WHAT IF Check report

This file was created 2013-12-26 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 pdb2xfz.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

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

Space group as read from CRYST card: P 21 21 21
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 2
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Z, symmetry, and molecular multiplicity disagree
Could it be that Z must be: 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: 852464.938
Volume of the Unit Cell V= 59251464.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 34.753
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.960 And remember, a matrix counting problem has been reported earlier already

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

5344 A3P   (1493-)  A  -

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

3084 ARG   (  38-)  L  -   NH2 4078 GLY   (   6-)  Y  -   N

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

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.

1970 LYS   (  22-)  D  -   NZ  bound to 4796  MG   (1685-)  D  -  MG

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

4118 ASP   (  46-)  Y  -   CB
4118 ASP   (  46-)  Y  -   CG
4118 ASP   (  46-)  Y  -   OD1
4118 ASP   (  46-)  Y  -   OD2

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

4118 ASP   (  46-)  Y  -   N
4118 ASP   (  46-)  Y  -   CA
4118 ASP   (  46-)  Y  -   C
4118 ASP   (  46-)  Y  -   O

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.

4802  MG   (1695-)  A  -

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: 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: Y

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

Warning: Missing atoms

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

   1 OGUA  (   3-)  A      N2

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 OGUA  (   3-)  A    High
   2 OURA  (   4-)  A    High
   3 OURA  (   5-)  A    High
   4 OGUA  (   6-)  A    High
   5 OGUA  (   7-)  A    High
   6 OADE  (   8-)  A    High
   8 OADE  (  10-)  A    High
  10 OURA  (  12-)  A    High
  12 OURA  (  14-)  A    High
  13 OGUA  (  15-)  A    High
  14 OADE  (  16-)  A    High
  15 OURA  (  17-)  A    High
  16 OCYT  (  18-)  A    High
  17 OCYT  (  19-)  A    High
  20 OGUA  (  22-)  A    High
  27 OGUA  (  29-)  A    High
  29 OGUA  (  31-)  A    High
  36 OGUA  (  38-)  A    High
  37 OGUA  (  39-)  A    High
  38 OCYT  (  40-)  A    High
  39 OGUA  (  41-)  A    High
  41 OCYT  (  43-)  A    High
  46 OCYT  (  48-)  A    High
  48 OADE  (  50-)  A    High
  51 OADE  (  53-)  A    High
And so on for a total of 3441 lines.

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

3901 LYS   (  26-)  U
3777 LYS   (  88-)  S
3622 ARG   ( 101-)  Q
3522 ALA   (  84-)  P
3290 GLY   ( 119-)  M
3172 ALA   ( 126-)  L
2928 VAL   ( 101-)  J
2308 GLU   ( 155-)  E
2157 ARG   ( 209-)  D
1949 ILE   ( 208-)  C
1742 GLU   ( 241-)  B

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

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: Y

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.

1993 ARG   (  47-)  D
1996 ARG   (  50-)  D
2064 ARG   ( 118-)  D
2099 ARG   ( 153-)  D
3849 ARG   (  89-)  T
4101 ARG   (  40-)  Y
4103 ARG   (  42-)  Y

Warning: Tyrosine convention problem

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

1532 TYR   (  31-)  B
1700 TYR   ( 199-)  B
1769 TYR   (  29-)  C
1973 TYR   (  27-)  D
2052 TYR   ( 106-)  D
2153 TYR   ( 207-)  D
2283 TYR   ( 133-)  E
2354 TYR   (  50-)  F
2367 TYR   (  63-)  F
2448 TYR   (  44-)  G
2489 TYR   (  85-)  G
2555 TYR   ( 151-)  G
2558 TYR   ( 154-)  G
2654 TYR   (  94-)  H
2811 TYR   ( 114-)  I
2822 TYR   ( 125-)  I
2963 TYR   (  50-)  K
3143 TYR   ( 102-)  L
3186 TYR   (  21-)  M
3188 TYR   (  23-)  M
4066 TYR   (   5-)  Y
4070 TYR   (   9-)  Y
4125 TYR   (  64-)  Y

Warning: Phenylalanine convention problem

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

1518 PHE   (  17-)  B
1529 PHE   (  28-)  B
1653 PHE   ( 152-)  B
1664 PHE   ( 163-)  B
2039 PHE   (  93-)  D
2715 PHE   (  18-)  I
2734 PHE   (  37-)  I
2798 PHE   ( 101-)  I
2834 PHE   (  11-)  J
3357 PHE   (  15-)  O
3676 PHE   (  81-)  R
4063 PHE   (   2-)  Y

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.

1561 ASP   (  60-)  B
1667 ASP   ( 166-)  B
1696 ASP   ( 195-)  B
1699 ASP   ( 198-)  B
1776 ASP   (  36-)  C
1923 ASP   ( 183-)  C
2387 ASP   (  83-)  F
2419 ASP   (  15-)  G
2449 ASP   (  45-)  G
2633 ASP   (  73-)  H
2757 ASP   (  60-)  I
2772 ASP   (  75-)  I
2835 ASP   (  12-)  J
3024 ASP   ( 111-)  K
3150 ASP   ( 109-)  L
3181 ASP   (  16-)  M
3248 ASP   (  83-)  M
3363 ASP   (  21-)  O
3460 ASP   (  29-)  P
3471 ASP   (  40-)  P
3559 ASP   (  46-)  Q
3628 ASP   (  33-)  R
3692 ASP   (  12-)  S
4148 ASP   (  87-)  Y

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.

1510 GLU   (   9-)  B
1553 GLU   (  52-)  B
1617 GLU   ( 116-)  B
1630 GLU   ( 129-)  B
1644 GLU   ( 143-)  B
1671 GLU   ( 170-)  B
1822 GLU   (  82-)  C
1830 GLU   (  90-)  C
1845 GLU   ( 105-)  C
1970 GLU   (  24-)  D
2027 GLU   (  81-)  D
2091 GLU   ( 145-)  D
2109 GLU   ( 163-)  D
2138 GLU   ( 192-)  D
2151 GLU   ( 205-)  D
2158 GLU   (   8-)  E
2261 GLU   ( 111-)  E
2287 GLU   ( 137-)  E
2299 GLU   ( 149-)  E
2326 GLU   (  22-)  F
2346 GLU   (  42-)  F
2382 GLU   (  78-)  F
2471 GLU   (  67-)  G
2478 GLU   (  74-)  G
2543 GLU   ( 139-)  G
2546 GLU   ( 142-)  G
2582 GLU   (  22-)  H
2594 GLU   (  34-)  H
2609 GLU   (  49-)  H
2683 GLU   ( 123-)  H
2906 GLU   (  83-)  J
2918 GLU   (  95-)  J
3054 GLU   (  13-)  L
3197 GLU   (  32-)  M
3328 GLU   (  46-)  N
3349 GLU   (   7-)  O
3383 GLU   (  41-)  O
3425 GLU   (  83-)  O
3485 GLU   (  54-)  P
3561 GLU   (  48-)  Q
3623 GLU   (  28-)  R
3633 GLU   (  38-)  R
3641 GLU   (  46-)  R
3697 GLU   (  17-)  S
3701 GLU   (  21-)  S
3707 GLU   (  27-)  S
3753 GLU   (  73-)  S
3766 GLU   (  86-)  S
3820 GLU   (  60-)  T

Warning: Phosphate group convention problem

The nucleic acid residues listed in the table below have the OP1 and OP2 atom names exchanged.

   5 OGUA  (   7-)  A
  47 OURA  (  49-)  A
  48 OADE  (  50-)  A
  49 OADE  (  51-)  A
  50 OGUA  (  52-)  A
  60 OURA  (  62-)  A
  61 OCYT  (  63-)  A
  63 OURA  (  65-)  A
  75 OGUA  (  79-)  A
  76 OGUA  (  80-)  A
 108 OGUA  ( 117-)  A
 113 OGUA  ( 122-)  A
 165 OURA  ( 173-)  A
 201 OADE  ( 197-)  A
 254 OURA  ( 261-)  A
 255 OADE  ( 262-)  A
 300 OCYT  ( 307-)  A
 318 OADE  ( 325-)  A
 336 OURA  ( 343-)  A
 337 OADE  ( 344-)  A
 338 OCYT  ( 345-)  A
 339 OGUA  ( 346-)  A
 340 OGUA  ( 347-)  A
 341 OGUA  ( 348-)  A
 343 OGUA  ( 350-)  A
And so on for a total of 122 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.

3943 OGUA  (  52-)  V      P    OP1   1.40   -5.2
3943 OGUA  (  52-)  V      C3'  O3'   1.49    4.8
3943 OGUA  (  52-)  V      P    O5'   1.50   -9.7
3943 OGUA  (  52-)  V      O5'  C5'   1.24  -12.4
3943 OGUA  (  52-)  V      O4'  C1'   1.33   -6.7
3943 OGUA  (  52-)  V      C1'  C2'   1.41  -11.9
3943 OGUA  (  52-)  V      C1'  N9    1.35  -11.9
3943 OGUA  (  52-)  V      N9   C4    1.17  -25.3
3943 OGUA  (  52-)  V      C8   N7    1.26   -8.2
3943 OGUA  (  52-)  V      N7   C5    1.24  -25.5
3943 OGUA  (  52-)  V      C5   C4    1.30  -10.8
3943 OGUA  (  52-)  V      N3   C4    1.27  -11.2
3943 OGUA  (  52-)  V      C2   N3    1.23  -11.6
3943 OGUA  (  52-)  V      C5   C6    1.20  -22.3
3943 OGUA  (  52-)  V      C6   O6    1.10  -14.7
3943 OGUA  (  52-)  V      C2   N2    1.26   -8.6
3943 OGUA  (  52-)  V      O2'  C2'   1.35   -4.7
3944 OGUA  (  53-)  V      P    OP1   1.37   -6.7
3944 OGUA  (  53-)  V      P    OP2   1.40   -4.8
3944 OGUA  (  53-)  V      P    O5'   1.40  -19.3
3944 OGUA  (  53-)  V      O5'  C5'   1.16  -17.6
3944 OGUA  (  53-)  V      C5'  C4'   1.45   -4.7
3944 OGUA  (  53-)  V      C4'  O4'   1.34   -9.2
3944 OGUA  (  53-)  V      O4'  C1'   1.32   -8.0
3944 OGUA  (  53-)  V      C1'  C2'   1.46   -6.9
And so on for a total of 97 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

 |  0.999554  0.000026  0.000276|
 |  0.000026  1.000050  0.000062|
 |  0.000276  0.000062  0.999814|
Proposed new scale matrix

 |  0.004718  0.000000 -0.000001|
 |  0.000000  0.002205  0.000000|
 |  0.000000  0.000000  0.001623|
With corresponding cell

    A    = 211.949  B   = 453.538  C    = 616.028
    Alpha=  90.006  Beta=  89.988  Gamma=  90.004

The CRYST1 cell dimensions

    A    = 212.041  B   = 453.514  C    = 616.103
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 75.925
(Under-)estimated Z-score: 6.422

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.

   1 OGUA  (   3-)  A      N9   C8   N7  113.90    5.6
   4 OGUA  (   6-)  A      N9   C8   N7  113.15    4.1
  13 OGUA  (  15-)  A      N9   C8   N7  113.23    4.3
  19 OGUA  (  21-)  A      N9   C8   N7  113.14    4.1
  20 OGUA  (  22-)  A      N9   C8   N7  113.13    4.1
  25 OGUA  (  27-)  A      N9   C8   N7  113.16    4.1
  26 OGUA  (  28-)  A      N9   C8   N7  113.35    4.5
  29 OGUA  (  31-)  A      N9   C8   N7  113.13    4.1
  33 OGUA  (  35-)  A      N9   C8   N7  113.18    4.2
  36 OGUA  (  38-)  A      N9   C8   N7  113.16    4.1
  40 OGUA  (  42-)  A      N9   C8   N7  113.19    4.2
  42 OGUA  (  44-)  A      N9   C8   N7  113.16    4.1
  50 OGUA  (  52-)  A      N9   C8   N7  113.16    4.1
  55 OGUA  (  57-)  A      N9   C8   N7  113.17    4.1
  59 OGUA  (  61-)  A      N9   C8   N7  113.18    4.2
  64 OGUA  (  66-)  A      N9   C8   N7  113.19    4.2
  67 OGUA  (  69-)  A      N9   C8   N7  113.14    4.1
  73 OGUA  (  77-)  A      N9   C8   N7  113.14    4.1
  74 OGUA  (  78-)  A      N9   C8   N7  113.13    4.1
  75 OGUA  (  79-)  A      N9   C8   N7  113.24    4.3
  76 OGUA  (  80-)  A      N9   C8   N7  113.14    4.1
  88 OGUA  (  97-)  A      N9   C8   N7  113.17    4.1
  89 OGUA  (  98-)  A      N9   C8   N7  113.29    4.4
  93 OGUA  ( 102-)  A      N9   C8   N7  113.21    4.2
  95 OGUA  ( 104-)  A      N9   C8   N7  113.11    4.0
And so on for a total of 669 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.

1510 GLU   (   9-)  B
1553 GLU   (  52-)  B
1561 ASP   (  60-)  B
1617 GLU   ( 116-)  B
1630 GLU   ( 129-)  B
1644 GLU   ( 143-)  B
1667 ASP   ( 166-)  B
1671 GLU   ( 170-)  B
1696 ASP   ( 195-)  B
1699 ASP   ( 198-)  B
1776 ASP   (  36-)  C
1822 GLU   (  82-)  C
1830 GLU   (  90-)  C
1845 GLU   ( 105-)  C
1923 ASP   ( 183-)  C
1970 GLU   (  24-)  D
1993 ARG   (  47-)  D
1996 ARG   (  50-)  D
2027 GLU   (  81-)  D
2064 ARG   ( 118-)  D
2091 GLU   ( 145-)  D
2099 ARG   ( 153-)  D
2109 GLU   ( 163-)  D
2138 GLU   ( 192-)  D
2151 GLU   ( 205-)  D
And so on for a total of 80 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.

4090 PRO   (  29-)  Y      N     -9.9   -34.89    -2.48
4099 GLY   (  38-)  Y      C      6.8     9.06     0.06
4105 THR   (  44-)  Y      C     -7.4   -10.78     0.30
4147 PRO   (  86-)  Y      N     -9.4   -33.27    -2.48
The average deviation= 0.716

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.

4095 GLN   (  34-)  Y    7.29
4108 LYS   (  47-)  Y    7.22
1557 ARG   (  56-)  B    6.36
3772 ALA   (  12-)  T    5.42
3580 LYS   (  67-)  Q    5.30
4105 THR   (  44-)  Y    5.20
4073 ALA   (  12-)  Y    5.14
4146 GLY   (  85-)  Y    5.13
4140 THR   (  79-)  Y    5.03
1673 ILE   ( 172-)  B    4.98
3836 ALA   (  76-)  T    4.88
4074 PRO   (  13-)  Y    4.81
2098 SER   ( 152-)  D    4.76
2018 GLU   (  72-)  D    4.74
1610 SER   ( 109-)  B    4.59
2549 ALA   ( 145-)  G    4.53
1816 VAL   (  76-)  C    4.46
1728 GLY   ( 227-)  B    4.45
3157 LYS   ( 116-)  L    4.45
4145 LYS   (  84-)  Y    4.37
4150 LYS   (  89-)  Y    4.33
4135 SER   (  74-)  Y    4.32
4091 LYS   (  30-)  Y    4.24
2551 ALA   ( 147-)  G    4.22
4132 HIS   (  71-)  Y    4.19
4144 LEU   (  83-)  Y    4.16
2499 ARG   (  95-)  G    4.12
2592 LYS   (  32-)  H    4.11
2281 ILE   ( 131-)  E    4.11
3774 LYS   (  14-)  T    4.09
3064 ALA   (  23-)  L    4.09
3484 VAL   (  53-)  P    4.05
4106 GLY   (  45-)  Y    4.04
2182 VAL   (  32-)  E    4.01

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

3894 OGUA  (   4-)  V    0.12
 Ramachandran Z-score : -6.657

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -6.657

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.

4076 THR   (  15-)  Y    -3.6
2584 THR   (  24-)  H    -3.2
4090 PRO   (  29-)  Y    -3.1
3833 HIS   (  73-)  T    -3.0
3795 THR   (  35-)  T    -2.9
1953 PRO   (   7-)  D    -2.8
3090 LEU   (  49-)  L    -2.8
2400 PRO   (  96-)  F    -2.8
2162 LEU   (  12-)  E    -2.8
3620 THR   (  25-)  R    -2.8
1996 ARG   (  50-)  D    -2.7
3229 TRP   (  64-)  M    -2.7
1520 HIS   (  19-)  B    -2.7
3044 THR   (   3-)  L    -2.7
4074 PRO   (  13-)  Y    -2.7
3065 LEU   (  24-)  L    -2.7
2268 ILE   ( 118-)  E    -2.7
4089 ILE   (  28-)  Y    -2.7
1518 PHE   (  17-)  B    -2.7
2391 ARG   (  87-)  F    -2.7
2954 THR   (  41-)  K    -2.7
4136 PHE   (  75-)  Y    -2.6
3677 THR   (  82-)  R    -2.6
1701 ILE   ( 200-)  B    -2.6
2915 THR   (  92-)  J    -2.6
And so on for a total of 173 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.

1517 HIS   (  16-)  B  Poor phi/psi
1520 HIS   (  19-)  B  Poor phi/psi
1521 GLU   (  20-)  B  Poor phi/psi
1523 LYS   (  22-)  B  Poor phi/psi
1525 TRP   (  24-)  B  Poor phi/psi
1527 PRO   (  26-)  B  Poor phi/psi
1538 ASN   (  37-)  B  Poor phi/psi
1567 GLY   (  66-)  B  Poor phi/psi
1574 THR   (  73-)  B  Poor phi/psi
1575 LYS   (  74-)  B  Poor phi/psi
1576 LYS   (  75-)  B  Poor phi/psi
1584 MET   (  83-)  B  Poor phi/psi
1602 MET   ( 101-)  B  Poor phi/psi
1607 LYS   ( 106-)  B  Poor phi/psi
1615 ARG   ( 114-)  B  Poor phi/psi
1620 GLU   ( 119-)  B  Poor phi/psi
1626 PRO   ( 125-)  B  Poor phi/psi
1631 ARG   ( 130-)  B  Poor phi/psi
1632 PRO   ( 131-)  B  Poor phi/psi
1651 SER   ( 150-)  B  Poor phi/psi
1654 ARG   ( 153-)  B  Poor phi/psi
1662 ALA   ( 161-)  B  Poor phi/psi
1669 THR   ( 168-)  B  Poor phi/psi
1670 LYS   ( 169-)  B  Poor phi/psi
1682 PHE   ( 181-)  B  Poor phi/psi
And so on for a total of 339 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.302

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.

3842 SER   (  82-)  T    0.35
3532 VAL   (  19-)  Q    0.36
3393 HIS   (  51-)  O    0.37

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!

   3 OURA  (   5-)  A      0
   4 OGUA  (   6-)  A      0
   5 OGUA  (   7-)  A      0
   6 OADE  (   8-)  A      0
   7 OGUA  (   9-)  A      0
   8 OADE  (  10-)  A      0
   9 OGUA  (  11-)  A      0
  10 OURA  (  12-)  A      0
  11 OURA  (  13-)  A      0
  12 OURA  (  14-)  A      0
  13 OGUA  (  15-)  A      0
  14 OADE  (  16-)  A      0
  15 OURA  (  17-)  A      0
  16 OCYT  (  18-)  A      0
  17 OCYT  (  19-)  A      0
  18 OURA  (  20-)  A      0
  19 OGUA  (  21-)  A      0
  20 OGUA  (  22-)  A      0
  21 OCYT  (  23-)  A      0
  22 OURA  (  24-)  A      0
  23 OCYT  (  25-)  A      0
  24 OADE  (  26-)  A      0
  25 OGUA  (  27-)  A      0
  26 OGUA  (  28-)  A      0
  27 OGUA  (  29-)  A      0
And so on for a total of 2816 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 : 2.782

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!

2656 GLY   (  96-)  H   2.90   13
3546 GLY   (  33-)  Q   2.43   44
3265 GLY   ( 100-)  M   2.00   55
3428 GLY   (  86-)  O   2.00   23
3863 GLY   ( 103-)  T   1.85   10
2719 GLY   (  22-)  I   1.85   18
1934 GLY   ( 194-)  C   1.70   24
1877 ALA   ( 137-)  C   1.67   25
2843 ALA   (  20-)  J   1.67   16
2812 GLY   ( 115-)  I   1.66   19
3649 ARG   (  54-)  R   1.65   11
2703 GLY   (   6-)  I   1.61   74
2603 GLY   (  43-)  H   1.55   80
3101 GLY   (  60-)  L   1.54   80
2989 GLY   (  76-)  K   1.52   29

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]

2864 PRO   (  41-)  J    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].

1997 PRO   (  51-)  D   108.2 envelop C-beta (108 degrees)
2135 PRO   ( 189-)  D  -119.3 half-chair C-delta/C-gamma (-126 degrees)
2587 PRO   (  27-)  H   102.3 envelop C-beta (108 degrees)
4074 PRO   (  13-)  Y   -43.3 envelop C-alpha (-36 degrees)
4138 PRO   (  77-)  Y   105.6 envelop C-beta (108 degrees)
4147 PRO   (  86-)  Y   120.6 half-chair C-beta/C-alpha (126 degrees)
4149 PRO   (  88-)  Y  -114.3 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

2822 TYR   ( 125-)  I      CB   <->  4821  MG   (1761-)  I     MG    1.79    1.41  INTRA BF
4631  MG   ( 657-)  Z     MG    <->  4957  MG   (3052-)  Z     MG    1.32    1.88  INTRA BL
4574  MG   ( 597-)  A     MG    <->  4774  MG   (1651-)  A     MG    1.30    1.90  INTRA BL
4283  MG   ( 159-)  A     MG    <->  4341  MG   ( 254-)  A     MG    1.29    1.91  INTRA BL
2822 TYR   ( 125-)  I      CG   <->  4821  MG   (1761-)  I     MG    1.20    2.00  INTRA BF
4702  MG   ( 742-)  Z     MG    <->  5184  MG   (3429-)  Z     MG    1.16    2.04  INTRA BL
1902 GLN   ( 162-)  C      CB   <->  4058 OADE  (  23-)  X      N7   1.14    1.96  INTRA BF
1902 GLN   ( 162-)  C      CG   <->  4058 OADE  (  23-)  X      N7   1.14    1.96  INTRA BF
1968 LYS   (  22-)  D      CD   <->  4785  MG   (1685-)  D     MG    1.14    1.66  INTRA BF
4938  MG   (3019-)  Z     MG    <->  5257  MG   (3542-)  Z     MG    1.13    2.07  INTRA BL
1743 ASN   (   3-)  C      CB   <->  4748  MG   (1603-)  C     MG    1.13    1.67  INTRA BF
1902 GLN   ( 162-)  C      CB   <->  4058 OADE  (  23-)  X      C5   1.10    2.10  INTRA BF
4471  MG   ( 476-)  A     MG    <->  4519  MG   ( 537-)  A     MG    1.05    2.15  INTRA BL
4482  MG   ( 491-)  A     MG    <->  4813  MG   (1740-)  A     MG    1.03    2.17  INTRA BL
4701  MG   ( 741-)  Z     MG    <->  5182  MG   (3421-)  Z     MG    1.03    2.17  INTRA BL
3082 THR   (  41-)  L      CG2  <->  4068 HIS   (   7-)  Y      CB   1.03    2.17  INTRA BF
4688  MG   ( 727-)  Z     MG    <->  5101  MG   (3291-)  Z     MG    1.02    2.18  INTRA BL
4708  MG   ( 748-)  Z     MG    <->  5043  MG   (3187-)  Z     MG    1.01    2.19  INTRA BF
2822 TYR   ( 125-)  I      CD1  <->  4821  MG   (1761-)  I     MG    1.01    2.19  INTRA BF
1467 OADE  (1492-)  A      O3'  <->  5333 A3P   (1493-)  A      P2   0.98    1.62  INTRA BF
1902 GLN   ( 162-)  C      CD   <->  4058 OADE  (  23-)  X      N7   0.98    2.12  INTRA BF
4647  MG   ( 683-)  Z     MG    <->  4991  MG   (3108-)  Z     MG    0.98    2.22  INTRA BL
4658  MG   ( 694-)  Z     MG    <->  5021  MG   (3158-)  Z     MG    0.97    2.23  INTRA BL
4961  MG   (3063-)  Z     MG    <->  5083  MG   (3259-)  Z     MG    0.97    2.23  INTRA BL
  87 OURA  (  96-)  A      C6   <->  4398  MG   ( 357-)  A     MG    0.96    2.24  INTRA BL
And so on for a total of 2938 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: 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: Y

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.

3761 ARG   (  81-)  S      -8.25
3889 ARG   (  24-)  U      -8.16
1819 ARG   (  79-)  C      -8.06
2408 ARG   (   4-)  G      -7.92
1995 ARG   (  49-)  D      -7.87
3430 ARG   (  88-)  O      -7.87
3269 ARG   ( 104-)  M      -7.59
3033 ARG   ( 120-)  K      -7.59
4095 GLN   (  34-)  Y      -7.54
2559 ARG   ( 155-)  G      -7.51
1988 GLN   (  42-)  D      -7.49
2763 ARG   (  66-)  I      -7.45
3459 ARG   (  28-)  P      -7.44
2628 ARG   (  68-)  H      -7.38
1950 TYR   (   4-)  D      -7.34
1912 ARG   ( 172-)  C      -7.27
3760 TYR   (  80-)  S      -7.18
4066 TYR   (   5-)  Y      -7.17
2170 GLN   (  20-)  E      -7.16
2407 ARG   (   3-)  G      -7.16
1984 TYR   (  38-)  D      -7.14
3576 ARG   (  63-)  Q      -7.13
2410 ARG   (   6-)  G      -7.13
3264 ARG   (  99-)  M      -7.13
3513 GLN   (  82-)  P      -7.12
And so on for a total of 197 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.

1516 VAL   (  15-)  B      1518 - PHE     17- ( B)         -4.80
1537 ARG   (  36-)  B      1539 - GLY     38- ( B)         -4.95
1597 ARG   (  96-)  B      1599 - LEU     98- ( B)         -5.22
1629 GLU   ( 128-)  B      1631 - ARG    130- ( B)         -4.67
1657 LYS   ( 156-)  B      1659 - LEU    158- ( B)         -5.45
1730 VAL   ( 229-)  B      1732 - GLU    231- ( B)         -4.56
1742 GLY   (   2-)  C      1745 - ILE      5- ( C)         -5.13
1910 GLN   ( 170-)  C      1912 - ARG    172- ( C)         -5.39
1991 GLN   (  45-)  D      1993 - ARG     47- ( D)         -5.64
2030 LYS   (  84-)  D      2032 - LYS     86- ( D)         -5.63
2168 ARG   (  18-)  E      2171 - ALA     21- ( E)         -5.59
2302 ARG   ( 152-)  E      2304 - GLY    154- ( E)         -5.11
2407 ARG   (   3-)  G      2410 - ARG      6- ( G)         -6.77
2414 ARG   (  10-)  G      2417 - GLN     13- ( G)         -5.06
2628 ARG   (  68-)  H      2630 - GLN     70- ( H)         -6.96
2664 ARG   ( 104-)  H      2666 - GLY    106- ( H)         -4.92
2706 ARG   (   9-)  I      2708 - LYS     11- ( I)         -4.63
2806 VAL   ( 109-)  I      2811 - TYR    114- ( I)         -5.00
2877 PHE   (  54-)  J      2880 - LYS     57- ( J)         -5.47
3055 LYS   (  14-)  L      3057 - ARG     16- ( L)         -4.81
3110 GLY   (  69-)  L      3112 - GLY     71- ( L)         -4.77
3164 LYS   ( 123-)  L      3166 - ALA    125- ( L)         -5.14
3279 ARG   ( 114-)  M      3283 - ALA    118- ( M)         -4.64
3355 GLN   (  13-)  O      3357 - PHE     15- ( O)         -4.55
3443 LYS   (  12-)  P      3445 - ASN     14- ( P)         -5.33
3684 SER   (   4-)  S      3687 - LYS      7- ( S)         -5.42
3708 LYS   (  28-)  S      3710 - LEU     30- ( S)         -5.81
3758 ARG   (  78-)  S      3763 - HIS     83- ( S)         -6.09
3765 LYS   (  85-)  S      3767 - ALA     87- ( S)         -5.64
3864 LEU   ( 104-)  T      3866 - ALA    106- ( T)         -4.71
4094 LYS   (  33-)  Y      4096 - ASN     35- ( Y)         -5.57

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 4157 : -1.941

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: Y

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.

1988 GLN   (  42-)  D   -3.61
2878 LYS   (  55-)  J   -3.31
4095 GLN   (  34-)  Y   -3.29
3269 ARG   ( 104-)  M   -3.12
2824 LYS   ( 127-)  I   -3.10
2923 THR   ( 100-)  J   -3.08
2821 GLN   ( 124-)  I   -3.07
2877 PHE   (  54-)  J   -3.03
2939 ASN   (  26-)  K   -3.03
4150 LYS   (  89-)  Y   -3.03
3313 ARG   (  31-)  N   -3.02
3758 ARG   (  78-)  S   -2.99
1743 ASN   (   3-)  C   -2.97
3772 ALA   (  12-)  T   -2.95
3770 LEU   (  10-)  T   -2.94
3734 GLY   (  54-)  S   -2.90
2810 LYS   ( 113-)  I   -2.88
1949 ARG   (   3-)  D   -2.87
2880 LYS   (  57-)  J   -2.87
2708 LYS   (  11-)  I   -2.87
2809 LYS   ( 112-)  I   -2.87
2879 HIS   (  56-)  J   -2.87
1742 GLY   (   2-)  C   -2.84
3303 TYR   (  21-)  N   -2.78
3271 ASN   ( 106-)  M   -2.77
And so on for a total of 54 lines.

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.

1741 GLN   ( 240-)  B     - 1745 ILE   (   5-)  C        -2.24
1901 GLU   ( 161-)  C     - 1904 ARG   ( 164-)  C        -2.12
2167 ALA   (  17-)  E     - 2172 GLY   (  22-)  E        -1.74
2405 ALA   ( 101-)  F     - 2409 ARG   (   5-)  G        -1.77
2484 VAL   (  80-)  G     - 2488 ASN   (  84-)  G        -1.87
2560 TRP   ( 156-)  G     - 2563 THR   (   3-)  H        -1.90
2807 GLU   ( 110-)  I     - 2812 GLY   ( 115-)  I        -2.34
2815 LYS   ( 118-)  I     - 2818 ARG   ( 121-)  I        -1.99
2820 PRO   ( 123-)  I     - 2825 ARG   ( 128-)  I        -2.51
2876 PRO   (  53-)  J     - 2881 ASP   (  58-)  J        -2.59
3028 PRO   ( 115-)  K     - 3033 ARG   ( 120-)  K        -2.11
3283 ALA   ( 118-)  M     - 3287 ALA   (   5-)  N        -1.96
3295 THR   (  13-)  N     - 3301 ARG   (  19-)  N        -2.01
3339 ARG   (  57-)  N     - 3342 SER   (  60-)  N        -1.95
3441 GLY   (  10-)  P     - 3444 HIS   (  13-)  P        -2.08
3457 ARG   (  26-)  P     - 3460 ASP   (  29-)  P        -2.09

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: 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: Y

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

1541 HIS   (  40-)  B
1595 ASN   (  94-)  B
1705 ASN   ( 204-)  B
1777 GLN   (  37-)  C
2008 GLN   (  62-)  D
2023 ASN   (  77-)  D
2107 ASN   ( 161-)  D
2280 ASN   ( 130-)  E
2311 ASN   (   7-)  F
2368 GLN   (  64-)  F
2404 ASN   ( 100-)  F
2441 ASN   (  37-)  G
2490 GLN   (  86-)  G
2552 ASN   ( 148-)  G
2638 GLN   (  78-)  H
2770 GLN   (  73-)  I
3006 GLN   (  93-)  K
3030 ASN   ( 117-)  K
3046 ASN   (   5-)  L
3047 GLN   (   6-)  L
3087 ASN   (  46-)  L
3227 ASN   (  62-)  M
3266 GLN   ( 101-)  M
3370 GLN   (  28-)  O
3496 GLN   (  65-)  P
3703 ASN   (  23-)  S
3850 GLN   (  90-)  T

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.

   4 OGUA  (   6-)  A      N1
  26 OGUA  (  28-)  A      N2
  29 OGUA  (  31-)  A      N2
  53 OADE  (  55-)  A      N6
  55 OGUA  (  57-)  A      N2
  71 OGUA  (  73-)  A      N1
  75 OGUA  (  79-)  A      N1
  75 OGUA  (  79-)  A      N2
  87 OURA  (  96-)  A      N3
  99 OGUA  ( 108-)  A      N1
  99 OGUA  ( 108-)  A      N2
 100 OADE  ( 109-)  A      N6
 101 OCYT  ( 110-)  A      N4
 106 OGUA  ( 115-)  A      N2
 152 OADE  ( 160-)  A      N6
 161 OCYT  ( 169-)  A      N4
 170 OCYT  ( 178-)  A      N4
 173 OGUA  ( 181-)  A      N1
 173 OGUA  ( 181-)  A      N2
 174 OURA  ( 182-)  A      N3
 179 OCYT  ( 187-)  A      N4
 181 OGUA  ( 189-)  A      N1
 194 OURA  ( 190-)  A      N3
 203 OGUA  ( 199-)  A      N2
 209 OGUA  ( 216-)  A      N1
And so on for a total of 688 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.

1513 GLU   (  12-)  B      OE1
1585 GLU   (  84-)  B      OE1
1667 ASP   ( 166-)  B      OD1
1671 GLU   ( 170-)  B      OE1
1677 GLU   ( 176-)  B      OE1
1690 ASP   ( 189-)  B      OD1
1706 ASP   ( 205-)  B      OD2
1776 ASP   (  36-)  C      OD1
1784 GLU   (  44-)  C      OE1
2023 ASN   (  77-)  D      OD1
2229 GLU   (  79-)  E      OE2
2280 ASN   ( 130-)  E      OD1
2311 ASN   (   7-)  F      OD1
2419 ASP   (  15-)  G      OD2
2700 GLN   (   3-)  I      OE1
2892 ASN   (  69-)  J      OD1
2980 ASP   (  67-)  K      OD1
3029 HIS   ( 116-)  K      NE2
3047 GLN   (   6-)  L      OE1
3173 GLU   (   8-)  M      OE2
3197 GLU   (  32-)  M      OE1
3266 GLN   ( 101-)  M      OE1
3328 GLU   (  46-)  N      OE1
3658 GLN   (  63-)  R      OE1
3703 ASN   (  23-)  S      OD1
3820 GLU   (  60-)  T      OE2
4116 ASP   (  55-)  Y      OD2

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+.

4169  MG   (   2-)  A   -.-  -.-  Too few ligands (1)
4170  MG   (   3-)  Z   -.-  -.-  Too few ligands (0)
4171  MG   (   4-)  A   -.-  -.-  Part of ionic cluster
4171  MG   (   4-)  A   -.-  -.-  Too few ligands (2)
4173  MG   (   6-)  Z   -.-  -.-  Low probability ion. B=113.3
4174  MG   (   7-)  Z   -.-  -.-  Too few ligands (0)
4175  MG   (   8-)  A   -.-  -.-  Part of ionic cluster
4175  MG   (   8-)  A   -.-  -.-  Too few ligands (1)
4176  MG   (   9-)  A   -.-  -.-  Low probability ion. B=118.7
4177  MG   (  10-)  A   -.-  -.-  Low probability ion. B=153.0
4178  MG   (  12-)  A   -.-  -.-  Part of ionic cluster
4178  MG   (  12-)  A   -.-  -.-  Too few ligands (1)
4179  MG   (  13-)  Z   -.-  -.-  Too few ligands (0)
4180  MG   (  14-)  A   -.-  -.-  Too few ligands (2)
4181  MG   (  15-)  A   -.-  -.-  Part of ionic cluster
4181  MG   (  15-)  A   -.-  -.-  Too few ligands (2)
4182  MG   (  17-)  A   -.-  -.-  Too few ligands (1)
4183  MG   (  18-)  Z   -.-  -.-  Low probability ion. B=104.6
4184  MG   (  19-)  Z   -.-  -.-  Part of ionic cluster
4184  MG   (  19-)  Z   -.-  -.-  Too few ligands (0)
4185  MG   (  20-)  Z   -.-  -.-  Low probability ion. B= 92.2
4186  MG   (  21-)  Z   -.-  -.-  Low probability ion. B=108.7
4187  MG   (  22-)  Z   -.-  -.-  Low probability ion. B= 84.6
4188  MG   (  28-)  Z   -.-  -.-  Too few ligands (0)
4189  MG   (  29-)  A   -.-  -.-  Too few ligands (1)
And so on for a total of 1431 lines.

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.

1551 GLU   (  50-)  B   H-bonding suggests Gln
1553 GLU   (  52-)  B   H-bonding suggests Gln
1561 ASP   (  60-)  B   H-bonding suggests Asn
1585 GLU   (  84-)  B   H-bonding suggests Gln
1587 GLU   (  86-)  B   H-bonding suggests Gln
1630 GLU   ( 129-)  B   H-bonding suggests Gln
1644 GLU   ( 143-)  B   H-bonding suggests Gln
1706 ASP   ( 205-)  B   H-bonding suggests Asn
1707 ASP   ( 206-)  B   H-bonding suggests Asn; but Alt-Rotamer
1757 ASP   (  17-)  C   H-bonding suggests Asn
1786 GLU   (  46-)  C   H-bonding suggests Gln
1796 ASP   (  56-)  C   H-bonding suggests Asn; but Alt-Rotamer
1830 GLU   (  90-)  C   H-bonding suggests Gln; but Alt-Rotamer
2090 ASP   ( 144-)  D   H-bonding suggests Asn
2139 ASP   ( 193-)  D   H-bonding suggests Asn
2272 GLU   ( 122-)  E   H-bonding suggests Gln; but Alt-Rotamer
2299 GLU   ( 149-)  E   H-bonding suggests Gln; but Alt-Rotamer
2359 ASP   (  55-)  F   H-bonding suggests Asn
2449 ASP   (  45-)  G   H-bonding suggests Asn
2585 ASP   (  25-)  H   H-bonding suggests Asn
2594 GLU   (  34-)  H   H-bonding suggests Gln
2612 ASP   (  52-)  H   H-bonding suggests Asn
2757 ASP   (  60-)  I   H-bonding suggests Asn
2881 ASP   (  58-)  J   H-bonding suggests Asn; but Alt-Rotamer
2896 ASP   (  73-)  J   H-bonding suggests Asn; but Alt-Rotamer
2906 GLU   (  83-)  J   H-bonding suggests Gln
2947 ASP   (  34-)  K   H-bonding suggests Asn
3234 GLU   (  69-)  M   H-bonding suggests Gln
3248 ASP   (  83-)  M   H-bonding suggests Asn; but Alt-Rotamer
3328 GLU   (  46-)  N   H-bonding suggests Gln
3568 ASP   (  55-)  Q   H-bonding suggests Asn; but Alt-Rotamer
3609 GLU   (  96-)  Q   H-bonding suggests Gln
3625 ASP   (  30-)  R   H-bonding suggests Asn; but Alt-Rotamer
3678 GLU   (  83-)  R   H-bonding suggests Gln
3692 ASP   (  12-)  S   H-bonding suggests Asn; but Alt-Rotamer
3707 GLU   (  27-)  S   H-bonding suggests Gln; but Alt-Rotamer
3853 GLU   (  93-)  T   H-bonding suggests Gln
4116 ASP   (  55-)  Y   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact

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 :  -3.602
  2nd generation packing quality :  -3.944 (poor)
  Ramachandran plot appearance   :  -6.657 (bad)
  chi-1/chi-2 rotamer normality  :  -4.302 (bad)
  Backbone conformation          :  -0.839

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.471 (tight)
  Bond angles                    :   0.712
  Omega angle restraints         :   0.506 (tight)
  Side chain planarity           :   0.216 (tight)
  Improper dihedral distribution :   0.670
  B-factor distribution          :   0.885
  Inside/Outside distribution    :   1.014

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.3
  2nd generation packing quality :  -1.6
  Ramachandran plot appearance   :  -3.5 (poor)
  chi-1/chi-2 rotamer normality  :  -1.9
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.471 (tight)
  Bond angles                    :   0.712
  Omega angle restraints         :   0.506 (tight)
  Side chain planarity           :   0.216 (tight)
  Improper dihedral distribution :   0.670
  B-factor distribution          :   0.885
  Inside/Outside distribution    :   1.014
==============

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.