WHAT IF Check report

This file was created 2012-01-05 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 pdb1o01.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 : 0.322
CA-only RMS fit for the two chains : 0.100

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 : 0.384
CA-only RMS fit for the two chains : 0.152

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 : 0.345
CA-only RMS fit for the two chains : 0.104

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 : 0.321
CA-only RMS fit for the two chains : 0.137

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 : 0.394
CA-only RMS fit for the two chains : 0.145

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 F

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.

3964 GAI   (4801-)  A  -
3965 NAD   (5501-)  A  -
3968 CRD   (4512-)  B  -
3969 GAI   (4802-)  B  -
3970 NAD   (5502-)  B  -
3973 CRD   (4513-)  C  -
3974 GAI   (4803-)  C  -
3976 NAD   (5503-)  C  -
3979 CRD   (4514-)  D  -
3980 GAI   (4804-)  D  -
3983 NAD   (5504-)  D  -
3986 CRD   (4515-)  E  -
3987 GAI   (4805-)  E  -
3989 NAD   (5505-)  E  -
3992 CRD   (4516-)  F  -
3993 GAI   (4806-)  F  -
3995 NAD   (5506-)  F  -
3998 GAI   (4807-)  G  -
4000 NAD   (5507-)  G  -
4005 NAD   (5508-)  H  -
4006 GAI   (4808-)  H  -
4007 CRD   (4517-)  G  -

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

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 989 GLN   (   6-)  C    0.75

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: 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

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.

  28 ARG   (  34-)  A
  84 ARG   (  90-)  A
  91 ARG   (  97-)  A
  93 ARG   (  99-)  A
 585 ARG   (  97-)  B
 587 ARG   (  99-)  B
 618 ARG   ( 130-)  B
 907 ARG   ( 419-)  B
1080 ARG   (  97-)  C
1082 ARG   (  99-)  C
1290 ARG   ( 307-)  C
1574 ARG   (  97-)  D
1576 ARG   (  99-)  D
1607 ARG   ( 130-)  D
1896 ARG   ( 419-)  D
2057 ARG   (  86-)  E
2061 ARG   (  90-)  E
2068 ARG   (  97-)  E
2070 ARG   (  99-)  E
2101 ARG   ( 130-)  E
2390 ARG   ( 419-)  E
2499 ARG   (  34-)  F
2551 ARG   (  86-)  F
2555 ARG   (  90-)  F
2562 ARG   (  97-)  F
2564 ARG   (  99-)  F
2595 ARG   ( 130-)  F
2884 ARG   ( 419-)  F
3045 ARG   (  86-)  G
3049 ARG   (  90-)  G
3056 ARG   (  97-)  G
3058 ARG   (  99-)  G
3089 ARG   ( 130-)  G
3378 ARG   ( 419-)  G
3539 ARG   (  86-)  H
3543 ARG   (  90-)  H
3550 ARG   (  97-)  H
3552 ARG   (  99-)  H
3583 ARG   ( 130-)  H
3872 ARG   ( 419-)  H

Warning: Tyrosine convention problem

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

 112 TYR   ( 118-)  A
 126 TYR   ( 132-)  A
 147 TYR   ( 153-)  A
 309 TYR   ( 315-)  A
 350 TYR   ( 356-)  A
 373 TYR   ( 379-)  A
 419 TYR   ( 425-)  A
 435 TYR   ( 441-)  A
 450 TYR   ( 456-)  A
 479 TYR   ( 485-)  A
 606 TYR   ( 118-)  B
 620 TYR   ( 132-)  B
 803 TYR   ( 315-)  B
 844 TYR   ( 356-)  B
 867 TYR   ( 379-)  B
 913 TYR   ( 425-)  B
 929 TYR   ( 441-)  B
 944 TYR   ( 456-)  B
 973 TYR   ( 485-)  B
1101 TYR   ( 118-)  C
1115 TYR   ( 132-)  C
1298 TYR   ( 315-)  C
1339 TYR   ( 356-)  C
1362 TYR   ( 379-)  C
1408 TYR   ( 425-)  C
And so on for a total of 75 lines.

Warning: Phenylalanine convention problem

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

  12 PHE   (  18-)  A
  31 PHE   (  37-)  A
 144 PHE   ( 150-)  A
 164 PHE   ( 170-)  A
 207 PHE   ( 213-)  A
 218 PHE   ( 224-)  A
 237 PHE   ( 243-)  A
 286 PHE   ( 292-)  A
 289 PHE   ( 295-)  A
 290 PHE   ( 296-)  A
 303 PHE   ( 309-)  A
 312 PHE   ( 318-)  A
 329 PHE   ( 335-)  A
 380 PHE   ( 386-)  A
 404 PHE   ( 410-)  A
 506 PHE   (  18-)  B
 525 PHE   (  37-)  B
 638 PHE   ( 150-)  B
 712 PHE   ( 224-)  B
 780 PHE   ( 292-)  B
 783 PHE   ( 295-)  B
 784 PHE   ( 296-)  B
 797 PHE   ( 309-)  B
 806 PHE   ( 318-)  B
 823 PHE   ( 335-)  B
And so on for a total of 104 lines.

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  24 ASP   (  30-)  A
 115 ASP   ( 121-)  A
 131 ASP   ( 137-)  A
 278 ASP   ( 284-)  A
 330 ASP   ( 336-)  A
 429 ASP   ( 435-)  A
 431 ASP   ( 437-)  A
 518 ASP   (  30-)  B
 609 ASP   ( 121-)  B
 625 ASP   ( 137-)  B
 772 ASP   ( 284-)  B
 923 ASP   ( 435-)  B
 925 ASP   ( 437-)  B
1013 ASP   (  30-)  C
1104 ASP   ( 121-)  C
1120 ASP   ( 137-)  C
1265 ASP   ( 282-)  C
1418 ASP   ( 435-)  C
1420 ASP   ( 437-)  C
1507 ASP   (  30-)  D
1598 ASP   ( 121-)  D
1614 ASP   ( 137-)  D
1761 ASP   ( 284-)  D
1853 ASP   ( 376-)  D
1912 ASP   ( 435-)  D
1914 ASP   ( 437-)  D
2001 ASP   (  30-)  E
2092 ASP   ( 121-)  E
2108 ASP   ( 137-)  E
2253 ASP   ( 282-)  E
2406 ASP   ( 435-)  E
2408 ASP   ( 437-)  E
2495 ASP   (  30-)  F
2586 ASP   ( 121-)  F
2602 ASP   ( 137-)  F
2900 ASP   ( 435-)  F
2902 ASP   ( 437-)  F
2989 ASP   (  30-)  G
3080 ASP   ( 121-)  G
3096 ASP   ( 137-)  G
3394 ASP   ( 435-)  G
3396 ASP   ( 437-)  G
3483 ASP   (  30-)  H
3574 ASP   ( 121-)  H
3590 ASP   ( 137-)  H
3789 ASP   ( 336-)  H
3888 ASP   ( 435-)  H
3890 ASP   ( 437-)  H

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.

  10 GLU   (  16-)  A
  51 GLU   (  57-)  A
  90 GLU   (  96-)  A
 100 GLU   ( 106-)  A
 189 GLU   ( 195-)  A
 204 GLU   ( 210-)  A
 242 GLU   ( 248-)  A
 306 GLU   ( 312-)  A
 311 GLU   ( 317-)  A
 392 GLU   ( 398-)  A
 393 GLU   ( 399-)  A
 473 GLU   ( 479-)  A
 481 GLU   ( 487-)  A
 584 GLU   (  96-)  B
 594 GLU   ( 106-)  B
 683 GLU   ( 195-)  B
 776 GLU   ( 288-)  B
 800 GLU   ( 312-)  B
 805 GLU   ( 317-)  B
 851 GLU   ( 363-)  B
 886 GLU   ( 398-)  B
 887 GLU   ( 399-)  B
 967 GLU   ( 479-)  B
 975 GLU   ( 487-)  B
 999 GLU   (  16-)  C
And so on for a total of 104 lines.

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

 |  0.998332  0.000053  0.000002|
 |  0.000053  0.998152  0.000146|
 |  0.000002  0.000146  0.998228|
Proposed new scale matrix

 |  0.007048  0.000000  0.000000|
 |  0.000000  0.006653  0.000000|
 |  0.000000  0.000000  0.005667|
With corresponding cell

    A    = 141.889  B   = 150.301  C    = 176.459
    Alpha=  90.002  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 142.133  B   = 150.571  C    = 176.782
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 390.745
(Under-)estimated Z-score: 14.568

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.

   6 ASN   (  12-)  A      N    CA   C    99.49   -4.2
 137 THR   ( 143-)  A      N    CA   C    98.80   -4.4
 500 ASN   (  12-)  B      N    CA   C    98.16   -4.7
 631 THR   ( 143-)  B      N    CA   C    98.90   -4.4
 995 ASN   (  12-)  C      N    CA   C    98.52   -4.5
1126 THR   ( 143-)  C      N    CA   C    99.98   -4.0
1620 THR   ( 143-)  D      N    CA   C    97.83   -4.8
2114 THR   ( 143-)  E      N    CA   C    98.07   -4.7
2161 VAL   ( 190-)  E      N    CA   C    99.60   -4.1
2971 ASN   (  12-)  G      N    CA   C    99.32   -4.2
3102 THR   ( 143-)  G      N    CA   C    99.37   -4.2
3596 THR   ( 143-)  H      N    CA   C    99.48   -4.2

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.

  10 GLU   (  16-)  A
  24 ASP   (  30-)  A
  28 ARG   (  34-)  A
  51 GLU   (  57-)  A
  84 ARG   (  90-)  A
  90 GLU   (  96-)  A
  91 ARG   (  97-)  A
  93 ARG   (  99-)  A
 100 GLU   ( 106-)  A
 115 ASP   ( 121-)  A
 131 ASP   ( 137-)  A
 189 GLU   ( 195-)  A
 204 GLU   ( 210-)  A
 242 GLU   ( 248-)  A
 278 ASP   ( 284-)  A
 306 GLU   ( 312-)  A
 311 GLU   ( 317-)  A
 330 ASP   ( 336-)  A
 392 GLU   ( 398-)  A
 393 GLU   ( 399-)  A
 429 ASP   ( 435-)  A
 431 ASP   ( 437-)  A
 473 GLU   ( 479-)  A
 481 GLU   ( 487-)  A
 518 ASP   (  30-)  B
And so on for a total of 192 lines.

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.

 193 LEU   ( 199-)  A    6.49
1676 LEU   ( 199-)  D    6.48
2664 LEU   ( 199-)  F    6.29
3158 LEU   ( 199-)  G    6.21
1182 LEU   ( 199-)  C    6.20
2170 LEU   ( 199-)  E    5.95
3652 LEU   ( 199-)  H    5.40
2777 GLU   ( 312-)  F    5.40
1295 GLU   ( 312-)  C    5.18
 800 GLU   ( 312-)  B    5.15
2160 VAL   ( 189-)  E    5.13
 687 LEU   ( 199-)  B    5.12
 677 VAL   ( 189-)  B    5.02
3404 ALA   ( 445-)  G    4.99
1666 VAL   ( 189-)  D    4.90
1620 THR   ( 143-)  D    4.90
3271 GLU   ( 312-)  G    4.84
2114 THR   ( 143-)  E    4.80
 183 VAL   ( 189-)  A    4.77
3642 VAL   ( 189-)  H    4.75
1789 GLU   ( 312-)  D    4.71
1172 VAL   ( 189-)  C    4.70
2283 GLU   ( 312-)  E    4.69
3148 VAL   ( 189-)  G    4.65
 306 GLU   ( 312-)  A    4.64
And so on for a total of 51 lines.

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.

3854 PHE   ( 401-)  H    -3.6
2866 PHE   ( 401-)  F    -3.5
2372 PHE   ( 401-)  E    -3.5
1384 PHE   ( 401-)  C    -3.5
1878 PHE   ( 401-)  D    -3.4
 889 PHE   ( 401-)  B    -3.4
 395 PHE   ( 401-)  A    -3.4
3360 PHE   ( 401-)  G    -3.4
2604 TYR   ( 139-)  F    -2.6
1644 PRO   ( 167-)  D    -2.6
 161 PRO   ( 167-)  A    -2.6
3098 TYR   ( 139-)  G    -2.6
 133 TYR   ( 139-)  A    -2.5
3126 PRO   ( 167-)  G    -2.5
1122 TYR   ( 139-)  C    -2.5
1150 PRO   ( 167-)  C    -2.5
2110 TYR   ( 139-)  E    -2.5
3592 TYR   ( 139-)  H    -2.5
1616 TYR   ( 139-)  D    -2.5
 627 TYR   ( 139-)  B    -2.4
2632 PRO   ( 167-)  F    -2.4
2138 PRO   ( 167-)  E    -2.4
 655 PRO   ( 167-)  B    -2.4
1154 PRO   ( 171-)  C    -2.4
 165 PRO   ( 171-)  A    -2.4
And so on for a total of 64 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.

  20 ASN   (  26-)  A  Poor phi/psi
  28 ARG   (  34-)  A  Poor phi/psi
 139 PRO   ( 145-)  A  Poor phi/psi
 221 THR   ( 227-)  A  Poor phi/psi
 254 SER   ( 260-)  A  Poor phi/psi
 256 LEU   ( 262-)  A  Poor phi/psi
 291 ASN   ( 297-)  A  Poor phi/psi
 292 GLN   ( 298-)  A  Poor phi/psi
 395 PHE   ( 401-)  A  Poor phi/psi
 397 PRO   ( 403-)  A  Poor phi/psi
 448 ASN   ( 454-)  A  Poor phi/psi
 463 LYS   ( 469-)  A  Poor phi/psi
 471 LEU   ( 477-)  A  Poor phi/psi
 514 ASN   (  26-)  B  Poor phi/psi
 522 ARG   (  34-)  B  Poor phi/psi
 633 PRO   ( 145-)  B  Poor phi/psi
 715 THR   ( 227-)  B  Poor phi/psi
 748 SER   ( 260-)  B  Poor phi/psi
 750 LEU   ( 262-)  B  Poor phi/psi
 757 LEU   ( 269-)  B  Poor phi/psi
 785 ASN   ( 297-)  B  Poor phi/psi
 786 GLN   ( 298-)  B  Poor phi/psi
 889 PHE   ( 401-)  B  Poor phi/psi
 891 PRO   ( 403-)  B  Poor phi/psi
 942 ASN   ( 454-)  B  Poor phi/psi
And so on for a total of 116 lines.

Warning: Unusual rotamers

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

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

 605 SER   ( 117-)  B    0.34
3076 SER   ( 117-)  G    0.35
3570 SER   ( 117-)  H    0.35
2582 SER   ( 117-)  F    0.36
1594 SER   ( 117-)  D    0.37
2088 SER   ( 117-)  E    0.37
1920 SER   ( 443-)  D    0.39

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!

   7 GLN   (  13-)  A      0
   8 GLN   (  14-)  A      0
  12 PHE   (  18-)  A      0
  13 CYS   (  19-)  A      0
  14 ASN   (  20-)  A      0
  20 ASN   (  26-)  A      0
  27 SER   (  33-)  A      0
  28 ARG   (  34-)  A      0
  29 LYS   (  35-)  A      0
  31 PHE   (  37-)  A      0
  42 ILE   (  48-)  A      0
  43 CYS   (  49-)  A      0
  66 LEU   (  72-)  A      0
 103 ASP   ( 109-)  A      0
 104 ASN   ( 110-)  A      0
 129 TRP   ( 135-)  A      0
 131 ASP   ( 137-)  A      0
 132 LYS   ( 138-)  A      0
 133 TYR   ( 139-)  A      0
 139 PRO   ( 145-)  A      0
 141 ASP   ( 147-)  A      0
 143 ASP   ( 149-)  A      0
 144 PHE   ( 150-)  A      0
 153 VAL   ( 159-)  A      0
 155 VAL   ( 161-)  A      0
And so on for a total of 1289 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 : 1.482

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!

2241 GLY   ( 270-)  E   1.64   15
2735 GLY   ( 270-)  F   1.63   14
3723 GLY   ( 270-)  H   1.59   13
 264 GLY   ( 270-)  A   1.55   14
1748 GLY   ( 271-)  D   1.53   17
1253 GLY   ( 270-)  C   1.52   14
 265 GLY   ( 271-)  A   1.52   12
3229 GLY   ( 270-)  G   1.51   17

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

2273 CYS   ( 302-)  E      SG  <-> 3986 CRD   (4515-)  E      CC4    0.83    2.57  INTRA
3261 CYS   ( 302-)  G      SG  <-> 4007 CRD   (4517-)  G      CC4    0.83    2.17  INTRA B3
1779 CYS   ( 302-)  D      SG  <-> 3979 CRD   (4514-)  D      CC4    0.79    2.61  INTRA
1779 CYS   ( 302-)  D      SG  <-> 3979 CRD   (4514-)  D      OC1    0.48    2.52  INTRA
1407 THR   ( 424-)  C      CG2 <-> 1453 MET   ( 470-)  C      SD     0.48    2.92  INTRA
 912 THR   ( 424-)  B      CG2 <->  958 MET   ( 470-)  B      SD     0.48    2.92  INTRA
2889 THR   ( 424-)  F      CG2 <-> 2935 MET   ( 470-)  F      SD     0.46    2.94  INTRA
3383 THR   ( 424-)  G      CG2 <-> 3429 MET   ( 470-)  G      SD     0.44    2.96  INTRA
3877 THR   ( 424-)  H      CG2 <-> 3923 MET   ( 470-)  H      SD     0.41    2.99  INTRA
2395 THR   ( 424-)  E      CG2 <-> 2441 MET   ( 470-)  E      SD     0.40    3.00  INTRA
1010 GLU   (  27-)  C      CG  <-> 1012 HIS   (  29-)  C      NE2    0.39    2.71  INTRA
 790 CYS   ( 302-)  B      SG  <-> 3968 CRD   (4512-)  B      CC4    0.36    3.04  INTRA
 418 THR   ( 424-)  A      CG2 <->  464 MET   ( 470-)  A      SD     0.36    3.04  INTRA
1901 THR   ( 424-)  D      CG2 <-> 1947 MET   ( 470-)  D      SD     0.34    3.06  INTRA
3045 ARG   (  86-)  G      NH1 <-> 4014 HOH   (2951 )  G      O      0.26    2.44  INTRA
3737 ASP   ( 284-)  H      OD1 <-> 3774 ARG   ( 321-)  H      NH1    0.26    2.44  INTRA
3378 ARG   ( 419-)  G      NH2 <-> 4014 HOH   (3094 )  G      O      0.24    2.46  INTRA
 229 HIS   ( 235-)  A      ND1 <->  231 ASP   ( 237-)  A      N      0.22    2.78  INTRA BL
 791 CYS   ( 303-)  B      SG  <->  947 PHE   ( 459-)  B      CZ     0.20    3.20  INTRA
1651 MET   ( 174-)  D      CE  <-> 1721 THR   ( 244-)  D      CG2    0.19    3.01  INTRA
1285 CYS   ( 302-)  C      SG  <-> 1286 CYS   ( 303-)  C      N      0.17    3.03  INTRA
1007 ILE   (  24-)  C      O   <-> 1010 GLU   (  27-)  C      CG     0.17    2.63  INTRA
2828 GLU   ( 363-)  F      OE2 <-> 2859 THR   ( 394-)  F      N      0.17    2.53  INTRA
3539 ARG   (  86-)  H      NH1 <-> 4015 HOH   (2161 )  H      O      0.17    2.53  INTRA
2643 LYS   ( 178-)  F      NZ  <-> 4013 HOH   (2336 )  F      O      0.16    2.54  INTRA
And so on for a total of 245 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

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.

1854 ARG   ( 377-)  D      -6.34
3336 ARG   ( 377-)  G      -6.16
 865 ARG   ( 377-)  B      -5.94
 501 GLN   (  13-)  B      -5.87
1490 GLN   (  13-)  D      -5.85
1984 GLN   (  13-)  E      -5.85
 996 GLN   (  13-)  C      -5.80
   7 GLN   (  13-)  A      -5.78
3466 GLN   (  13-)  H      -5.72
2478 GLN   (  13-)  F      -5.72
1839 GLN   ( 362-)  D      -5.67
1360 ARG   ( 377-)  C      -5.66
2333 GLN   ( 362-)  E      -5.66
1345 GLN   ( 362-)  C      -5.64
2912 GLN   ( 447-)  F      -5.64
3815 GLN   ( 362-)  H      -5.62
 356 GLN   ( 362-)  A      -5.59
2827 GLN   ( 362-)  F      -5.59
3321 GLN   ( 362-)  G      -5.59
2972 GLN   (  13-)  G      -5.58
 850 GLN   ( 362-)  B      -5.56
 371 ARG   ( 377-)  A      -5.55
1430 GLN   ( 447-)  C      -5.52
3830 ARG   ( 377-)  H      -5.51
2348 ARG   ( 377-)  E      -5.50
And so on for a total of 64 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

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.

2842 ARG   ( 377-)  F   -2.88
3220 ASN   ( 261-)  G   -2.67
2992 SER   (  33-)  G   -2.64
2232 ASN   ( 261-)  E   -2.63
3714 ASN   ( 261-)  H   -2.58
1440 ASP   ( 457-)  C   -2.54
 749 ASN   ( 261-)  B   -2.52
 451 ASP   ( 457-)  A   -2.52
2922 ASP   ( 457-)  F   -2.51
 624 ALA   ( 136-)  B   -2.51
1613 ALA   ( 136-)  D   -2.50

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

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.

4009 HOH   (5635 )  B      O     35.86  120.71  112.78
4009 HOH   (5806 )  B      O     50.16  115.70   74.72
4009 HOH   (5957 )  B      O     65.68   85.28   66.10
4010 HOH   (5667 )  C      O     97.68  156.73   88.79
4010 HOH   (5737 )  C      O     55.07  111.82  170.60
4011 HOH   (5664 )  D      O     86.62  102.81  161.97
4011 HOH   (5842 )  D      O    100.69   49.63   76.39
4011 HOH   (5960 )  D      O     83.22  102.84  161.60
4012 HOH   (5507 )  E      O     86.27   46.34   14.66
4012 HOH   (5706 )  E      O     46.03   18.66   33.15
4013 HOH   (2214 )  F      O     42.07   90.23  150.29
4013 HOH   (2377 )  F      O     82.50    0.32   90.42
4013 HOH   (2558 )  F      O     62.10   33.85    1.39

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.

4009 HOH   (5803 )  B      O
4012 HOH   (5874 )  E      O
4012 HOH   (5879 )  E      O
4013 HOH   (2506 )  F      O
4014 HOH   (1756 )  G      O
4014 HOH   (1804 )  G      O
ERROR. No convergence in HB2STD
Old,New value: 5891.956 5891.993
ERROR. No convergence in HB2STD
Old,New value: 5913.934 5913.984

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.

  35 ASN   (  41-)  A
 169 GLN   ( 175-)  A
 343 GLN   ( 349-)  A
 352 ASN   ( 358-)  A
 356 GLN   ( 362-)  A
 850 GLN   ( 362-)  B
1054 GLN   (  71-)  C
1158 GLN   ( 175-)  C
1237 GLN   ( 254-)  C
1341 ASN   ( 358-)  C
1502 ASN   (  25-)  D
1503 ASN   (  26-)  D
1826 GLN   ( 349-)  D
1883 GLN   ( 406-)  D
1917 ASN   ( 440-)  D
1997 ASN   (  26-)  E
2225 GLN   ( 254-)  E
2246 ASN   ( 275-)  E
2988 HIS   (  29-)  G
3234 ASN   ( 275-)  G
3466 GLN   (  13-)  H
3524 GLN   (  71-)  H
3728 ASN   ( 275-)  H
3811 ASN   ( 358-)  H
3815 GLN   ( 362-)  H

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.

  13 CYS   (  19-)  A      N
  24 ASP   (  30-)  A      N
 104 ASN   ( 110-)  A      ND2
 117 ASP   ( 123-)  A      N
 150 HIS   ( 156-)  A      NE2
 162 TRP   ( 168-)  A      N
 169 GLN   ( 175-)  A      NE2
 186 LYS   ( 192-)  A      NZ
 187 VAL   ( 193-)  A      N
 191 THR   ( 197-)  A      OG1
 238 THR   ( 244-)  A      OG1
 340 ASP   ( 346-)  A      N
 396 GLY   ( 402-)  A      N
 408 GLU   ( 414-)  A      N
 449 CYS   ( 455-)  A      N
 451 ASP   ( 457-)  A      N
 452 VAL   ( 458-)  A      N
 457 SER   ( 463-)  A      OG
 474 TYR   ( 480-)  A      OH
 611 ASP   ( 123-)  B      N
 619 TYR   ( 131-)  B      OH
 656 TRP   ( 168-)  B      N
 657 ASN   ( 169-)  B      ND2
 663 GLN   ( 175-)  B      NE2
 681 VAL   ( 193-)  B      N
And so on for a total of 163 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 150 HIS   ( 156-)  A      ND1
 158 GLN   ( 164-)  A      OE1
 269 ASN   ( 275-)  A      OD1
 400 GLN   ( 406-)  A      OE1
 451 ASP   ( 457-)  A      OD1
 644 HIS   ( 156-)  B      ND1
 652 GLN   ( 164-)  B      OE1
 763 ASN   ( 275-)  B      OD1
 894 GLN   ( 406-)  B      OE1
 945 ASP   ( 457-)  B      OD1
1033 GLN   (  50-)  C      OE1
1139 HIS   ( 156-)  C      ND1
1147 GLN   ( 164-)  C      OE1
1258 ASN   ( 275-)  C      OD1
1332 GLN   ( 349-)  C      OE1
1389 GLN   ( 406-)  C      OE1
1440 ASP   ( 457-)  C      OD1
1641 GLN   ( 164-)  D      OE1
1752 ASN   ( 275-)  D      OD1
1883 GLN   ( 406-)  D      OE1
1934 ASP   ( 457-)  D      OD1
2135 GLN   ( 164-)  E      OE1
2246 ASN   ( 275-)  E      OD1
2377 GLN   ( 406-)  E      OE1
2428 ASP   ( 457-)  E      OD1
2629 GLN   ( 164-)  F      OE1
2740 ASN   ( 275-)  F      OD1
2871 GLN   ( 406-)  F      OE1
2922 ASP   ( 457-)  F      OD1
3123 GLN   ( 164-)  G      OE1
3234 ASN   ( 275-)  G      OD1
3365 GLN   ( 406-)  G      OE1
3416 ASP   ( 457-)  G      OD1
3617 GLN   ( 164-)  H      OE1
3728 ASN   ( 275-)  H      OD1
3802 GLN   ( 349-)  H      OE1
3859 GLN   ( 406-)  H      OE1
3910 ASP   ( 457-)  H      OD1

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+.

3962  MG   (4601-)  A     0.41   0.82 Is perhaps NA *1
3966  MG   (4602-)  B   -.-  -.-  Too few ligands (3)
3971  MG   (4603-)  C     0.40   0.80 Is perhaps NA *1
3977  MG   (4604-)  D     0.47   0.93 Is perhaps NA *1
3984  MG   (4605-)  E     0.49   0.97 Is perhaps NA *1
3990  MG   (4606-)  F     0.63   1.02 Is perhaps CA (Few ligands (4) )
3996  MG   (4607-)  G     0.52   1.05 Is perhaps NA (Few ligands (4) ) *1
4001  MG   (4608-)  H     0.38   0.76 Is perhaps NA *1

Warning: Unusual water packing

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

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

4008 HOH   (5588 )  A      O  0.91  K  4 NCS 3/3
4008 HOH   (5634 )  A      O  0.88  K  4 NCS 3/3
4008 HOH   (5941 )  A      O  1.00  K  4 NCS 2/2
4009 HOH   (5709 )  B      O  0.87  K  4 NCS 3/3
4009 HOH   (5831 )  B      O  1.01  K  4 NCS 3/3
4009 HOH   (5919 )  B      O  1.12  K  4 NCS 2/2
4009 HOH   (5936 )  B      O  0.90  K  4 NCS 2/2
4010 HOH   (5603 )  C      O  0.98  K  4 NCS 2/2
4010 HOH   (5637 )  C      O  0.95  K  4 NCS 3/3
4010 HOH   (5650 )  C      O  0.86  K  4 NCS 2/2
4010 HOH   (5733 )  C      O  1.03  K  4 NCS 1/1
4010 HOH   (5812 )  C      O  0.99  K  4 Ion-B NCS 2/2
4011 HOH   (5738 )  D      O  0.89  K  4 NCS 3/3
4011 HOH   (5877 )  D      O  0.94  K  4 NCS 2/2
4012 HOH   (5548 )  E      O  0.86  K  4 Ion-B
4012 HOH   (5869 )  E      O  0.92  K  4 NCS 7/7
4013 HOH   (2330 )  F      O  1.12  K  4 NCS 4/4
4013 HOH   (2351 )  F      O  1.13  K  4 NCS 5/5
4013 HOH   (2422 )  F      O  0.95  K  4 Ion-B NCS 3/3
4013 HOH   (2441 )  F      O  0.95  K  4 Ion-B NCS 4/4
4014 HOH   (1636 )  G      O  0.89  K  4 H2O-B NCS 6/6
4014 HOH   (2984 )  G      O  1.07  K  4 NCS 7/7
4015 HOH   (3495 )  H      O  0.97  K  4 NCS 7/7

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.

 115 ASP   ( 121-)  A   H-bonding suggests Asn
 262 GLU   ( 268-)  A   H-bonding suggests Gln; but Alt-Rotamer
 393 GLU   ( 399-)  A   H-bonding suggests Gln; Ligand-contact
 756 GLU   ( 268-)  B   H-bonding suggests Gln; but Alt-Rotamer
1104 ASP   ( 121-)  C   H-bonding suggests Asn
1251 GLU   ( 268-)  C   H-bonding suggests Gln; but Alt-Rotamer
1745 GLU   ( 268-)  D   H-bonding suggests Gln; but Alt-Rotamer
2239 GLU   ( 268-)  E   H-bonding suggests Gln; but Alt-Rotamer
2733 GLU   ( 268-)  F   H-bonding suggests Gln; but Alt-Rotamer
3227 GLU   ( 268-)  G   H-bonding suggests Gln; but Alt-Rotamer
3721 GLU   ( 268-)  H   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.155
  2nd generation packing quality :  -1.035
  Ramachandran plot appearance   :  -0.455
  chi-1/chi-2 rotamer normality  :  -0.350
  Backbone conformation          :  -0.078

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.286 (tight)
  Bond angles                    :   0.561 (tight)
  Omega angle restraints         :   0.269 (tight)
  Side chain planarity           :   0.283 (tight)
  Improper dihedral distribution :   0.665
  B-factor distribution          :   0.579
  Inside/Outside distribution    :   1.055

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.15


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :   0.7
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.286 (tight)
  Bond angles                    :   0.561 (tight)
  Omega angle restraints         :   0.269 (tight)
  Side chain planarity           :   0.283 (tight)
  Improper dihedral distribution :   0.665
  B-factor distribution          :   0.579
  Inside/Outside distribution    :   1.055
==============

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.