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 pdb1o05.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 : 0.346
CA-only RMS fit for the two chains : 0.113

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 B

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 : 0.365
CA-only RMS fit for the two chains : 0.134

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 C

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 : 0.328
CA-only RMS fit for the two chains : 0.120

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 : 0.343
CA-only RMS fit for the two chains : 0.150

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 E

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 : 0.395
CA-only RMS fit for the two chains : 0.153

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

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: 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.

2794 VAL   ( 330-)  F
3367 LYS   ( 409-)  G
3748 PHE   ( 296-)  H

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) :110.000

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
  80 ARG   (  86-)  A
  84 ARG   (  90-)  A
  91 ARG   (  97-)  A
  93 ARG   (  99-)  A
 124 ARG   ( 130-)  A
 413 ARG   ( 419-)  A
 522 ARG   (  34-)  B
 574 ARG   (  86-)  B
 578 ARG   (  90-)  B
 585 ARG   (  97-)  B
 587 ARG   (  99-)  B
 618 ARG   ( 130-)  B
 739 ARG   ( 251-)  B
 907 ARG   ( 419-)  B
1016 ARG   (  34-)  C
1068 ARG   (  86-)  C
1072 ARG   (  90-)  C
1079 ARG   (  97-)  C
1081 ARG   (  99-)  C
1112 ARG   ( 130-)  C
1233 ARG   ( 251-)  C
1401 ARG   ( 419-)  C
1510 ARG   (  34-)  D
1562 ARG   (  86-)  D
And so on for a total of 59 lines.

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
 620 TYR   ( 132-)  B
 641 TYR   ( 153-)  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
1100 TYR   ( 118-)  C
1114 TYR   ( 132-)  C
1135 TYR   ( 153-)  C
1338 TYR   ( 356-)  C
1361 TYR   ( 379-)  C
1407 TYR   ( 425-)  C
1438 TYR   ( 456-)  C
And so on for a total of 69 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
 218 PHE   ( 224-)  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
 374 PHE   ( 380-)  A
 380 PHE   ( 386-)  A
 404 PHE   ( 410-)  A
 453 PHE   ( 459-)  A
 506 PHE   (  18-)  B
 638 PHE   ( 150-)  B
 658 PHE   ( 170-)  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
 276 ASP   ( 282-)  A
 370 ASP   ( 376-)  A
 429 ASP   ( 435-)  A
 431 ASP   ( 437-)  A
 518 ASP   (  30-)  B
 609 ASP   ( 121-)  B
 625 ASP   ( 137-)  B
 864 ASP   ( 376-)  B
 923 ASP   ( 435-)  B
 925 ASP   ( 437-)  B
1012 ASP   (  30-)  C
1103 ASP   ( 121-)  C
1119 ASP   ( 137-)  C
1417 ASP   ( 435-)  C
1419 ASP   ( 437-)  C
1506 ASP   (  30-)  D
1597 ASP   ( 121-)  D
1613 ASP   ( 137-)  D
1911 ASP   ( 435-)  D
1913 ASP   ( 437-)  D
2000 ASP   (  30-)  E
2091 ASP   ( 121-)  E
2107 ASP   ( 137-)  E
2346 ASP   ( 376-)  E
2405 ASP   ( 435-)  E
2407 ASP   ( 437-)  E
2494 ASP   (  30-)  F
2585 ASP   ( 121-)  F
2601 ASP   ( 137-)  F
2840 ASP   ( 376-)  F
2899 ASP   ( 435-)  F
2901 ASP   ( 437-)  F
2988 ASP   (  30-)  G
3079 ASP   ( 121-)  G
3095 ASP   ( 137-)  G
3393 ASP   ( 435-)  G
3395 ASP   ( 437-)  G
3482 ASP   (  30-)  H
3573 ASP   ( 121-)  H
3589 ASP   ( 137-)  H
3887 ASP   ( 435-)  H
3889 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
 204 GLU   ( 210-)  A
 242 GLU   ( 248-)  A
 282 GLU   ( 288-)  A
 306 GLU   ( 312-)  A
 311 GLU   ( 317-)  A
 341 GLU   ( 347-)  A
 357 GLU   ( 363-)  A
 392 GLU   ( 398-)  A
 473 GLU   ( 479-)  A
 481 GLU   ( 487-)  A
 504 GLU   (  16-)  B
 584 GLU   (  96-)  B
 594 GLU   ( 106-)  B
 683 GLU   ( 195-)  B
 698 GLU   ( 210-)  B
 736 GLU   ( 248-)  B
 776 GLU   ( 288-)  B
 800 GLU   ( 312-)  B
 805 GLU   ( 317-)  B
 808 GLU   ( 320-)  B
 851 GLU   ( 363-)  B
And so on for a total of 120 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

 |  0.998339  0.000073 -0.000004|
 |  0.000073  0.998321  0.000098|
 | -0.000004  0.000098  0.998381|
Proposed new scale matrix

 |  0.007095  0.000000  0.000000|
 |  0.000000  0.006593  0.000000|
 |  0.000000  0.000000  0.005655|
With corresponding cell

    A    = 140.949  B   = 151.674  C    = 176.830
    Alpha=  90.002  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 141.180  B   = 151.940  C    = 177.120
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 343.634
(Under-)estimated Z-score: 13.662

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    98.65   -4.5
 137 THR   ( 143-)  A      N    CA   C    99.06   -4.3
 500 ASN   (  12-)  B      N    CA   C    97.94   -4.7
 631 THR   ( 143-)  B      N    CA   C    99.30   -4.3
 644 HIS   ( 156-)  B      CG   ND1  CE1 109.63    4.0
 994 ASN   (  12-)  C      N    CA   C    99.08   -4.3
1125 THR   ( 143-)  C      N    CA   C    98.98   -4.4
1138 HIS   ( 156-)  C      CG   ND1  CE1 109.65    4.0
1172 VAL   ( 190-)  C      N    CA   C    99.58   -4.1
1488 ASN   (  12-)  D      N    CA   C    98.89   -4.4
1505 HIS   (  29-)  D      CG   ND1  CE1 109.62    4.0
1619 THR   ( 143-)  D      N    CA   C    99.00   -4.4
1632 HIS   ( 156-)  D      CG   ND1  CE1 109.67    4.1
1982 ASN   (  12-)  E      N    CA   C    99.41   -4.2
2113 THR   ( 143-)  E      N    CA   C    99.22   -4.3
2476 ASN   (  12-)  F      N    CA   C    99.05   -4.3
2607 THR   ( 143-)  F      N    CA   C    99.75   -4.1
2970 ASN   (  12-)  G      N    CA   C    99.73   -4.1
3101 THR   ( 143-)  G      N    CA   C    99.42   -4.2
3114 HIS   ( 156-)  G      CG   ND1  CE1 109.92    4.3
3464 ASN   (  12-)  H      N    CA   C    97.68   -4.8
3595 THR   ( 143-)  H      N    CA   C    99.69   -4.1
3608 HIS   ( 156-)  H      CG   ND1  CE1 109.65    4.0

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
  80 ARG   (  86-)  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
 124 ARG   ( 130-)  A
 131 ASP   ( 137-)  A
 204 GLU   ( 210-)  A
 242 GLU   ( 248-)  A
 276 ASP   ( 282-)  A
 282 GLU   ( 288-)  A
 306 GLU   ( 312-)  A
 311 GLU   ( 317-)  A
 341 GLU   ( 347-)  A
 357 GLU   ( 363-)  A
 370 ASP   ( 376-)  A
 392 GLU   ( 398-)  A
 413 ARG   ( 419-)  A
 429 ASP   ( 435-)  A
And so on for a total of 224 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.

1181 LEU   ( 199-)  C    6.69
3157 LEU   ( 199-)  G    6.22
 193 LEU   ( 199-)  A    6.06
 800 GLU   ( 312-)  B    5.76
2663 LEU   ( 199-)  F    5.71
2776 GLU   ( 312-)  F    5.66
2169 LEU   ( 199-)  E    5.61
 687 LEU   ( 199-)  B    5.55
3651 LEU   ( 199-)  H    5.53
 677 VAL   ( 189-)  B    5.35
3764 GLU   ( 312-)  H    5.25
 183 VAL   ( 189-)  A    5.17
1171 VAL   ( 189-)  C    4.99
1665 VAL   ( 189-)  D    4.96
3147 VAL   ( 189-)  G    4.91
1675 LEU   ( 199-)  D    4.89
3270 GLU   ( 312-)  G    4.77
1788 GLU   ( 312-)  D    4.76
2159 VAL   ( 189-)  E    4.67
3641 VAL   ( 189-)  H    4.61
3464 ASN   (  12-)  H    4.60
 500 ASN   (  12-)  B    4.51
 933 ALA   ( 445-)  B    4.48
1125 THR   ( 143-)  C    4.42
1619 THR   ( 143-)  D    4.41
 137 THR   ( 143-)  A    4.38
2759 PHE   ( 295-)  F    4.36
2653 VAL   ( 189-)  F    4.35
2113 THR   ( 143-)  E    4.31
 631 THR   ( 143-)  B    4.28
   6 ASN   (  12-)  A    4.28
3101 THR   ( 143-)  G    4.23
1427 ALA   ( 445-)  C    4.21
1277 PHE   ( 295-)  C    4.21
 439 ALA   ( 445-)  A    4.20
1488 ASN   (  12-)  D    4.20
3593 GLY   ( 141-)  H    4.20
3403 ALA   ( 445-)  G    4.18
1172 VAL   ( 190-)  C    4.17
1771 PHE   ( 295-)  D    4.15
2415 ALA   ( 445-)  E    4.15
2476 ASN   (  12-)  F    4.15
 994 ASN   (  12-)  C    4.14
2235 VAL   ( 265-)  E    4.12
3595 THR   ( 143-)  H    4.12
2607 THR   ( 143-)  F    4.09
 528 VAL   (  40-)  B    4.05
1982 ASN   (  12-)  E    4.03
2998 VAL   (  40-)  G    4.03
1066 ARG   (  84-)  C    4.02

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.

1877 PHE   ( 401-)  D    -3.6
2371 PHE   ( 401-)  E    -3.5
 395 PHE   ( 401-)  A    -3.5
3359 PHE   ( 401-)  G    -3.5
3853 PHE   ( 401-)  H    -3.5
2865 PHE   ( 401-)  F    -3.3
 889 PHE   ( 401-)  B    -3.3
1383 PHE   ( 401-)  C    -3.3
 133 TYR   ( 139-)  A    -2.7
2141 PRO   ( 171-)  E    -2.7
1615 TYR   ( 139-)  D    -2.6
3591 TYR   ( 139-)  H    -2.6
2109 TYR   ( 139-)  E    -2.5
3097 TYR   ( 139-)  G    -2.5
1121 TYR   ( 139-)  C    -2.5
 627 TYR   ( 139-)  B    -2.4
2603 TYR   ( 139-)  F    -2.4
3391 THR   ( 433-)  G    -2.3
1909 THR   ( 433-)  D    -2.3
1627 PHE   ( 151-)  D    -2.3
 522 ARG   (  34-)  B    -2.3
1153 PRO   ( 171-)  C    -2.3
1944 TYR   ( 468-)  D    -2.3
 984 PRO   ( 496-)  B    -2.2
2897 THR   ( 433-)  F    -2.2
And so on for a total of 55 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
 263 LEU   ( 269-)  A  Poor phi/psi
 291 ASN   ( 297-)  A  Poor phi/psi
 292 GLN   ( 298-)  A  Poor phi/psi
 382 ASP   ( 388-)  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
 451 ASP   ( 457-)  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
 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
 867 TYR   ( 379-)  B  Poor phi/psi
And so on for a total of 123 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.

1593 SER   ( 117-)  D    0.34
3075 SER   ( 117-)  G    0.35
3569 SER   ( 117-)  H    0.36
 605 SER   ( 117-)  B    0.36
 111 SER   ( 117-)  A    0.38
1099 SER   ( 117-)  C    0.38
2581 SER   ( 117-)  F    0.38
2087 SER   ( 117-)  E    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
 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
 162 TRP   ( 168-)  A      0
And so on for a total of 1295 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 : 1.393

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!

2240 GLY   ( 270-)  E   1.66   17
2734 GLY   ( 270-)  F   1.56   17
3228 GLY   ( 270-)  G   1.51   15

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 490 PRO   ( 496-)  A    0.46 HIGH
3948 PRO   ( 496-)  H    0.46 HIGH

Warning: Unusual PRO puckering phases

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

3103 PRO   ( 145-)  G    51.9 half-chair C-delta/C-gamma (54 degrees)

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.

3876 THR   ( 424-)  H      CG2 <-> 3922 MET   ( 470-)  H      SD     0.46    2.94  INTRA
 790 CYS   ( 302-)  B      SG  <-> 3970 HOH   (5117 )  B      O      0.37    2.63  INTRA
1284 CYS   ( 302-)  C      SG  <-> 3971 HOH   (5134 )  C      O      0.36    2.64  INTRA
 296 CYS   ( 302-)  A      SG  <-> 3969 HOH   (5107 )  A      O      0.32    2.68  INTRA
1900 THR   ( 424-)  D      CG2 <-> 1946 MET   ( 470-)  D      SD     0.27    3.13  INTRA
 572 ARG   (  84-)  B      NH2 <-> 3970 HOH   (5177 )  B      O      0.27    2.43  INTRA
1273 HIS   ( 291-)  C      NE2 <-> 1311 ARG   ( 329-)  C      NH1    0.26    2.74  INTRA BL
3754 CYS   ( 302-)  H      SG  <-> 3976 HOH   (2265 )  H      O      0.25    2.75  INTRA
2056 ARG   (  86-)  E      NH1 <-> 3973 HOH   (2346 )  E      O      0.25    2.45  INTRA
2054 ARG   (  84-)  E      NH2 <-> 3973 HOH   (2286 )  E      O      0.24    2.46  INTRA
3914 GLN   ( 462-)  H      NE2 <-> 3976 HOH   (2615 )  H      O      0.24    2.46  INTRA
3260 CYS   ( 302-)  G      SG  <-> 3975 HOH   (2156 )  G      O      0.24    2.76  INTRA
 273 SER   ( 279-)  A      N   <->  305 GLN   ( 311-)  A      OE1    0.23    2.47  INTRA
2054 ARG   (  84-)  E      NH1 <-> 2154 ALA   ( 184-)  E      O      0.23    2.47  INTRA BL
1566 ARG   (  90-)  D      NH1 <-> 3972 HOH   ( 720 )  D      O      0.21    2.49  INTRA
1444 GLN   ( 462-)  C      NE2 <-> 3971 HOH   (5086 )  C      O      0.20    2.50  INTRA BL
2394 THR   ( 424-)  E      CG2 <-> 2440 MET   ( 470-)  E      SD     0.20    3.20  INTRA
2550 ARG   (  86-)  F      NH1 <-> 3974 HOH   (2040 )  F      O      0.20    2.50  INTRA
2827 GLU   ( 363-)  F      OE2 <-> 2858 THR   ( 394-)  F      N      0.19    2.51  INTRA
 574 ARG   (  86-)  B      NH1 <-> 3970 HOH   (5040 )  B      O      0.19    2.51  INTRA
2478 GLN   (  14-)  F      NE2 <-> 3974 HOH   (2674 )  F      O      0.18    2.52  INTRA
 502 GLN   (  14-)  B      NE2 <-> 3970 HOH   (5281 )  B      O      0.18    2.52  INTRA
 568 ASP   (  80-)  B      OD1 <-> 1480 LYS   ( 498-)  C      NZ     0.17    2.53  INTRA BL
2971 GLN   (  13-)  G      NE2 <-> 3975 HOH   (2988 )  G      O      0.17    2.53  INTRA
3731 SER   ( 279-)  H      N   <-> 3763 GLN   ( 311-)  H      OE1    0.16    2.54  INTRA
And so on for a total of 304 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.

3335 ARG   ( 377-)  G      -6.58
2347 ARG   ( 377-)  E      -6.01
 865 ARG   ( 377-)  B      -5.93
1489 GLN   (  13-)  D      -5.81
   7 GLN   (  13-)  A      -5.79
2911 GLN   ( 447-)  F      -5.76
1983 GLN   (  13-)  E      -5.75
1429 GLN   ( 447-)  C      -5.73
2971 GLN   (  13-)  G      -5.73
3829 ARG   ( 377-)  H      -5.72
2477 GLN   (  13-)  F      -5.72
 371 ARG   ( 377-)  A      -5.68
1853 ARG   ( 377-)  D      -5.68
1838 GLN   ( 362-)  D      -5.67
 995 GLN   (  13-)  C      -5.65
 356 GLN   ( 362-)  A      -5.65
2826 GLN   ( 362-)  F      -5.64
3320 GLN   ( 362-)  G      -5.63
2332 GLN   ( 362-)  E      -5.62
 501 GLN   (  13-)  B      -5.62
3405 GLN   ( 447-)  G      -5.60
1344 GLN   ( 362-)  C      -5.60
1923 GLN   ( 447-)  D      -5.59
 850 GLN   ( 362-)  B      -5.58
3465 GLN   (  13-)  H      -5.58
And so on for a total of 63 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.

1243 ASN   ( 261-)  C   -2.78
1737 ASN   ( 261-)  D   -2.71
3219 ASN   ( 261-)  G   -2.62
 749 ASN   ( 261-)  B   -2.59
 624 ALA   ( 136-)  B   -2.55
3713 ASN   ( 261-)  H   -2.54
1439 ASP   ( 457-)  C   -2.53
2600 ALA   ( 136-)  F   -2.53
3094 ALA   ( 136-)  G   -2.53
3588 ALA   ( 136-)  H   -2.52
 945 ASP   ( 457-)  B   -2.52
 130 ALA   ( 136-)  A   -2.52
1118 ALA   ( 136-)  C   -2.51
1933 ASP   ( 457-)  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.

3969 HOH   (5275 )  A      O     29.17   26.88   97.68
3970 HOH   (5015 )  B      O     27.16  129.03  113.80
3970 HOH   (5380 )  B      O     31.80  125.80  121.05
3971 HOH   (5337 )  C      O     94.13  131.29   70.77
3972 HOH   ( 847 )  D      O     87.70  120.77  166.55
3973 HOH   (1960 )  E      O    108.24  121.64   97.34
3973 HOH   (1977 )  E      O    103.10   98.46  103.73
3973 HOH   (2416 )  E      O     98.85  114.78   86.14
3973 HOH   (2442 )  E      O     79.43   47.06    9.78
3973 HOH   (3055 )  E      O     86.23   46.40   14.88
3974 HOH   (1518 )  F      O    107.68    3.73   90.54
3974 HOH   (2304 )  F      O     96.01   -0.88   87.60
3976 HOH   (2865 )  H      O     24.77  133.45   89.05

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.

3971 HOH   (5400 )  C      O
3972 HOH   ( 864 )  D      O

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.

  20 ASN   (  26-)  A
  35 ASN   (  41-)  A
 169 GLN   ( 175-)  A
 190 GLN   ( 196-)  A
 269 ASN   ( 275-)  A
 294 GLN   ( 300-)  A
 352 ASN   ( 358-)  A
 501 GLN   (  13-)  B
 502 GLN   (  14-)  B
 514 ASN   (  26-)  B
 529 ASN   (  41-)  B
 663 GLN   ( 175-)  B
 684 GLN   ( 196-)  B
 788 GLN   ( 300-)  B
1008 ASN   (  26-)  C
1023 ASN   (  41-)  C
1282 GLN   ( 300-)  C
1502 ASN   (  26-)  D
1517 ASN   (  41-)  D
1651 GLN   ( 175-)  D
1672 GLN   ( 196-)  D
1751 ASN   ( 275-)  D
1776 GLN   ( 300-)  D
1825 GLN   ( 349-)  D
1834 ASN   ( 358-)  D
1996 ASN   (  26-)  E
2011 ASN   (  41-)  E
2145 GLN   ( 175-)  E
2166 GLN   ( 196-)  E
2245 ASN   ( 275-)  E
2270 GLN   ( 300-)  E
2639 GLN   ( 175-)  F
2764 GLN   ( 300-)  F
2984 ASN   (  26-)  G
2999 ASN   (  41-)  G
3154 GLN   ( 196-)  G
3233 ASN   ( 275-)  G
3258 GLN   ( 300-)  G
3307 GLN   ( 349-)  G
3420 GLN   ( 462-)  G
3478 ASN   (  26-)  H
3493 ASN   (  41-)  H
3627 GLN   ( 175-)  H
3648 GLN   ( 196-)  H
3727 ASN   ( 275-)  H
3752 GLN   ( 300-)  H
3914 GLN   ( 462-)  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
 104 ASN   ( 110-)  A      ND2
 117 ASP   ( 123-)  A      N
 146 SER   ( 152-)  A      N
 148 THR   ( 154-)  A      OG1
 162 TRP   ( 168-)  A      N
 169 GLN   ( 175-)  A      NE2
 187 VAL   ( 193-)  A      N
 238 THR   ( 244-)  A      OG1
 265 GLY   ( 271-)  A      N
 267 SER   ( 273-)  A      OG
 340 ASP   ( 346-)  A      N
 422 ALA   ( 428-)  A      N
 449 CYS   ( 455-)  A      N
 450 TYR   ( 456-)  A      N
 451 ASP   ( 457-)  A      N
 452 VAL   ( 458-)  A      N
 457 SER   ( 463-)  A      OG
 598 ASN   ( 110-)  B      ND2
 663 GLN   ( 175-)  B      NE2
 681 VAL   ( 193-)  B      N
 786 GLN   ( 298-)  B      NE2
 789 CYS   ( 301-)  B      N
 834 ASP   ( 346-)  B      N
 878 GLN   ( 390-)  B      N
And so on for a total of 135 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
 262 GLU   ( 268-)  A      OE2
 269 ASN   ( 275-)  A      OD1
 400 GLN   ( 406-)  A      OE1
 451 ASP   ( 457-)  A      OD1
 652 GLN   ( 164-)  B      OE1
 763 ASN   ( 275-)  B      OD1
 894 GLN   ( 406-)  B      OE1
 945 ASP   ( 457-)  B      OD1
1146 GLN   ( 164-)  C      OE1
1388 GLN   ( 406-)  C      OE1
1439 ASP   ( 457-)  C      OD1
1640 GLN   ( 164-)  D      OE1
1744 GLU   ( 268-)  D      OE2
1751 ASN   ( 275-)  D      OD1
1882 GLN   ( 406-)  D      OE1
1933 ASP   ( 457-)  D      OD1
2126 HIS   ( 156-)  E      ND1
2134 GLN   ( 164-)  E      OE1
2245 ASN   ( 275-)  E      OD1
2376 GLN   ( 406-)  E      OE1
2427 ASP   ( 457-)  E      OD1
2620 HIS   ( 156-)  F      ND1
2628 GLN   ( 164-)  F      OE1
2739 ASN   ( 275-)  F      OD1
2870 GLN   ( 406-)  F      OE1
2921 ASP   ( 457-)  F      OD1
3122 GLN   ( 164-)  G      OE1
3226 GLU   ( 268-)  G      OE2
3233 ASN   ( 275-)  G      OD1
3364 GLN   ( 406-)  G      OE1
3415 ASP   ( 457-)  G      OD1
3498 GLU   (  46-)  H      OE2
3608 HIS   ( 156-)  H      ND1
3616 GLN   ( 164-)  H      OE1
3727 ASN   ( 275-)  H      OD1
3858 GLN   ( 406-)  H      OE1
3909 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+.

3963  NA   (5003-)  B     0.61   1.08 Is perhaps  K (Few ligands (4) )
3964  NA   (5004-)  C     0.47   0.70 Scores about as good as  K (Few ligands (4) )
3966  NA   (5006-)  F   -.-  -.-  Too few ligands (3)

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.

3969 HOH   (5076 )  A      O  1.01  K  4 NCS 3/3
3969 HOH   (5119 )  A      O  0.99  K  4 NCS 3/3
3969 HOH   (5158 )  A      O  0.93  K  4 NCS 3/3
3970 HOH   (5042 )  B      O  0.89  K  4 NCS 2/2
3970 HOH   (5062 )  B      O  0.89  K  4 Ion-B NCS 1/1
3970 HOH   (5077 )  B      O  1.01  K  4 NCS 3/3
3970 HOH   (5115 )  B      O  0.99  K  4 NCS 3/3
3970 HOH   (5125 )  B      O  0.86  K  4 NCS 2/2
3971 HOH   (5144 )  C      O  1.01  K  4 NCS 3/3
3971 HOH   (5363 )  C      O  0.90  K  4 Ion-B NCS 1/1
3972 HOH   ( 546 )  D      O  0.87 NA  6 *1 NCS 1/1
3972 HOH   ( 565 )  D      O  1.02  K  4 NCS 2/2
3972 HOH   ( 622 )  D      O  0.87  K  4 NCS 3/3
3972 HOH   ( 644 )  D      O  1.04  K  4 NCS 3/3
3973 HOH   (2355 )  E      O  0.96  K  5 Ion-B NCS 7/7
3974 HOH   (1426 )  F      O  0.97  K  4 NCS 7/7
3974 HOH   (1481 )  F      O  0.95  K  4 NCS 7/7
3974 HOH   (2070 )  F      O  0.91  K  5 NCS 6/6
3975 HOH   (2157 )  G      O  0.87  K  5 NCS 6/6
3976 HOH   (2231 )  H      O  0.87  K  4 NCS 7/7
3976 HOH   (2370 )  H      O  0.85  K  4 Ion-B NCS 5/5

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.

  54 ASP   (  60-)  A   H-bonding suggests Asn
  87 ASP   (  93-)  A   H-bonding suggests Asn
 262 GLU   ( 268-)  A   H-bonding suggests Gln; but Alt-Rotamer
 515 GLU   (  27-)  B   H-bonding suggests Gln; but Alt-Rotamer
 609 ASP   ( 121-)  B   H-bonding suggests Asn; but Alt-Rotamer
 756 GLU   ( 268-)  B   H-bonding suggests Gln; but Alt-Rotamer
1042 ASP   (  60-)  C   H-bonding suggests Asn; but Alt-Rotamer
1103 ASP   ( 121-)  C   H-bonding suggests Asn; but Alt-Rotamer
1250 GLU   ( 268-)  C   H-bonding suggests Gln; but Alt-Rotamer
1536 ASP   (  60-)  D   H-bonding suggests Asn
1744 GLU   ( 268-)  D   H-bonding suggests Gln; but Alt-Rotamer
2238 GLU   ( 268-)  E   H-bonding suggests Gln; but Alt-Rotamer
2573 ASP   ( 109-)  F   H-bonding suggests Asn
2732 GLU   ( 268-)  F   H-bonding suggests Gln; but Alt-Rotamer
3720 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 :   0.138
  2nd generation packing quality :  -1.042
  Ramachandran plot appearance   :  -0.661
  chi-1/chi-2 rotamer normality  :  -0.838
  Backbone conformation          :  -0.123

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.294 (tight)
  Bond angles                    :   0.571 (tight)
  Omega angle restraints         :   0.253 (tight)
  Side chain planarity           :   0.298 (tight)
  Improper dihedral distribution :   0.678
  B-factor distribution          :   0.636
  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 : 2.25


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :   0.4
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.294 (tight)
  Bond angles                    :   0.571 (tight)
  Omega angle restraints         :   0.253 (tight)
  Side chain planarity           :   0.298 (tight)
  Improper dihedral distribution :   0.678
  B-factor distribution          :   0.636
  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.