WHAT IF Check report

This file was created 2013-04-18 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 pdb2wj8.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.105
CA-only RMS fit for the two chains : 0.103

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 C

All-atom RMS fit for the two chains : 0.188
CA-only RMS fit for the two chains : 0.171

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 D

All-atom RMS fit for the two chains : 0.274
CA-only RMS fit for the two chains : 0.188

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

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 E

All-atom RMS fit for the two chains : 0.128
CA-only RMS fit for the two chains : 0.125

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 F

All-atom RMS fit for the two chains : 0.079
CA-only RMS fit for the two chains : 0.075

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

7640 BO4   (2001-)  A  -         Atom types
7641 BO4   (2001-)  B  -         Atom types
7642 BO4   (2001-)  C  -         Atom types
7643 BO4   (2001-)  D  -         Atom types
7644 BO4   (2001-)  H  -         Atom types
7645 BO4   (2001-)  I  -         Atom types
7646 BO4   (2001-)  K  -         Atom types
7647 BO4   (2001-)  L  -         Atom types
7648 BO4   (2001-)  M  -         Atom types
7649 BO4   (2001-)  N  -         Atom types
7650 BO4   (2001-)  O  -         Atom types
7651 BO4   (2001-)  T  -         Atom types

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.

7500 OCYT  (1001-)  A  -   P   7569 OCYT  (1007-)  J  -   O3'
7506 OCYT  (1007-)  A  -   O3' 7507 OCYT  (1001-)  B  -   P
7513 OCYT  (1007-)  B  -   O3' 7514 OCYT  (1001-)  C  -   P
7520 OCYT  (1007-)  C  -   O3' 7521 OCYT  (1001-)  D  -   P
7527 OCYT  (1007-)  D  -   O3' 7528 OCYT  (1001-)  E  -   P
7534 OCYT  (1007-)  E  -   O3' 7535 OCYT  (1001-)  F  -   P
7541 OCYT  (1007-)  F  -   O3' 7542 OCYT  (1001-)  G  -   P
7548 OCYT  (1007-)  G  -   O3' 7549 OCYT  (1001-)  H  -   P
7555 OCYT  (1007-)  H  -   O3' 7556 OCYT  (1001-)  I  -   P
7562 OCYT  (1007-)  I  -   O3' 7563 OCYT  (1001-)  J  -   P
7570 OCYT  (1001-)  K  -   P   7639 OCYT  (1007-)  T  -   O3'
7576 OCYT  (1007-)  K  -   O3' 7577 OCYT  (1001-)  L  -   P
7583 OCYT  (1007-)  L  -   O3' 7584 OCYT  (1001-)  M  -   P
7590 OCYT  (1007-)  M  -   O3' 7591 OCYT  (1001-)  N  -   P
7597 OCYT  (1007-)  N  -   O3' 7598 OCYT  (1001-)  O  -   P
7604 OCYT  (1007-)  O  -   O3' 7605 OCYT  (1001-)  P  -   P
7611 OCYT  (1007-)  P  -   O3' 7612 OCYT  (1001-)  Q  -   P
7618 OCYT  (1007-)  Q  -   O3' 7619 OCYT  (1001-)  R  -   P
7625 OCYT  (1007-)  R  -   O3' 7626 OCYT  (1001-)  S  -   P
7632 OCYT  (1007-)  S  -   O3' 7633 OCYT  (1001-)  T  -   P

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.

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

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.

 876 GLU   ( 128-)  C
3130 GLU   ( 128-)  I
4999 GLU   ( 128-)  N
6839 ASN   (  93-)  S

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.

   4 LYS   (   5-)  A    High
   6 LYS   (   7-)  A    High
  21 LYS   (  22-)  A    High
  25 GLN   (  26-)  A    High
  30 ASP   (  31-)  A    High
  54 GLU   (  55-)  A    High
  55 ASP   (  56-)  A    High
  59 LYS   (  60-)  A    High
  75 ARG   (  76-)  A    High
  76 GLU   (  77-)  A    High
  80 LYS   (  81-)  A    High
  83 ARG   (  84-)  A    High
  90 LYS   (  91-)  A    High
  92 ASN   (  93-)  A    High
  99 HIS   ( 100-)  A    High
 100 ARG   ( 101-)  A    High
 101 GLN   ( 102-)  A    High
 102 ASP   ( 103-)  A    High
 103 ILE   ( 104-)  A    High
 104 ASN   ( 105-)  A    High
 105 GLY   ( 106-)  A    High
 106 LYS   ( 107-)  A    High
 107 GLU   ( 108-)  A    High
 108 MET   ( 109-)  A    High
 109 LYS   ( 110-)  A    High
And so on for a total of 1577 lines.

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :200.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Nomenclature related problems

Warning: Tyrosine convention problem

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

 134 TYR   ( 135-)  A
 250 TYR   ( 251-)  A
 508 TYR   ( 135-)  B
 624 TYR   ( 251-)  B
 883 TYR   ( 135-)  C
 999 TYR   ( 251-)  C
1260 TYR   ( 135-)  D
1376 TYR   ( 251-)  D
1634 TYR   ( 135-)  E
1750 TYR   ( 251-)  E
2008 TYR   ( 135-)  F
2124 TYR   ( 251-)  F
2385 TYR   ( 135-)  G
2501 TYR   ( 251-)  G
2762 TYR   ( 135-)  H
2878 TYR   ( 251-)  H
3137 TYR   ( 135-)  I
3253 TYR   ( 251-)  I
3511 TYR   ( 135-)  J
3627 TYR   ( 251-)  J
3881 TYR   ( 135-)  K
3997 TYR   ( 251-)  K
4255 TYR   ( 135-)  L
4371 TYR   ( 251-)  L
4632 TYR   ( 135-)  M
4748 TYR   ( 251-)  M
5006 TYR   ( 135-)  N
5122 TYR   ( 251-)  N
5384 TYR   ( 135-)  O
5500 TYR   ( 251-)  O
5757 TYR   ( 135-)  P
5873 TYR   ( 251-)  P
6131 TYR   ( 135-)  Q
6247 TYR   ( 251-)  Q
6505 TYR   ( 135-)  R
6621 TYR   ( 251-)  R
6881 TYR   ( 135-)  S
6997 TYR   ( 251-)  S
7259 TYR   ( 135-)  T
7375 TYR   ( 251-)  T

Warning: Phenylalanine convention problem

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

 299 PHE   ( 300-)  A
 673 PHE   ( 300-)  B
1048 PHE   ( 300-)  C
1425 PHE   ( 300-)  D
1799 PHE   ( 300-)  E
2173 PHE   ( 300-)  F
2550 PHE   ( 300-)  G
2927 PHE   ( 300-)  H
3302 PHE   ( 300-)  I
3676 PHE   ( 300-)  J
4046 PHE   ( 300-)  K
4420 PHE   ( 300-)  L
4797 PHE   ( 300-)  M
5171 PHE   ( 300-)  N
5549 PHE   ( 300-)  O
5922 PHE   ( 300-)  P
6296 PHE   ( 300-)  Q
6670 PHE   ( 300-)  R
7046 PHE   ( 300-)  S
7424 PHE   ( 300-)  T

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.

  33 ASP   (  34-)  A
  84 ASP   (  85-)  A
 102 ASP   ( 103-)  A
 174 ASP   ( 175-)  A
 407 ASP   (  34-)  B
 458 ASP   (  85-)  B
 476 ASP   ( 103-)  B
 548 ASP   ( 175-)  B
 782 ASP   (  34-)  C
 833 ASP   (  85-)  C
 851 ASP   ( 103-)  C
 923 ASP   ( 175-)  C
1159 ASP   (  34-)  D
1210 ASP   (  85-)  D
1228 ASP   ( 103-)  D
1300 ASP   ( 175-)  D
1533 ASP   (  34-)  E
1584 ASP   (  85-)  E
1602 ASP   ( 103-)  E
1674 ASP   ( 175-)  E
1907 ASP   (  34-)  F
1958 ASP   (  85-)  F
1976 ASP   ( 103-)  F
2048 ASP   ( 175-)  F
2284 ASP   (  34-)  G
And so on for a total of 80 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.

  54 GLU   (  55-)  A
  76 GLU   (  77-)  A
 107 GLU   ( 108-)  A
 111 GLU   ( 112-)  A
 428 GLU   (  55-)  B
 450 GLU   (  77-)  B
 481 GLU   ( 108-)  B
 485 GLU   ( 112-)  B
 803 GLU   (  55-)  C
 825 GLU   (  77-)  C
 856 GLU   ( 108-)  C
 860 GLU   ( 112-)  C
1180 GLU   (  55-)  D
1202 GLU   (  77-)  D
1233 GLU   ( 108-)  D
1237 GLU   ( 112-)  D
1554 GLU   (  55-)  E
1576 GLU   (  77-)  E
1607 GLU   ( 108-)  E
1928 GLU   (  55-)  F
1950 GLU   (  77-)  F
1981 GLU   ( 108-)  F
1985 GLU   ( 112-)  F
2305 GLU   (  55-)  G
2327 GLU   (  77-)  G
And so on for a total of 78 lines.

Error: Chain names not unique

The chain names listed below are given for more than one protein/DNA molecule in the structure ('-' represents a chain without chain identifier).

Chain identifier(s): A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T

Geometric checks

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

 |  0.996758  0.000005  0.000061|
 |  0.000005  0.996824 -0.000013|
 |  0.000061 -0.000013  0.996900|
Proposed new scale matrix

 |  0.004598  0.000000  0.000247|
 |  0.000000  0.004539  0.000000|
 |  0.000000  0.000000  0.004606|
With corresponding cell

    A    = 217.491  B   = 220.293  C    = 217.410
    Alpha=  90.002  Beta=  93.082  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 218.200  B   = 220.990  C    = 218.100
    Alpha=  90.000  Beta=  93.090  Gamma=  90.000

Variance: 3022.808
(Under-)estimated Z-score: 40.520

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.

 303 LEU   ( 304-)  A      N    CA   C    99.37   -4.2
 677 LEU   ( 304-)  B      N    CA   C    99.35   -4.2
 981 THR   ( 233-)  C      CA   CB   CG2 117.44    4.1
1052 LEU   ( 304-)  C      N    CA   C    99.37   -4.2
1429 LEU   ( 304-)  D      N    CA   C    99.29   -4.3
1489 ASN   ( 364-)  D      N    CA   CB  118.27    4.6
1489 ASN   ( 364-)  D      CA   CB   CG  117.51    4.9
1500 LEU   ( 375-)  D      N    CA   C   126.08    5.3
1803 LEU   ( 304-)  E      N    CA   C    99.39   -4.2
2177 LEU   ( 304-)  F      N    CA   C    99.43   -4.2
2483 THR   ( 233-)  G      CA   CB   CG2 117.42    4.1
2554 LEU   ( 304-)  G      N    CA   C    99.28   -4.3
2860 THR   ( 233-)  H      CA   CB   CG2 117.40    4.1
2931 LEU   ( 304-)  H      N    CA   C    99.35   -4.2
3306 LEU   ( 304-)  I      N    CA   C    99.30   -4.3
3680 LEU   ( 304-)  J      N    CA   C    99.25   -4.3
4050 LEU   ( 304-)  K      N    CA   C    99.38   -4.2
4424 LEU   ( 304-)  L      N    CA   C    99.38   -4.2
4730 THR   ( 233-)  M      CA   CB   CG2 117.41    4.1
4801 LEU   ( 304-)  M      N    CA   C    99.33   -4.2
5104 THR   ( 233-)  N      CA   CB   CG2 117.36    4.0
5175 LEU   ( 304-)  N      N    CA   C    99.28   -4.3
5553 LEU   ( 304-)  O      N    CA   C    99.37   -4.2
5926 LEU   ( 304-)  P      N    CA   C    99.30   -4.3
6300 LEU   ( 304-)  Q      N    CA   C    99.27   -4.3
And so on for a total of 230 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.

  33 ASP   (  34-)  A
  54 GLU   (  55-)  A
  76 GLU   (  77-)  A
  84 ASP   (  85-)  A
 102 ASP   ( 103-)  A
 107 GLU   ( 108-)  A
 111 GLU   ( 112-)  A
 174 ASP   ( 175-)  A
 407 ASP   (  34-)  B
 428 GLU   (  55-)  B
 450 GLU   (  77-)  B
 458 ASP   (  85-)  B
 476 ASP   ( 103-)  B
 481 GLU   ( 108-)  B
 485 GLU   ( 112-)  B
 548 ASP   ( 175-)  B
 782 ASP   (  34-)  C
 803 GLU   (  55-)  C
 825 GLU   (  77-)  C
 833 ASP   (  85-)  C
 851 ASP   ( 103-)  C
 856 GLU   ( 108-)  C
 860 GLU   ( 112-)  C
 923 ASP   ( 175-)  C
1159 ASP   (  34-)  D
And so on for a total of 158 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.

1500 LEU   ( 375-)  D      CA    -8.9    20.56    34.19
The average deviation= 1.138

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.

1500 LEU   ( 375-)  D    6.01
4027 MET   ( 281-)  K    4.88
4401 MET   ( 281-)  L    4.88
7428 LEU   ( 304-)  T    4.87
3680 LEU   ( 304-)  J    4.87
2531 MET   ( 281-)  G    4.87
5530 MET   ( 281-)  O    4.87
6300 LEU   ( 304-)  Q    4.86
2554 LEU   ( 304-)  G    4.86
1780 MET   ( 281-)  E    4.86
5175 LEU   ( 304-)  N    4.86
1429 LEU   ( 304-)  D    4.86
3306 LEU   ( 304-)  I    4.85
5926 LEU   ( 304-)  P    4.85
2908 MET   ( 281-)  H    4.85
5903 MET   ( 281-)  P    4.85
6651 MET   ( 281-)  R    4.84
4801 LEU   ( 304-)  M    4.84
 677 LEU   ( 304-)  B    4.83
2931 LEU   ( 304-)  H    4.83
6277 MET   ( 281-)  Q    4.83
1029 MET   ( 281-)  C    4.83
 303 LEU   ( 304-)  A    4.82
7405 MET   ( 281-)  T    4.82
4778 MET   ( 281-)  M    4.82
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.

1489 ASN   ( 364-)  D    7.37
7051 ASN   ( 305-)  S    5.45

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.

6741 THR   ( 371-)  R    -2.6
5242 THR   ( 371-)  N    -2.6
4117 THR   ( 371-)  K    -2.6
5993 THR   ( 371-)  P    -2.6
 744 THR   ( 371-)  B    -2.6
6367 THR   ( 371-)  Q    -2.6
1496 THR   ( 371-)  D    -2.6
3373 THR   ( 371-)  I    -2.6
1119 THR   ( 371-)  C    -2.6
2998 THR   ( 371-)  H    -2.6
4868 THR   ( 371-)  M    -2.6
1870 THR   ( 371-)  E    -2.6
2621 THR   ( 371-)  G    -2.6
7495 THR   ( 371-)  T    -2.6
5620 THR   ( 371-)  O    -2.6
7117 THR   ( 371-)  S    -2.6
2244 THR   ( 371-)  F    -2.6
4491 THR   ( 371-)  L    -2.6
 370 THR   ( 371-)  A    -2.6
6493 ILE   ( 123-)  R    -2.5
5745 ILE   ( 123-)  P    -2.5
4243 ILE   ( 123-)  L    -2.5
 496 ILE   ( 123-)  B    -2.5
3869 ILE   ( 123-)  K    -2.5
3125 ILE   ( 123-)  I    -2.5
And so on for a total of 259 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.

  55 ASP   (  56-)  A  Poor phi/psi
  75 ARG   (  76-)  A  Poor phi/psi
 104 ASN   ( 105-)  A  Poor phi/psi
 175 ARG   ( 176-)  A  Poor phi/psi
 189 LEU   ( 190-)  A  Poor phi/psi
 267 LYS   ( 268-)  A  Poor phi/psi
 304 ASN   ( 305-)  A  Poor phi/psi
 334 GLY   ( 335-)  A  omega poor
 359 ASN   ( 360-)  A  Poor phi/psi
 368 ASP   ( 369-)  A  Poor phi/psi
 370 THR   ( 371-)  A  Poor phi/psi
 429 ASP   (  56-)  B  Poor phi/psi
 449 ARG   (  76-)  B  Poor phi/psi
 478 ASN   ( 105-)  B  Poor phi/psi
 549 ARG   ( 176-)  B  Poor phi/psi
 563 LEU   ( 190-)  B  Poor phi/psi
 641 LYS   ( 268-)  B  Poor phi/psi
 678 ASN   ( 305-)  B  Poor phi/psi
 708 GLY   ( 335-)  B  omega poor
 733 ASN   ( 360-)  B  Poor phi/psi
 742 ASP   ( 369-)  B  Poor phi/psi
 744 THR   ( 371-)  B  Poor phi/psi
 804 ASP   (  56-)  C  Poor phi/psi
 824 ARG   (  76-)  C  Poor phi/psi
 853 ASN   ( 105-)  C  Poor phi/psi
And so on for a total of 219 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 : -4.070

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!

   5 VAL   (   6-)  A      0
   6 LYS   (   7-)  A      0
   9 ASP   (  10-)  A      0
  19 SER   (  20-)  A      0
  28 THR   (  29-)  A      0
  30 ASP   (  31-)  A      0
  52 ILE   (  53-)  A      0
  54 GLU   (  55-)  A      0
  73 LEU   (  74-)  A      0
 141 MET   ( 142-)  A      0
 143 GLU   ( 144-)  A      0
 150 HIS   ( 151-)  A      0
 169 LYS   ( 170-)  A      0
 172 ALA   ( 173-)  A      0
 174 ASP   ( 175-)  A      0
 175 ARG   ( 176-)  A      0
 176 SER   ( 177-)  A      0
 189 LEU   ( 190-)  A      0
 195 ARG   ( 196-)  A      0
 196 TYR   ( 197-)  A      0
 233 ARG   ( 234-)  A      0
 236 SER   ( 237-)  A      0
 250 TYR   ( 251-)  A      0
 254 GLN   ( 255-)  A      0
 255 VAL   ( 256-)  A      0
And so on for a total of 2115 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 : 1.788

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!

1109 GLY   ( 361-)  C   1.84   42
3363 GLY   ( 361-)  I   1.83   42
3737 GLY   ( 361-)  J   1.78   57
 734 GLY   ( 361-)  B   1.76   42
6731 GLY   ( 361-)  R   1.76   47
2988 GLY   ( 361-)  H   1.76   47
1860 GLY   ( 361-)  E   1.76   46
4459 GLY   ( 339-)  L   1.76   19
 712 GLY   ( 339-)  B   1.75   19
2212 GLY   ( 339-)  F   1.75   19
5210 GLY   ( 339-)  N   1.75   19
1838 GLY   ( 339-)  E   1.75   19
2966 GLY   ( 339-)  H   1.75   19
1087 GLY   ( 339-)  C   1.75   19
 338 GLY   ( 339-)  A   1.75   19
3341 GLY   ( 339-)  I   1.75   19
6709 GLY   ( 339-)  R   1.75   19
1486 GLY   ( 361-)  D   1.75   44
4836 GLY   ( 339-)  M   1.75   19
7085 GLY   ( 339-)  S   1.75   19
2589 GLY   ( 339-)  G   1.75   19
4085 GLY   ( 339-)  K   1.75   19
4858 GLY   ( 361-)  M   1.75   51
 360 GLY   ( 361-)  A   1.75   49
1464 GLY   ( 339-)  D   1.75   19
And so on for a total of 80 lines.

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 153 PRO   ( 154-)  A  -112.1 envelop C-gamma (-108 degrees)
 317 PRO   ( 318-)  A  -113.7 envelop C-gamma (-108 degrees)
 527 PRO   ( 154-)  B  -112.1 envelop C-gamma (-108 degrees)
 691 PRO   ( 318-)  B  -113.8 envelop C-gamma (-108 degrees)
 902 PRO   ( 154-)  C  -112.1 envelop C-gamma (-108 degrees)
1066 PRO   ( 318-)  C  -113.7 envelop C-gamma (-108 degrees)
1279 PRO   ( 154-)  D  -112.2 envelop C-gamma (-108 degrees)
1443 PRO   ( 318-)  D  -113.6 envelop C-gamma (-108 degrees)
1653 PRO   ( 154-)  E  -112.3 envelop C-gamma (-108 degrees)
1817 PRO   ( 318-)  E  -113.7 envelop C-gamma (-108 degrees)
2027 PRO   ( 154-)  F  -112.1 envelop C-gamma (-108 degrees)
2191 PRO   ( 318-)  F  -113.8 envelop C-gamma (-108 degrees)
2404 PRO   ( 154-)  G  -112.3 envelop C-gamma (-108 degrees)
2568 PRO   ( 318-)  G  -113.7 envelop C-gamma (-108 degrees)
2781 PRO   ( 154-)  H  -112.2 envelop C-gamma (-108 degrees)
2945 PRO   ( 318-)  H  -113.6 envelop C-gamma (-108 degrees)
3156 PRO   ( 154-)  I  -112.1 envelop C-gamma (-108 degrees)
3320 PRO   ( 318-)  I  -113.6 envelop C-gamma (-108 degrees)
3530 PRO   ( 154-)  J  -112.2 envelop C-gamma (-108 degrees)
3694 PRO   ( 318-)  J  -113.8 envelop C-gamma (-108 degrees)
3900 PRO   ( 154-)  K  -112.2 envelop C-gamma (-108 degrees)
4064 PRO   ( 318-)  K  -113.6 envelop C-gamma (-108 degrees)
4274 PRO   ( 154-)  L  -112.3 envelop C-gamma (-108 degrees)
4438 PRO   ( 318-)  L  -113.7 envelop C-gamma (-108 degrees)
4651 PRO   ( 154-)  M  -112.2 envelop C-gamma (-108 degrees)
4815 PRO   ( 318-)  M  -113.6 envelop C-gamma (-108 degrees)
5025 PRO   ( 154-)  N  -112.4 envelop C-gamma (-108 degrees)
5189 PRO   ( 318-)  N  -113.6 envelop C-gamma (-108 degrees)
5403 PRO   ( 154-)  O  -112.2 envelop C-gamma (-108 degrees)
5567 PRO   ( 318-)  O  -113.8 envelop C-gamma (-108 degrees)
5776 PRO   ( 154-)  P  -112.3 envelop C-gamma (-108 degrees)
5940 PRO   ( 318-)  P  -113.6 envelop C-gamma (-108 degrees)
6150 PRO   ( 154-)  Q  -112.1 envelop C-gamma (-108 degrees)
6314 PRO   ( 318-)  Q  -113.6 envelop C-gamma (-108 degrees)
6524 PRO   ( 154-)  R  -112.2 envelop C-gamma (-108 degrees)
6688 PRO   ( 318-)  R  -113.8 envelop C-gamma (-108 degrees)
6900 PRO   ( 154-)  S  -112.2 envelop C-gamma (-108 degrees)
7064 PRO   ( 318-)  S  -113.7 envelop C-gamma (-108 degrees)
7278 PRO   ( 154-)  T  -112.2 envelop C-gamma (-108 degrees)
7442 PRO   ( 318-)  T  -113.7 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.

7575 OCYT  (1006-)  K      N4   <->  7662 HOH   (3041 )  K      O    0.21    2.49  INTRA BL
6540 LYS   ( 170-)  R      NZ   <->  7669 HOH   (3024 )  R      O    0.21    2.49  INTRA BF
4606 MET   ( 109-)  M      CE   <->  4608 PHE   ( 111-)  M      CZ   0.20    3.00  INTRA BF
3933 ASN   ( 187-)  K      ND2  <->  3940 MET   ( 194-)  K      SD   0.18    3.12  INTRA BL
1686 ASN   ( 187-)  E      ND2  <->  1693 MET   ( 194-)  E      SD   0.18    3.12  INTRA BL
5809 ASN   ( 187-)  P      ND2  <->  5816 MET   ( 194-)  P      SD   0.18    3.12  INTRA BL
3189 ASN   ( 187-)  I      ND2  <->  3196 MET   ( 194-)  I      SD   0.18    3.12  INTRA BF
6557 ASN   ( 187-)  R      ND2  <->  6564 MET   ( 194-)  R      SD   0.18    3.12  INTRA BF
3563 ASN   ( 187-)  J      ND2  <->  3570 MET   ( 194-)  J      SD   0.18    3.12  INTRA BF
6183 ASN   ( 187-)  Q      ND2  <->  6190 MET   ( 194-)  Q      SD   0.18    3.12  INTRA BF
4684 ASN   ( 187-)  M      ND2  <->  4691 MET   ( 194-)  M      SD   0.18    3.12  INTRA BF
1312 ASN   ( 187-)  D      ND2  <->  1319 MET   ( 194-)  D      SD   0.18    3.12  INTRA BL
4307 ASN   ( 187-)  L      ND2  <->  4314 MET   ( 194-)  L      SD   0.18    3.12  INTRA BF
5058 ASN   ( 187-)  N      ND2  <->  5065 MET   ( 194-)  N      SD   0.18    3.12  INTRA BL
7311 ASN   ( 187-)  T      ND2  <->  7318 MET   ( 194-)  T      SD   0.18    3.12  INTRA BL
 560 ASN   ( 187-)  B      ND2  <->   567 MET   ( 194-)  B      SD   0.18    3.12  INTRA BF
5436 ASN   ( 187-)  O      ND2  <->  5443 MET   ( 194-)  O      SD   0.18    3.12  INTRA BF
2437 ASN   ( 187-)  G      ND2  <->  2444 MET   ( 194-)  G      SD   0.18    3.12  INTRA BF
 186 ASN   ( 187-)  A      ND2  <->   193 MET   ( 194-)  A      SD   0.18    3.12  INTRA BF
2814 ASN   ( 187-)  H      ND2  <->  2821 MET   ( 194-)  H      SD   0.18    3.12  INTRA BL
2060 ASN   ( 187-)  F      ND2  <->  2067 MET   ( 194-)  F      SD   0.18    3.12  INTRA BF
7604 OCYT  (1007-)  O      N3   <->  7666 HOH   (3033 )  O      O    0.17    2.53  INTRA BL
6933 ASN   ( 187-)  S      ND2  <->  6940 MET   ( 194-)  S      SD   0.17    3.13  INTRA BL
 935 ASN   ( 187-)  C      ND2  <->   942 MET   ( 194-)  C      SD   0.17    3.13  INTRA BL
6937 LYS   ( 191-)  S      NZ   <->  7670 HOH   (3016 )  S      O    0.17    2.53  INTRA BF
And so on for a total of 251 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

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.

3552 ARG   ( 176-)  J      -5.71
5047 ARG   ( 176-)  N      -5.71
5798 ARG   ( 176-)  P      -5.71
6172 ARG   ( 176-)  Q      -5.70
3178 ARG   ( 176-)  I      -5.70
2049 ARG   ( 176-)  F      -5.70
1675 ARG   ( 176-)  E      -5.70
2426 ARG   ( 176-)  G      -5.70
2803 ARG   ( 176-)  H      -5.70
4673 ARG   ( 176-)  M      -5.70
 924 ARG   ( 176-)  C      -5.69
6546 ARG   ( 176-)  R      -5.66
 175 ARG   ( 176-)  A      -5.66
4296 ARG   ( 176-)  L      -5.66
6922 ARG   ( 176-)  S      -5.65
1301 ARG   ( 176-)  D      -5.65
3922 ARG   ( 176-)  K      -5.65
7300 ARG   ( 176-)  T      -5.65
5425 ARG   ( 176-)  O      -5.64
 549 ARG   ( 176-)  B      -5.64
4083 TYR   ( 337-)  K      -5.45
2964 TYR   ( 337-)  H      -5.45
7461 TYR   ( 337-)  T      -5.45
1836 TYR   ( 337-)  E      -5.44
1462 TYR   ( 337-)  D      -5.44
And so on for a total of 123 lines.

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

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.

 546 ALA   ( 173-)  B   -3.37
2423 ALA   ( 173-)  G   -3.37
5795 ALA   ( 173-)  P   -3.37
7297 ALA   ( 173-)  T   -3.37
6543 ALA   ( 173-)  R   -3.37
2046 ALA   ( 173-)  F   -3.37
1298 ALA   ( 173-)  D   -3.37
6919 ALA   ( 173-)  S   -3.37
4670 ALA   ( 173-)  M   -3.37
 172 ALA   ( 173-)  A   -3.37
4293 ALA   ( 173-)  L   -3.37
3549 ALA   ( 173-)  J   -3.37
 921 ALA   ( 173-)  C   -3.37
6169 ALA   ( 173-)  Q   -3.37
3919 ALA   ( 173-)  K   -3.37
5044 ALA   ( 173-)  N   -3.37
1672 ALA   ( 173-)  E   -3.37
3175 ALA   ( 173-)  I   -3.37
5422 ALA   ( 173-)  O   -3.37
2800 ALA   ( 173-)  H   -3.37
3687 LEU   ( 311-)  J   -2.69
1059 LEU   ( 311-)  C   -2.69
2184 LEU   ( 311-)  F   -2.69
4431 LEU   ( 311-)  L   -2.69
1436 LEU   ( 311-)  D   -2.69
6307 LEU   ( 311-)  Q   -2.69
2938 LEU   ( 311-)  H   -2.69
5182 LEU   ( 311-)  N   -2.69
6681 LEU   ( 311-)  R   -2.69
2561 LEU   ( 311-)  G   -2.69
7435 LEU   ( 311-)  T   -2.69
7057 LEU   ( 311-)  S   -2.69
 684 LEU   ( 311-)  B   -2.69
1810 LEU   ( 311-)  E   -2.69
5933 LEU   ( 311-)  P   -2.68
4057 LEU   ( 311-)  K   -2.68
 310 LEU   ( 311-)  A   -2.68

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

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.

7659 HOH   (3006 )  H      O      3.26   71.39  201.63
7660 HOH   (3010 )  I      O    -20.73   44.75  215.93
7669 HOH   (3004 )  R      O    -72.32   72.33  174.93

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.

7652 HOH   (3007 )  A      O
7652 HOH   (3008 )  A      O
7652 HOH   (3018 )  A      O
7652 HOH   (3020 )  A      O
7652 HOH   (3022 )  A      O
7652 HOH   (3024 )  A      O
7652 HOH   (3025 )  A      O
7652 HOH   (3026 )  A      O
7653 HOH   (3004 )  B      O
7653 HOH   (3007 )  B      O
7653 HOH   (3015 )  B      O
7653 HOH   (3016 )  B      O
7653 HOH   (3017 )  B      O
7653 HOH   (3020 )  B      O
7653 HOH   (3027 )  B      O
7653 HOH   (3028 )  B      O
7654 HOH   (3010 )  C      O
7654 HOH   (3011 )  C      O
7654 HOH   (3015 )  C      O
7654 HOH   (3023 )  C      O
7654 HOH   (3025 )  C      O
7655 HOH   (3008 )  D      O
7655 HOH   (3024 )  D      O
7655 HOH   (3027 )  D      O
7655 HOH   (3028 )  D      O
And so on for a total of 127 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.

 277 GLN   ( 278-)  A
 291 GLN   ( 292-)  A
 651 GLN   ( 278-)  B
 665 GLN   ( 292-)  B
1026 GLN   ( 278-)  C
1040 GLN   ( 292-)  C
1168 HIS   (  43-)  D
1403 GLN   ( 278-)  D
1417 GLN   ( 292-)  D
1588 HIS   (  89-)  E
1686 ASN   ( 187-)  E
1777 GLN   ( 278-)  E
1791 GLN   ( 292-)  E
2089 HIS   ( 216-)  F
2151 GLN   ( 278-)  F
2165 GLN   ( 292-)  F
2528 GLN   ( 278-)  G
2542 GLN   ( 292-)  G
2905 GLN   ( 278-)  H
2919 GLN   ( 292-)  H
3218 HIS   ( 216-)  I
3280 GLN   ( 278-)  I
3294 GLN   ( 292-)  I
3592 HIS   ( 216-)  J
3654 GLN   ( 278-)  J
And so on for a total of 52 lines.

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   5 VAL   (   6-)  A      N
   7 LEU   (   8-)  A      N
  21 LYS   (  22-)  A      N
  37 TYR   (  38-)  A      N
  41 LYS   (  42-)  A      N
  56 ALA   (  57-)  A      N
  60 PHE   (  61-)  A      N
  76 GLU   (  77-)  A      N
  89 VAL   (  90-)  A      N
 102 ASP   ( 103-)  A      N
 106 LYS   ( 107-)  A      N
 118 LEU   ( 119-)  A      N
 121 GLU   ( 122-)  A      N
 122 ILE   ( 123-)  A      N
 147 GLU   ( 148-)  A      N
 150 HIS   ( 151-)  A      N
 151 ASP   ( 152-)  A      N
 171 ALA   ( 172-)  A      N
 179 THR   ( 180-)  A      N
 184 ARG   ( 185-)  A      NH1
 192 GLU   ( 193-)  A      N
 209 TYR   ( 210-)  A      OH
 234 GLY   ( 235-)  A      N
 238 VAL   ( 239-)  A      N
 256 MET   ( 257-)  A      N
And so on for a total of 643 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.

  42 HIS   (  43-)  A      ND1
 150 HIS   ( 151-)  A      ND1
 416 HIS   (  43-)  B      ND1
 524 HIS   ( 151-)  B      ND1
 566 GLU   ( 193-)  B      OE1
 791 HIS   (  43-)  C      ND1
 899 HIS   ( 151-)  C      ND1
1218 ASN   (  93-)  D      OD1
1276 HIS   ( 151-)  D      ND1
1318 GLU   ( 193-)  D      OE1
1542 HIS   (  43-)  E      ND1
1588 HIS   (  89-)  E      ND1
1650 HIS   ( 151-)  E      ND1
1692 GLU   ( 193-)  E      OE1
1916 HIS   (  43-)  F      ND1
2024 HIS   ( 151-)  F      ND1
2066 GLU   ( 193-)  F      OE1
2293 HIS   (  43-)  G      ND1
2401 HIS   ( 151-)  G      ND1
2670 HIS   (  43-)  H      ND1
2778 HIS   ( 151-)  H      ND1
2820 GLU   ( 193-)  H      OE1
3045 HIS   (  43-)  I      ND1
3153 HIS   ( 151-)  I      ND1
3419 HIS   (  43-)  J      ND1
And so on for a total of 51 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.

  95 ASP   (  96-)  A   H-bonding suggests Asn
 347 ASP   ( 348-)  A   H-bonding suggests Asn
 358 GLU   ( 359-)  A   H-bonding suggests Gln
 469 ASP   (  96-)  B   H-bonding suggests Asn
 721 ASP   ( 348-)  B   H-bonding suggests Asn
 732 GLU   ( 359-)  B   H-bonding suggests Gln
 844 ASP   (  96-)  C   H-bonding suggests Asn
1096 ASP   ( 348-)  C   H-bonding suggests Asn
1107 GLU   ( 359-)  C   H-bonding suggests Gln
1203 ASP   (  78-)  D   H-bonding suggests Asn
1221 ASP   (  96-)  D   H-bonding suggests Asn
1473 ASP   ( 348-)  D   H-bonding suggests Asn
1484 GLU   ( 359-)  D   H-bonding suggests Gln
1595 ASP   (  96-)  E   H-bonding suggests Asn
1847 ASP   ( 348-)  E   H-bonding suggests Asn
1858 GLU   ( 359-)  E   H-bonding suggests Gln
1969 ASP   (  96-)  F   H-bonding suggests Asn
2221 ASP   ( 348-)  F   H-bonding suggests Asn
2232 GLU   ( 359-)  F   H-bonding suggests Gln
2346 ASP   (  96-)  G   H-bonding suggests Asn
2598 ASP   ( 348-)  G   H-bonding suggests Asn
2609 GLU   ( 359-)  G   H-bonding suggests Gln
2723 ASP   (  96-)  H   H-bonding suggests Asn
2975 ASP   ( 348-)  H   H-bonding suggests Asn
2986 GLU   ( 359-)  H   H-bonding suggests Gln
And so on for a total of 63 lines.

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 :  -0.416
  2nd generation packing quality :  -1.481
  Ramachandran plot appearance   :  -1.348
  chi-1/chi-2 rotamer normality  :  -4.070 (bad)
  Backbone conformation          :  -0.349

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.447 (tight)
  Bond angles                    :   0.789
  Omega angle restraints         :   0.325 (tight)
  Side chain planarity           :   0.896
  Improper dihedral distribution :   1.013
  B-factor distribution          :   0.708
  Inside/Outside distribution    :   0.943

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 : 3.29


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.9
  2nd generation packing quality :   0.6
  Ramachandran plot appearance   :   1.5
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.447 (tight)
  Bond angles                    :   0.789
  Omega angle restraints         :   0.325 (tight)
  Side chain planarity           :   0.896
  Improper dihedral distribution :   1.013
  B-factor distribution          :   0.708
  Inside/Outside distribution    :   0.943
==============

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.