89 PRO   (  90-)  A      0
  91 MET   (  92-)  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
 123 THR   ( 124-)  A      0
 125 TRP   ( 126-)  A      0
 127 VAL   ( 128-)  A      0
 128 TYR   ( 129-)  A      0
 129 PRO   ( 130-)  A      0
 137 HIS   ( 138-)  A      0
 138 ALA   ( 139-)  A      0
 140 ALA   ( 141-)  A      0
And so on for a total of 1100 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.591

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   2.01   80
3246 GLY   (  47-)  U   2.01   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...

1341 HIS   (  94-)  F   3.37

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]

 266 PRO   ( 267-)  A    0.45 HIGH
 642 PRO   ( 130-)  B    0.45 HIGH
1103 PRO   ( 108-)  D    0.45 HIGH
1160 PRO   (  22-)  E    0.46 HIGH
2292 PRO   (   4-)  O    0.46 HIGH
2418 PRO   ( 130-)  O    0.45 HIGH
2586 PRO   (  73-)  P    0.45 HIGH
2623 PRO   ( 110-)  P    0.47 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].

 314 PRO   ( 315-)  A  -112.1 envelop C-gamma (-108 degrees)
1394 PRO   (  49-)  G    36.1 envelop C-delta (36 degrees)
2016 PRO   ( 241-)  N   100.0 envelop C-beta (108 degrees)
2090 PRO   ( 315-)  N  -116.9 envelop C-gamma (-108 degrees)
3170 PRO   (  49-)  T    49.0 half-chair C-delta/C-gamma (54 degrees)
3220 PRO   (  21-)  U   -60.7 half-chair C-beta/C-alpha (-54 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  1.74    1.36  INTRA BL
 239 HIS   ( 240-)  A      NE2  <->   243 TYR   ( 244-)  A      CE2  1.73    1.37  INTRA BL
2290 ALA   (   2-)  O      N    <->  3628 FME   (   1-)  O      C    1.37    1.33  INTRA B3
3285 THR   (   2-)  V      N    <->  3627 SAC   (   1-)  V      C    1.37    1.33  INTRA BF
2015 HIS   ( 240-)  N      CE1  <->  2019 TYR   ( 244-)  N      CE2  0.88    2.32  INTRA BL
2015 HIS   ( 240-)  N      NE2  <->  2019 TYR   ( 244-)  N      CD2  0.87    2.23  INTRA BL
 239 HIS   ( 240-)  A      CE1  <->   243 TYR   ( 244-)  A      CE2  0.84    2.36  INTRA BL
 239 HIS   ( 240-)  A      NE2  <->   243 TYR   ( 244-)  A      CD2  0.82    2.28  INTRA BL
2290 ALA   (   2-)  O      CA   <->  3628 FME   (   1-)  O      C    0.76    2.44  INTRA
3285 THR   (   2-)  V      CA   <->  3627 SAC   (   1-)  V      C    0.76    2.44  INTRA BF
2015 HIS   ( 240-)  N      CD2  <->  2019 TYR   ( 244-)  N      CE2  0.70    2.50  INTRA BL
 239 HIS   ( 240-)  A      CD2  <->   243 TYR   ( 244-)  A      CE2  0.70    2.50  INTRA BL
2745 HIS   ( 232-)  P      NE2  <->  3618 UNX   (4262-)  P     UNK   0.67    2.43  INTRA
 885 HIS   ( 148-)  C      NE2  <->  3592 UNX   (3262-)  C     UNK   0.66    2.44  INTRA BF
 969 HIS   ( 232-)  C      NE2  <->  3592 UNX   (3262-)  C     UNK   0.65    2.45  INTRA
2661 HIS   ( 148-)  P      NE2  <->  3618 UNX   (4262-)  P     UNK   0.65    2.45  INTRA
2015 HIS   ( 240-)  N      NE2  <->  2019 TYR   ( 244-)  N      CZ   0.61    2.49  INTRA BL
 239 HIS   ( 240-)  A      NE2  <->   243 TYR   ( 244-)  A      CZ   0.60    2.50  INTRA BL
3117 HIS   (  94-)  S      CD2  <->  3118 GLN   (  95-)  S      N    0.37    2.63  INTRA BF
2015 HIS   ( 240-)  N      CD2  <->  2019 TYR   ( 244-)  N      CD2  0.37    2.83  INTRA BL
2421 LEU   ( 133-)  O      CD1  <->  3628 FME   (   1-)  O      SD   0.36    3.04  INTRA
3348 LYS   (  65-)  V      O    <->  3463 ARG   (  54-)  X      NH2  0.35    2.35  INTRA BF
 377 HIS   ( 378-)  A      NE2  <->  3578 HEA   ( 515-)  A      NC   0.35    2.65  INTRA BL
 239 HIS   ( 240-)  A      CD2  <->   243 TYR   ( 244-)  A      CD2  0.35    2.85  INTRA BL
3482 ARG   (  20-)  Y      NH1  <->  3653 HOH   (1514 )  Y      O    0.34    2.36  INTRA BF
And so on for a total of 302 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      -6.55
1507 LYS   (  84-)  H      -6.49
2401 TYR   ( 113-)  O      -6.41
3283 LYS   (  84-)  U      -6.41
2347 GLN   (  59-)  O      -6.35
 571 GLN   (  59-)  B      -6.23
1342 GLN   (  95-)  F      -6.12
1353 HIS   (   8-)  G      -6.01
1387 ARG   (  42-)  G      -6.00
2875 TYR   ( 104-)  Q      -5.97
3129 HIS   (   8-)  T      -5.97
3118 GLN   (  95-)  S      -5.94
 859 HIS   ( 122-)  C      -5.84
2635 HIS   ( 122-)  P      -5.83
3551 LYS   (  42-)  Z      -5.81
2476 ARG   ( 188-)  O      -5.78
1099 TYR   ( 104-)  D      -5.78
 700 ARG   ( 188-)  B      -5.77
1775 LYS   (  42-)  M      -5.73
1818 GLN   (  43-)  N      -5.73
3195 ARG   (  74-)  T      -5.72
3051 GLN   (  28-)  S      -5.71
3163 ARG   (  42-)  T      -5.67
3048 ARG   (  25-)  S      -5.63
1389 ARG   (  44-)  G      -5.58
And so on for a total of 79 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.

 772 PHE   (  35-)  C       774 - PHE     37- ( C)         -4.65
1386 HIS   (  41-)  G      1389 - ARG     44- ( G)         -5.23
1430 LYS   (   7-)  H      1433 - ASN     10- ( H)         -4.65
1689 TYR   (   3-)  L      1691 - GLU      5- ( L)         -4.78
2548 PHE   (  35-)  P      2550 - PHE     37- ( P)         -4.60
3162 HIS   (  41-)  T      3165 - ARG     44- ( T)         -5.14
3465 TYR   (   3-)  Y      3467 - GLU      5- ( Y)         -4.95

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.

1432 LYS   (   9-)  H   -2.90
3221 ASN   (  22-)  U   -2.80
3196 VAL   (  75-)  T   -2.79
3208 LYS   (   9-)  U   -2.76
1420 VAL   (  75-)  G   -2.76
1277 PRO   (  30-)  F   -2.63
2066 HIS   ( 291-)  N   -2.57
 290 HIS   ( 291-)  A   -2.55
1475 VAL   (  52-)  H   -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.

 285 ILE   ( 286-)  A     -  288 ALA   ( 289-)  A        -1.78

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

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

3630 HOH   (4154 )  B      O     34.76  292.64  255.18
3630 HOH   (4166 )  B      O     41.37  299.55  243.05
3630 HOH   (4231 )  B      O     34.56  291.81  250.87
3639 HOH   (  87 )  K      O     57.22  312.06  236.27
3644 HOH   (1484 )  P      O    143.03  317.18  146.12

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.

3629 HOH   (3639 )  A      O
3629 HOH   (3680 )  A      O
3629 HOH   (3749 )  A      O
3629 HOH   (3751 )  A      O
3630 HOH   (4181 )  B      O
3630 HOH   (4244 )  B      O
3631 HOH   (3526 )  C      O
3631 HOH   (3541 )  C      O
3631 HOH   (3617 )  C      O
3631 HOH   (3618 )  C      O
3631 HOH   (3635 )  C      O
3631 HOH   (3640 )  C      O
3632 HOH   (3560 )  D      O
3632 HOH   (3579 )  D      O
3632 HOH   (3582 )  D      O
3633 HOH   (3249 )  E      O
3633 HOH   (3284 )  E      O
3634 HOH   ( 147 )  F      O
3635 HOH   (2474 )  G      O
3635 HOH   (2634 )  G      O
3636 HOH   ( 664 )  H      O
3636 HOH   (2652 )  H      O
3636 HOH   (2662 )  H      O
3637 HOH   ( 532 )  I      O
3637 HOH   (2599 )  I      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.

  79 ASN   (  80-)  A
  97 ASN   (  98-)  A
 177 GLN   ( 178-)  A
 179 GLN   ( 180-)  A
 522 GLN   (  10-)  B
 740 HIS   (   3-)  C
 787 ASN   (  50-)  C
 805 GLN   (  68-)  C
 813 GLN   (  76-)  C
 967 ASN   ( 230-)  C
1032 GLN   (  37-)  D
1216 HIS   (  78-)  E
1232 ASN   (  94-)  E
1353 HIS   (   8-)  G
1379 ASN   (  34-)  G
1454 GLN   (  31-)  H
1515 GLN   (   8-)  I
1668 GLN   (  35-)  K
1855 ASN   (  80-)  N
1873 ASN   (  98-)  N
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
2800 HIS   (  29-)  Q
2808 GLN   (  37-)  Q
2992 HIS   (  78-)  R
3077 ASN   (  54-)  S
3103 GLN   (  80-)  S
3155 ASN   (  34-)  T
3230 GLN   (  31-)  U
3291 GLN   (   8-)  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
  90 ASP   (  91-)  A      N
  95 ARG   (  96-)  A      N
  95 ARG   (  96-)  A      NE
  95 ARG   (  96-)  A      NH2
 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
 243 TYR   ( 244-)  A      OH
 265 GLU   ( 266-)  A      N
 288 ALA   ( 289-)  A      N
 300 THR   ( 301-)  A      N
 301 ARG   ( 302-)  A      NH2
 367 HIS   ( 368-)  A      ND1
 370 TYR   ( 371-)  A      OH
 421 ASN   ( 422-)  A      ND2
 427 GLN   ( 428-)  A      NE2
 437 ARG   ( 438-)  A      NH2
 438 ARG   ( 439-)  A      N
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.

  54 ASN   (  55-)  A      OD1
 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
 574 GLU   (  62-)  B      OE1
 746 HIS   (   9-)  C      ND1
 808 HIS   (  71-)  C      NE2
 840 HIS   ( 103-)  C      ND1
 870 ASN   ( 133-)  C      OD1
 895 HIS   ( 158-)  C      NE2
1301 ASN   (  54-)  F      OD1
1352 ASP   (   7-)  G      OD2
1379 ASN   (  34-)  G      OD1
1383 HIS   (  38-)  G      NE2
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
2522 HIS   (   9-)  P      ND1
2584 HIS   (  71-)  P      NE2
2603 GLU   (  90-)  P      OE1
2616 HIS   ( 103-)  P      ND1
2646 ASN   ( 133-)  P      OD1
2661 HIS   ( 148-)  P      NE2
2671 HIS   ( 158-)  P      NE2
2674 GLN   ( 161-)  P      OE1
2720 HIS   ( 207-)  P      NE2
2745 HIS   ( 232-)  P      NE2
2880 HIS   ( 109-)  Q      ND1
3117 HIS   (  94-)  S      ND1
3118 GLN   (  95-)  S      OE1
3128 ASP   (   7-)  T      OD2
3129 HIS   (   8-)  T      ND1
3155 ASN   (  34-)  T      OD1

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+.

3577  NA   (3519-)  A     1.16   0.96 Scores about as good as CA
3603  NA   (4519-)  N     1.19   0.99 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.

3629 HOH   (3652 )  A      O  1.00  K  4 NCS 1/1
3629 HOH   (3720 )  A      O  0.91  K  4 NCS 1/1
3630 HOH   (4104 )  B      O  1.01  K  4 NCS 1/1
3630 HOH   (4158 )  B      O  0.93  K  4
3636 HOH   (2099 )  H      O  1.00  K  4
3647 HOH   (1507 )  S      O  0.87  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.

 211 ASP   ( 212-)  A   H-bonding suggests Asn; but Alt-Rotamer
 572 GLU   (  60-)  B   H-bonding suggests Gln
1039 GLU   (  44-)  D   H-bonding suggests Gln
1107 GLU   ( 112-)  D   H-bonding suggests Gln
1497 ASP   (  74-)  H   H-bonding suggests Asn
1987 ASP   ( 212-)  N   H-bonding suggests Asn; but Alt-Rotamer
2348 GLU   (  60-)  O   H-bonding suggests Gln
3234 ASP   (  35-)  U   H-bonding suggests Asn; but Alt-Rotamer
3272 ASP   (  73-)  U   H-bonding suggests Asn
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 :  -0.555
  2nd generation packing quality :  -1.272
  Ramachandran plot appearance   :  -0.046
  chi-1/chi-2 rotamer normality  :  -1.154
  Backbone conformation          :  -0.095

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.449 (tight)
  Bond angles                    :   0.722
  Omega angle restraints         :   0.289 (tight)
  Side chain planarity           :   0.539 (tight)
  Improper dihedral distribution :   0.915
  B-factor distribution          :   0.594
  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 : 1.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :   0.0
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.449 (tight)
  Bond angles                    :   0.722
  Omega angle restraints         :   0.289 (tight)
  Side chain planarity           :   0.539 (tight)
  Improper dihedral distribution :   0.915
  B-factor distribution          :   0.594
  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.