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 pdb1pdw.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 : 0.713
CA-only RMS fit for the two chains : 0.468

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 : 0.634
CA-only RMS fit for the two chains : 0.310

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 : 0.701
CA-only RMS fit for the two chains : 0.467

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 : 0.592
CA-only RMS fit for the two chains : 0.346

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 : 0.620
CA-only RMS fit for the two chains : 0.382

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: 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

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 2.09

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: Tyrosine convention problem

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

 253 TYR   ( 267-)  B

Warning: Phenylalanine convention problem

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

 118 PHE   ( 119-)  A
 161 PHE   ( 162-)  A
 305 PHE   ( 319-)  B
 348 PHE   ( 362-)  B
 492 PHE   (1119-)  C
 535 PHE   (1162-)  C
 679 PHE   (1319-)  D
 722 PHE   (1362-)  D
 866 PHE   (2119-)  E
 909 PHE   (2162-)  E
1055 PHE   (2319-)  F
1098 PHE   (2362-)  F
1242 PHE   (3119-)  G
1285 PHE   (3162-)  G
1433 PHE   (3319-)  H
1476 PHE   (3362-)  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.

  14 GLU   (  15-)  A
  89 GLU   (  90-)  A
 146 GLU   ( 147-)  A
 169 GLU   ( 170-)  A
 201 GLU   ( 215-)  B
 280 GLU   ( 294-)  B
 333 GLU   ( 347-)  B
 362 GLU   ( 376-)  B
 388 GLU   (1015-)  C
 520 GLU   (1147-)  C
 543 GLU   (1170-)  C
 549 GLU   (1176-)  C
 575 GLU   (1215-)  D
 703 GLU   (1343-)  D
 707 GLU   (1347-)  D
 730 GLU   (1370-)  D
 762 GLU   (2015-)  E
 894 GLU   (2147-)  E
 917 GLU   (2170-)  E
 951 GLU   (2215-)  F
1083 GLU   (2347-)  F
1106 GLU   (2370-)  F
1138 GLU   (3015-)  G
1182 GLU   (3059-)  G
1213 GLU   (3090-)  G
1270 GLU   (3147-)  G
1293 GLU   (3170-)  G
1329 GLU   (3215-)  H
1484 GLU   (3370-)  H

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

 |  0.999404 -0.000076  0.000056|
 | -0.000076  0.999145 -0.000148|
 |  0.000056 -0.000148  0.998834|
Proposed new scale matrix

 |  0.014042  0.000001  0.002617|
 |  0.000000  0.011963  0.000002|
 |  0.000000  0.000001  0.008920|
With corresponding cell

    A    =  71.214  B   =  83.589  C    = 114.033
    Alpha=  90.016  Beta= 100.559  Gamma=  90.005

The CRYST1 cell dimensions

    A    =  71.256  B   =  83.664  C    = 114.159
    Alpha=  90.000  Beta= 100.560  Gamma=  90.000

Variance: 35.668
(Under-)estimated Z-score: 4.402

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.

 529 ARG   (1156-)  C      N    CA   C   123.78    4.5
 716 ARG   (1356-)  D      N    CA   C   124.73    4.8
1092 ARG   (2356-)  F      N    CA   C   122.74    4.1
1470 ARG   (3356-)  H      N    CA   C   123.41    4.4

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.

  14 GLU   (  15-)  A
  89 GLU   (  90-)  A
 146 GLU   ( 147-)  A
 169 GLU   ( 170-)  A
 201 GLU   ( 215-)  B
 280 GLU   ( 294-)  B
 333 GLU   ( 347-)  B
 362 GLU   ( 376-)  B
 388 GLU   (1015-)  C
 520 GLU   (1147-)  C
 543 GLU   (1170-)  C
 549 GLU   (1176-)  C
 575 GLU   (1215-)  D
 703 GLU   (1343-)  D
 707 GLU   (1347-)  D
 730 GLU   (1370-)  D
 762 GLU   (2015-)  E
 894 GLU   (2147-)  E
 917 GLU   (2170-)  E
 951 GLU   (2215-)  F
1083 GLU   (2347-)  F
1106 GLU   (2370-)  F
1138 GLU   (3015-)  G
1182 GLU   (3059-)  G
1213 GLU   (3090-)  G
1270 GLU   (3147-)  G
1293 GLU   (3170-)  G
1329 GLU   (3215-)  H
1484 GLU   (3370-)  H

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.

 716 ARG   (1356-)  D    5.03
 529 ARG   (1156-)  C    4.67
 369 ALA   ( 383-)  B    4.64
 206 VAL   ( 220-)  B    4.60
1470 ARG   (3356-)  H    4.53
 580 VAL   (1220-)  D    4.49
 576 GLU   (1216-)  D    4.39
1139 GLU   (3016-)  G    4.38
 548 LYS   (1175-)  C    4.35
 952 GLU   (2216-)  F    4.35
 930 ALA   (2183-)  E    4.29
1092 ARG   (2356-)  F    4.28
1143 VAL   (3020-)  G    4.15
1436 LYS   (3322-)  H    4.04
 956 VAL   (2220-)  F    4.03

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.

 292 CYS   ( 306-)  B    -2.5
 372 VAL   ( 386-)  B    -2.5
 105 CYS   ( 106-)  A    -2.5
1420 CYS   (3306-)  H    -2.5
 853 CYS   (2106-)  E    -2.4
 479 CYS   (1106-)  C    -2.4
 185 VAL   ( 186-)  A    -2.4
1500 VAL   (3386-)  H    -2.3
1229 CYS   (3106-)  G    -2.2
 666 CYS   (1306-)  D    -2.2
1042 CYS   (2306-)  F    -2.2
 563 SER   (1203-)  D    -2.2
1122 VAL   (2386-)  F    -2.2
 559 VAL   (1186-)  C    -2.1
 933 VAL   (2186-)  E    -2.1
 323 GLY   ( 337-)  B    -2.1
1260 GLY   (3137-)  G    -2.1
1437 VAL   (3323-)  H    -2.1
1413 LYS   (3299-)  H    -2.1
 659 LYS   (1299-)  D    -2.1
1079 GLU   (2343-)  F    -2.0
 516 GLU   (1143-)  C    -2.0
 126 PRO   ( 127-)  A    -2.0
1383 VAL   (3269-)  H    -2.0
 142 GLU   ( 143-)  A    -2.0
 472 LYS   (1099-)  C    -2.0

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.

  48 ASP   (  49-)  A  Poor phi/psi
  64 GLY   (  65-)  A  Poor phi/psi
  98 LYS   (  99-)  A  Poor phi/psi
 105 CYS   ( 106-)  A  Poor phi/psi
 185 VAL   ( 186-)  A  Poor phi/psi
 235 ASP   ( 249-)  B  Poor phi/psi
 242 ALA   ( 256-)  B  Poor phi/psi
 250 GLU   ( 264-)  B  Poor phi/psi
 251 GLY   ( 265-)  B  Poor phi/psi
 285 LYS   ( 299-)  B  Poor phi/psi
 292 CYS   ( 306-)  B  Poor phi/psi
 372 VAL   ( 386-)  B  Poor phi/psi
 422 ASP   (1049-)  C  Poor phi/psi
 437 GLU   (1064-)  C  Poor phi/psi
 438 GLY   (1065-)  C  Poor phi/psi
 472 LYS   (1099-)  C  Poor phi/psi
 479 CYS   (1106-)  C  Poor phi/psi
 559 VAL   (1186-)  C  Poor phi/psi
 563 SER   (1203-)  D  Poor phi/psi
 609 ASP   (1249-)  D  Poor phi/psi
 666 CYS   (1306-)  D  Poor phi/psi
 746 VAL   (1386-)  D  Poor phi/psi
 796 ASP   (2049-)  E  Poor phi/psi
 811 GLU   (2064-)  E  Poor phi/psi
 812 GLY   (2065-)  E  Poor phi/psi
 846 LYS   (2099-)  E  Poor phi/psi
 853 CYS   (2106-)  E  Poor phi/psi
 933 VAL   (2186-)  E  Poor phi/psi
 985 ASP   (2249-)  F  Poor phi/psi
1035 LYS   (2299-)  F  Poor phi/psi
1042 CYS   (2306-)  F  Poor phi/psi
1122 VAL   (2386-)  F  Poor phi/psi
1172 ASP   (3049-)  G  Poor phi/psi
1187 GLU   (3064-)  G  Poor phi/psi
1188 GLY   (3065-)  G  Poor phi/psi
1222 LYS   (3099-)  G  Poor phi/psi
1229 CYS   (3106-)  G  Poor phi/psi
1309 VAL   (3186-)  G  Poor phi/psi
1317 SER   (3203-)  H  Poor phi/psi
1363 ASP   (3249-)  H  Poor phi/psi
1413 LYS   (3299-)  H  Poor phi/psi
1420 CYS   (3306-)  H  Poor phi/psi
1500 VAL   (3386-)  H  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.111

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.

 643 SER   (1283-)  D    0.36

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!

  11 LYS   (  12-)  A      0
  16 MSE   (  17-)  A      0
  25 MSE   (  26-)  A      0
  38 ALA   (  39-)  A      0
  40 LYS   (  41-)  A      0
  47 ARG   (  48-)  A      0
  63 GLU   (  64-)  A      0
  65 PRO   (  66-)  A      0
  67 ASP   (  68-)  A      0
 104 ILE   ( 105-)  A      0
 105 CYS   ( 106-)  A      0
 106 ALA   ( 107-)  A      0
 116 ILE   ( 117-)  A      0
 118 PHE   ( 119-)  A      0
 127 LEU   ( 128-)  A      0
 128 ALA   ( 129-)  A      0
 132 MSE   ( 133-)  A      0
 133 MSE   ( 134-)  A      0
 137 HIS   ( 138-)  A      0
 143 ASN   ( 144-)  A      0
 144 ARG   ( 145-)  A      0
 148 ASP   ( 149-)  A      0
 150 LEU   ( 151-)  A      0
 155 ARG   ( 156-)  A      0
 160 SER   ( 161-)  A      0
And so on for a total of 431 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 : 1.229

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!

 438 GLY   (1065-)  C   1.90   11
 787 GLY   (2040-)  E   1.51   13

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.

1128 ARG   (3005-)  G      NH2 <-> 1187 GLU   (3064-)  G      O      0.45    2.25  INTRA
 479 CYS   (1106-)  C      SG  <-> 1505 HOH   (4027 )  C      O      0.43    2.57  INTRA
1176 CYS   (3053-)  G      SG  <-> 1367 CYS   (3253-)  H      SG     0.42    3.03  INTRA
 191 ARG   ( 205-)  B      NH2 <->  251 GLY   ( 265-)  B      CA     0.35    2.75  INTRA BF
 565 ARG   (1205-)  D      NH2 <->  625 GLY   (1265-)  D      C      0.33    2.77  INTRA
 666 CYS   (1306-)  D      SG  <-> 1506 HOH   (4145 )  D      O      0.33    2.67  INTRA
 299 LEU   ( 313-)  B      CB  <->  319 MSE   ( 333-)  B      CE     0.31    2.89  INTRA
1106 GLU   (2370-)  F      OE2 <-> 1111 LYS   (2375-)  F      NZ     0.30    2.40  INTRA
 800 CYS   (2053-)  E      SG  <->  989 CYS   (2253-)  F      SG     0.29    3.16  INTRA
 426 CYS   (1053-)  C      SG  <->  613 CYS   (1253-)  D      SG     0.28    3.17  INTRA
  14 GLU   (  15-)  A      OE2 <->  214 ARG   ( 228-)  B      NH2    0.28    2.42  INTRA
 378 ARG   (1005-)  C      NH2 <->  437 GLU   (1064-)  C      O      0.27    2.43  INTRA
 191 ARG   ( 205-)  B      NH2 <->  251 GLY   ( 265-)  B      C      0.26    2.84  INTRA BF
 748 LYS   (1388-)  D      NZ  <-> 1506 HOH   (5001 )  D      O      0.26    2.44  INTRA
1229 CYS   (3106-)  G      SG  <-> 1509 HOH   (4677 )  G      O      0.25    2.75  INTRA
1072 GLY   (2336-)  F      N   <-> 1508 HOH   (4015 )  F      O      0.24    2.46  INTRA BL
  52 CYS   (  53-)  A      SG  <->  239 CYS   ( 253-)  B      SG     0.23    3.22  INTRA
 267 ASN   ( 281-)  B      ND2 <-> 1504 HOH   (4295 )  B      O      0.23    2.47  INTRA
 565 ARG   (1205-)  D      NH2 <->  624 GLU   (1264-)  D      O      0.23    2.47  INTRA
 462 LYS   (1089-)  C      NZ  <->  488 HIS   (1115-)  C      CD2    0.22    2.88  INTRA
1128 ARG   (3005-)  G      NH1 <-> 1189 PRO   (3066-)  G      O      0.22    2.48  INTRA
 565 ARG   (1205-)  D      NH2 <->  625 GLY   (1265-)  D      CA     0.22    2.88  INTRA
  97 ARG   (  98-)  A      NH2 <-> 1503 HOH   (4348 )  A      O      0.21    2.49  INTRA
 935 LYS   (2188-)  E      NZ  <->  937 LEU   (2190-)  E      CD1    0.21    2.89  INTRA BF
 649 LYS   (1289-)  D      NZ  <->  675 HIS   (1315-)  D      CD2    0.20    2.90  INTRA
And so on for a total of 265 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.

1314 GLU   (3191-)  G      -6.23
 414 LYS   (1041-)  C      -6.01
 788 LYS   (2041-)  E      -5.91
 977 LYS   (2241-)  F      -5.91
1164 LYS   (3041-)  G      -5.82
 601 LYS   (1241-)  D      -5.78
1355 LYS   (3241-)  H      -5.67
 658 ARG   (1298-)  D      -5.66
1221 ARG   (3098-)  G      -5.65
  40 LYS   (  41-)  A      -5.62
 845 ARG   (2098-)  E      -5.62
 882 ASN   (2135-)  E      -5.58
1034 ARG   (2298-)  F      -5.53
 227 LYS   ( 241-)  B      -5.48
1258 ASN   (3135-)  G      -5.43
 284 ARG   ( 298-)  B      -5.43
 321 ASN   ( 335-)  B      -5.42
1071 ASN   (2335-)  F      -5.42
 134 ASN   ( 135-)  A      -5.41
 508 ASN   (1135-)  C      -5.40
  97 ARG   (  98-)  A      -5.38
 471 ARG   (1098-)  C      -5.36
1342 ARG   (3228-)  H      -5.36
 214 ARG   ( 228-)  B      -5.33
 964 ARG   (2228-)  F      -5.31
 401 ARG   (1028-)  C      -5.29
1151 ARG   (3028-)  G      -5.27
 588 ARG   (1228-)  D      -5.27
 546 ASN   (1173-)  C      -5.26
1109 ASN   (2373-)  F      -5.25
1487 ASN   (3373-)  H      -5.24
 172 ASN   ( 173-)  A      -5.23
 775 ARG   (2028-)  E      -5.22
1412 ARG   (3298-)  H      -5.22
  27 ARG   (  28-)  A      -5.21
 733 ASN   (1373-)  D      -5.18
 359 ASN   ( 373-)  B      -5.17
 920 ASN   (2173-)  E      -5.15
1296 ASN   (3173-)  G      -5.14
1378 GLU   (3264-)  H      -5.02

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.

 935 LYS   (2188-)  E   -3.01
 897 GLY   (2150-)  E   -2.86
 523 GLY   (1150-)  C   -2.70
1259 GLY   (3136-)  G   -2.64
 215 ALA   ( 229-)  B   -2.60
 402 ALA   (1029-)  C   -2.57
1251 LEU   (3128-)  G   -2.56
 589 ALA   (1229-)  D   -2.55
 480 ALA   (1107-)  C   -2.54
1152 ALA   (3029-)  G   -2.51
1072 GLY   (2336-)  F   -2.51

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

1441 PRO   (3327-)  H     - 1444 LYS   (3330-)  H        -1.58

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.

1503 HOH   (4792 )  A      O    -25.77   24.94   69.72
1503 HOH   (5005 )  A      O     53.64    8.65  -28.04
1504 HOH   (4985 )  B      O    -27.53   -7.13   69.67
1505 HOH   (4913 )  C      O     35.92  -18.70    0.09
1505 HOH   (4983 )  C      O     -0.33    0.94   89.34
1505 HOH   (5015 )  C      O     15.42   52.05   28.63
1506 HOH   (4817 )  D      O     30.63   20.57   -3.20
1506 HOH   (5016 )  D      O     32.12   20.21   -5.63
1508 HOH   (4605 )  F      O     21.32   -0.80  -20.17
1508 HOH   (4651 )  F      O     -2.84   33.58   22.16
1508 HOH   (4973 )  F      O     -4.60   30.74   28.86
1508 HOH   (4991 )  F      O     -1.47   33.94   20.02
1509 HOH   (4848 )  G      O     -5.70    6.32   21.26
1510 HOH   (4998 )  H      O     -2.78   42.57  -14.40

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.

1503 HOH   (4427 )  A      O
1507 HOH   (4541 )  E      O
1509 HOH   (4750 )  G      O
1510 HOH   (4593 )  H      O
1510 HOH   (4993 )  H      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.

  80 ASN   (  81-)  A
  96 ASN   (  97-)  A
 114 HIS   ( 115-)  A
 125 HIS   ( 126-)  A
 301 HIS   ( 315-)  B
 312 HIS   ( 326-)  B
 330 ASN   ( 344-)  B
 449 ASN   (1076-)  C
 454 ASN   (1081-)  C
 488 HIS   (1115-)  C
 499 HIS   (1126-)  C
 517 ASN   (1144-)  C
 553 GLN   (1180-)  C
 675 HIS   (1315-)  D
 686 HIS   (1326-)  D
 704 ASN   (1344-)  D
 733 ASN   (1373-)  D
 740 GLN   (1380-)  D
 828 ASN   (2081-)  E
 873 HIS   (2126-)  E
 891 ASN   (2144-)  E
1012 ASN   (2276-)  F
1051 HIS   (2315-)  F
1062 HIS   (2326-)  F
1199 ASN   (3076-)  G
1204 ASN   (3081-)  G
1220 ASN   (3097-)  G
1249 HIS   (3126-)  G
1315 HIS   (3192-)  G
1429 HIS   (3315-)  H
1440 HIS   (3326-)  H
1458 ASN   (3344-)  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.

  39 GLY   (  40-)  A      N
  41 ASP   (  42-)  A      N
  47 ARG   (  48-)  A      N
  74 GLY   (  75-)  A      N
 127 LEU   ( 128-)  A      N
 138 TYR   ( 139-)  A      N
 140 TYR   ( 141-)  A      OH
 172 ASN   ( 173-)  A      ND2
 184 LEU   ( 185-)  A      N
 234 ARG   ( 248-)  B      N
 261 GLY   ( 275-)  B      N
 325 TYR   ( 339-)  B      N
 331 ARG   ( 345-)  B      NE
 359 ASN   ( 373-)  B      ND2
 363 VAL   ( 377-)  B      N
 374 LYS   ( 388-)  B      N
 512 TYR   (1139-)  C      N
 546 ASN   (1173-)  C      ND2
 602 ASP   (1242-)  D      N
 608 ARG   (1248-)  D      N
 622 LYS   (1262-)  D      NZ
 699 TYR   (1339-)  D      N
 716 ARG   (1356-)  D      NH1
 795 ARG   (2048-)  E      N
 804 SER   (2057-)  E      N
 822 GLY   (2075-)  E      N
 886 TYR   (2139-)  E      N
 903 ARG   (2156-)  E      NH1
 935 LYS   (2188-)  E      N
 938 ALA   (2202-)  F      N
1011 GLY   (2275-)  F      N
1075 TYR   (2339-)  F      N
1247 THR   (3124-)  G      OG1
1362 ARG   (3248-)  H      N
1453 TYR   (3339-)  H      N

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.

  17 GLU   (  18-)  A      OE2
  23 ASP   (  24-)  A      OD2
 204 GLU   ( 218-)  B      OE2
 210 ASP   ( 224-)  B      OD2
 397 ASP   (1024-)  C      OD2
 578 GLU   (1218-)  D      OE2
 584 ASP   (1224-)  D      OD2
 733 ASN   (1373-)  D      OD1
 765 GLU   (2018-)  E      OE2
 771 ASP   (2024-)  E      OD2
 844 ASN   (2097-)  E      OD1
 862 HIS   (2115-)  E      ND1
 954 GLU   (2218-)  F      OE2
 960 ASP   (2224-)  F      OD2
1141 GLU   (3018-)  G      OE2
1147 ASP   (3024-)  G      OD2
1238 HIS   (3115-)  G      ND1
1338 ASP   (3224-)  H      OD2

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.

1505 HOH   (4175 )  C      O  1.02  K  4
1508 HOH   (4973 )  F      O  0.86 NA  5 ION-B
1509 HOH   (5006 )  G      O  0.85 NA  4 ION-B
1510 HOH   (4057 )  H      O  1.10  K  4
1510 HOH   (4753 )  H      O  1.02  K  4

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.

 628 ASP   (1268-)  D   H-bonding suggests Asn

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 :  -0.039
  2nd generation packing quality :  -0.253
  Ramachandran plot appearance   :  -1.187
  chi-1/chi-2 rotamer normality  :  -1.111
  Backbone conformation          :   0.737

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.266 (tight)
  Bond angles                    :   0.587 (tight)
  Omega angle restraints         :   0.223 (tight)
  Side chain planarity           :   0.239 (tight)
  Improper dihedral distribution :   0.576
  B-factor distribution          :   0.671
  Inside/Outside distribution    :   0.928

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 : 2.20


Structure Z-scores, positive is better than average:

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

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.266 (tight)
  Bond angles                    :   0.587 (tight)
  Omega angle restraints         :   0.223 (tight)
  Side chain planarity           :   0.239 (tight)
  Improper dihedral distribution :   0.576
  B-factor distribution          :   0.671
  Inside/Outside distribution    :   0.928
==============

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.