WHAT IF Check report

This file was created 2011-12-28 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 pdb1iwa.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 C

All-atom RMS fit for the two chains : 0.398
CA-only RMS fit for the two chains : 0.206

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 E

All-atom RMS fit for the two chains : 0.339
CA-only RMS fit for the two chains : 0.199

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 G

All-atom RMS fit for the two chains : 0.514
CA-only RMS fit for the two chains : 0.377

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 G

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 I

All-atom RMS fit for the two chains : 0.392
CA-only RMS fit for the two chains : 0.202

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 I

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 K

All-atom RMS fit for the two chains : 0.477
CA-only RMS fit for the two chains : 0.322

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 K

Warning: Ligands for which a topology was generated automatically

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

4897 SO4   (4001-)  A  -
4898 SO4   (4002-)  C  -
4899 SO4   (4003-)  E  -
4900 SO4   (4004-)  G  -
4901 SO4   (4005-)  I  -
4902 SO4   (4008-)  K  -
4903 SO4   (4006-)  M  -
4904 SO4   (4007-)  O  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

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

Warning: Missing atoms

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

   1 THR   (   6-)  A      CG2
 612 THR   (   6-)  C      CG2
1223 THR   (   6-)  E      CG2
1834 THR   (   6-)  G      CG2
2445 THR   (   6-)  I      CG2
3056 THR   (   6-)  K      CG2
3667 THR   (   6-)  M      CG2
4278 THR   (   6-)  O      CG2

Warning: B-factors outside the range 0.0 - 100.0

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

1840 ARG   (  12-)  G    High
3512 TRP   ( 462-)  K    High
3668 ARG   (   7-)  M    High
4279 ARG   (   7-)  O    High

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

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.

   2 ARG   (   7-)  A
 211 ARG   ( 215-)  A
 213 ARG   ( 217-)  A
 822 ARG   ( 215-)  C
 824 ARG   ( 217-)  C
1433 ARG   ( 215-)  E
1435 ARG   ( 217-)  E
2044 ARG   ( 215-)  G
2046 ARG   ( 217-)  G
2655 ARG   ( 215-)  I
2657 ARG   ( 217-)  I
3266 ARG   ( 215-)  K
3268 ARG   ( 217-)  K
3877 ARG   ( 215-)  M
3879 ARG   ( 217-)  M
4488 ARG   ( 215-)  O
4490 ARG   ( 217-)  O

Warning: Tyrosine convention problem

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

   8 TYR   (  13-)  A
 601 TYR   ( 145-)  B
 604 TYR   ( 148-)  B
 611 TYR   ( 155-)  B
 619 TYR   (  13-)  C
1163 TYR   (  98-)  D
1212 TYR   ( 145-)  D
1215 TYR   ( 148-)  D
1222 TYR   ( 155-)  D
1230 TYR   (  13-)  E
1403 TYR   ( 185-)  E
1823 TYR   ( 145-)  F
1826 TYR   ( 148-)  F
1833 TYR   ( 155-)  F
1841 TYR   (  13-)  G
2343 TYR   (  44-)  H
2385 TYR   (  98-)  H
2429 TYR   ( 140-)  H
2434 TYR   ( 145-)  H
2437 TYR   ( 148-)  H
2444 TYR   ( 155-)  H
2452 TYR   (  13-)  I
3040 TYR   ( 140-)  J
3045 TYR   ( 145-)  J
3048 TYR   ( 148-)  J
3055 TYR   ( 155-)  J
3148 TYR   (  97-)  K
3656 TYR   ( 145-)  L
3659 TYR   ( 148-)  L
3666 TYR   ( 155-)  L
4267 TYR   ( 145-)  N
4270 TYR   ( 148-)  N
4277 TYR   ( 155-)  N
4741 TYR   ( 469-)  O
4787 TYR   (  44-)  P
4829 TYR   (  98-)  P
4873 TYR   ( 140-)  P
4878 TYR   ( 145-)  P
4881 TYR   ( 148-)  P
4888 TYR   ( 155-)  P

Warning: Phenylalanine convention problem

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

 216 PHE   ( 220-)  A
 340 PHE   ( 345-)  A
 483 PHE   (  17-)  B
 827 PHE   ( 220-)  C
 951 PHE   ( 345-)  C
1094 PHE   (  17-)  D
1438 PHE   ( 220-)  E
1562 PHE   ( 345-)  E
1705 PHE   (  17-)  F
2049 PHE   ( 220-)  G
2173 PHE   ( 345-)  G
2316 PHE   (  17-)  H
2660 PHE   ( 220-)  I
2784 PHE   ( 345-)  I
2927 PHE   (  17-)  J
3271 PHE   ( 220-)  K
3395 PHE   ( 345-)  K
3538 PHE   (  17-)  L
3882 PHE   ( 220-)  M
4006 PHE   ( 345-)  M
4149 PHE   (  17-)  N
4493 PHE   ( 220-)  O
4617 PHE   ( 345-)  O
4760 PHE   (  17-)  P
4859 PHE   ( 126-)  P

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   (  28-)  A
  29 ASP   (  33-)  A
  45 ASP   (  49-)  A
 159 ASP   ( 163-)  A
 199 ASP   ( 203-)  A
 281 ASP   ( 286-)  A
 283 ASP   ( 288-)  A
 360 ASP   ( 365-)  A
 406 ASP   ( 411-)  A
 431 ASP   ( 436-)  A
 459 ASP   ( 464-)  A
 513 ASP   (  47-)  B
 640 ASP   (  33-)  C
 656 ASP   (  49-)  C
 695 ASP   (  88-)  C
 770 ASP   ( 163-)  C
 810 ASP   ( 203-)  C
 892 ASP   ( 286-)  C
 894 ASP   ( 288-)  C
 971 ASP   ( 365-)  C
1017 ASP   ( 411-)  C
1042 ASP   ( 436-)  C
1124 ASP   (  47-)  D
1246 ASP   (  28-)  E
1251 ASP   (  33-)  E
And so on for a total of 104 lines.

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  91 GLU   (  95-)  A
 154 GLU   ( 158-)  A
 156 GLU   ( 160-)  A
 230 GLU   ( 234-)  A
 331 GLU   ( 336-)  A
 355 GLU   ( 360-)  A
 362 GLU   ( 367-)  A
 428 GLU   ( 433-)  A
 442 GLU   ( 447-)  A
 522 GLU   (  68-)  B
 540 GLU   (  86-)  B
 579 GLU   ( 123-)  B
 702 GLU   (  95-)  C
 765 GLU   ( 158-)  C
 767 GLU   ( 160-)  C
 841 GLU   ( 234-)  C
 866 GLU   ( 259-)  C
 942 GLU   ( 336-)  C
 966 GLU   ( 360-)  C
 973 GLU   ( 367-)  C
1039 GLU   ( 433-)  C
1053 GLU   ( 447-)  C
1133 GLU   (  68-)  D
1151 GLU   (  86-)  D
1313 GLU   (  95-)  E
And so on for a total of 98 lines.

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

1356 MET   ( 138-)  E      SD   CE    1.54   -4.2

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

 |  0.998984  0.000084 -0.000184|
 |  0.000084  0.999137  0.000088|
 | -0.000184  0.000088  0.999013|
Proposed new scale matrix

 |  0.004972  0.000000  0.000859|
 |  0.000000  0.006809  0.000000|
 |  0.000000  0.000000  0.005150|
With corresponding cell

    A    = 201.119  B   = 146.867  C    = 197.047
    Alpha=  90.002  Beta=  99.800  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 201.327  B   = 146.988  C    = 197.233
    Alpha=  90.000  Beta=  99.790  Gamma=  90.000

Variance: 150.259
(Under-)estimated Z-score: 9.034

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.

 196 VAL   ( 200-)  A      N    CA   C    99.54   -4.2
 360 ASP   ( 365-)  A      N    CA   C    99.06   -4.3
 643 VAL   (  36-)  C      N    CA   C    99.84   -4.1
 691 ALA   (  84-)  C      N    CA   C    98.93   -4.4
 807 VAL   ( 200-)  C      N    CA   C    98.42   -4.6
 971 ASP   ( 365-)  C      N    CA   C    99.42   -4.2
1089 GLN   (  12-)  D      N    CA   C    99.32   -4.2
1122 THR   (  45-)  D      C    CA   CB  102.22   -4.1
1259 ARG   (  41-)  E      N    CA   C    99.02   -4.3
1302 ALA   (  84-)  E      N    CA   C    99.75   -4.1
1418 VAL   ( 200-)  E      N    CA   C    98.24   -4.6
1582 ASP   ( 365-)  E      N    CA   C    97.79   -4.8
1700 GLN   (  12-)  F      N    CA   C    98.90   -4.4
1865 VAL   (  36-)  G      N    CA   C    98.90   -4.4
1870 ARG   (  41-)  G      N    CA   C    99.58   -4.2
2193 ASP   ( 365-)  G      N    CA   C    99.57   -4.2
2481 ARG   (  41-)  I      N    CA   C    99.10   -4.3
2640 VAL   ( 200-)  I      N    CA   C    99.12   -4.3
2804 ASP   ( 365-)  I      N    CA   C    98.97   -4.4
3251 VAL   ( 200-)  K      N    CA   C    98.99   -4.4
3415 ASP   ( 365-)  K      N    CA   C    97.57   -4.9
3533 GLN   (  12-)  L      N    CA   C    98.35   -4.6
3584 PHE   (  75-)  L      N    CA   C   123.23    4.3
3862 VAL   ( 200-)  M      N    CA   C    99.99   -4.0
3991 THR   ( 330-)  M      N    CA   C    96.95   -5.1
4026 ASP   ( 365-)  M      N    CA   C    97.69   -4.8
4144 GLN   (  12-)  N      N    CA   C    99.62   -4.1
4314 ARG   (  41-)  O      N    CA   C    98.75   -4.4
4602 THR   ( 330-)  O      N    CA   C    99.71   -4.1
4637 ASP   ( 365-)  O      N    CA   C    99.37   -4.2
4755 GLN   (  12-)  P      N    CA   C    99.54   -4.2

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

   2 ARG   (   7-)  A
  24 ASP   (  28-)  A
  29 ASP   (  33-)  A
  45 ASP   (  49-)  A
  91 GLU   (  95-)  A
 154 GLU   ( 158-)  A
 156 GLU   ( 160-)  A
 159 ASP   ( 163-)  A
 199 ASP   ( 203-)  A
 211 ARG   ( 215-)  A
 213 ARG   ( 217-)  A
 230 GLU   ( 234-)  A
 281 ASP   ( 286-)  A
 283 ASP   ( 288-)  A
 331 GLU   ( 336-)  A
 355 GLU   ( 360-)  A
 360 ASP   ( 365-)  A
 362 GLU   ( 367-)  A
 406 ASP   ( 411-)  A
 428 GLU   ( 433-)  A
 431 ASP   ( 436-)  A
 442 GLU   ( 447-)  A
 459 ASP   ( 464-)  A
 513 ASP   (  47-)  B
 522 GLU   (  68-)  B
And so on for a total of 219 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.

 424 LEU   ( 429-)  A    5.74
4622 LEU   ( 350-)  O    5.73
 956 LEU   ( 350-)  C    5.60
1432 TRP   ( 214-)  E    5.15
3533 GLN   (  12-)  L    5.11
3786 VAL   ( 124-)  M    5.05
 821 TRP   ( 214-)  C    4.99
4314 ARG   (  41-)  O    4.94
1700 GLN   (  12-)  F    4.90
3400 LEU   ( 350-)  K    4.90
1035 LEU   ( 429-)  C    4.88
1259 ARG   (  41-)  E    4.82
4591 ARG   ( 319-)  O    4.79
2481 ARG   (  41-)  I    4.78
1418 VAL   ( 200-)  E    4.78
1953 VAL   ( 124-)  G    4.77
3991 THR   ( 330-)  M    4.77
1089 GLN   (  12-)  D    4.73
 807 VAL   ( 200-)  C    4.70
4755 GLN   (  12-)  P    4.65
4397 VAL   ( 124-)  O    4.65
3415 ASP   ( 365-)  K    4.64
3584 PHE   (  75-)  L    4.62
4144 GLN   (  12-)  N    4.62
4026 ASP   ( 365-)  M    4.60
And so on for a total of 66 lines.

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 698 PRO   (  91-)  C    -3.1
1309 PRO   (  91-)  E    -3.1
4364 PRO   (  91-)  O    -3.1
1920 PRO   (  91-)  G    -3.1
2531 PRO   (  91-)  I    -3.0
3753 PRO   (  91-)  M    -3.0
  87 PRO   (  91-)  A    -2.9
2505 THR   (  65-)  I    -2.7
4180 ILE   (  48-)  N    -2.7
1736 ILE   (  48-)  F    -2.7
1125 ILE   (  48-)  D    -2.7
3569 ILE   (  48-)  L    -2.7
4791 ILE   (  48-)  P    -2.7
3142 PRO   (  91-)  K    -2.6
2958 ILE   (  48-)  J    -2.6
1034 ILE   ( 428-)  C    -2.6
2256 ILE   ( 428-)  G    -2.5
1569 PRO   ( 352-)  E    -2.5
2310 THR   (  11-)  H    -2.5
1645 ILE   ( 428-)  E    -2.5
   2 ARG   (   7-)  A    -2.5
1283 THR   (  65-)  E    -2.4
 334 PRO   ( 339-)  A    -2.4
4089 ILE   ( 428-)  M    -2.4
 813 ILE   ( 206-)  C    -2.4
And so on for a total of 123 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.

   6 SER   (  11-)  A  Poor phi/psi
  58 SER   (  62-)  A  Poor phi/psi
  59 THR   (  63-)  A  Poor phi/psi
  72 ALA   (  76-)  A  Poor phi/psi
  87 PRO   (  91-)  A  Poor phi/psi
 159 ASP   ( 163-)  A  Poor phi/psi
 171 LYS   ( 175-)  A  PRO omega poor
 192 GLY   ( 196-)  A  Poor phi/psi
 203 ASN   ( 207-)  A  Poor phi/psi
 208 MET   ( 212-)  A  Poor phi/psi
 290 ARG   ( 295-)  A  Poor phi/psi
 291 ALA   ( 296-)  A  Poor phi/psi
 317 GLY   ( 322-)  A  Poor phi/psi
 326 VAL   ( 331-)  A  Poor phi/psi
 364 ALA   ( 369-)  A  Poor phi/psi
 365 SER   ( 370-)  A  Poor phi/psi
 429 ASN   ( 434-)  A  Poor phi/psi
 436 GLY   ( 441-)  A  Poor phi/psi
 529 PHE   (  75-)  B  Poor phi/psi
 530 ASP   (  76-)  B  Poor phi/psi
 574 ASN   ( 118-)  B  Poor phi/psi
 589 ASP   ( 133-)  B  Poor phi/psi
 591 SER   ( 135-)  B  Poor phi/psi
 617 SER   (  11-)  C  Poor phi/psi
 669 SER   (  62-)  C  Poor phi/psi
And so on for a total of 161 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.

2669 SER   ( 229-)  I    0.36
3891 SER   ( 229-)  M    0.36
4502 SER   ( 229-)  O    0.36
3556 SER   (  35-)  L    0.37
 836 SER   ( 229-)  C    0.39
2058 SER   ( 229-)  G    0.40

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   5 ASN   (  10-)  A      0
   6 SER   (  11-)  A      0
   7 ARG   (  12-)  A      0
  10 SER   (  15-)  A      0
  18 MET   (  22-)  A      0
  20 TYR   (  24-)  A      0
  21 TRP   (  25-)  A      0
  25 TYR   (  29-)  A      0
  42 PRO   (  46-)  A      0
  57 SER   (  61-)  A      0
  58 SER   (  62-)  A      0
  59 THR   (  63-)  A      0
  60 ALA   (  64-)  A      0
  62 TRP   (  66-)  A      0
  66 TRP   (  70-)  A      0
  70 LEU   (  74-)  A      0
  72 ALA   (  76-)  A      0
  81 TYR   (  85-)  A      0
  84 ASP   (  88-)  A      0
  85 GLN   (  89-)  A      0
  88 ASN   (  92-)  A      0
  89 ASN   (  93-)  A      0
  92 GLN   (  96-)  A      0
 106 GLU   ( 110-)  A      0
 116 ILE   ( 120-)  A      0
And so on for a total of 1803 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 : 1.279

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!

4652 GLY   ( 380-)  O   2.94   11
4041 GLY   ( 380-)  M   2.80   11
 943 GLY   ( 337-)  C   2.32   12
2776 GLY   ( 337-)  I   2.17   11
 332 GLY   ( 337-)  A   2.09   10
3455 GLY   ( 405-)  K   2.08   15
4066 GLY   ( 405-)  M   1.79   80
3387 GLY   ( 337-)  K   1.65   16
4677 GLY   ( 405-)  O   1.63   80
1622 GLY   ( 405-)  E   1.62   80
 789 GLY   ( 182-)  C   1.52   15
 400 GLY   ( 405-)  A   1.52   62
3677 GLY   (  16-)  M   1.51   18

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].

  87 PRO   (  91-)  A   105.4 envelop C-beta (108 degrees)
 698 PRO   (  91-)  C   104.9 envelop C-beta (108 degrees)
1217 PRO   ( 150-)  D  -116.5 envelop C-gamma (-108 degrees)
1268 PRO   (  50-)  E  -112.6 envelop C-gamma (-108 degrees)
1309 PRO   (  91-)  E   103.7 envelop C-beta (108 degrees)
1879 PRO   (  50-)  G  -114.7 envelop C-gamma (-108 degrees)
1920 PRO   (  91-)  G    99.9 envelop C-beta (108 degrees)
2490 PRO   (  50-)  I  -117.2 half-chair C-delta/C-gamma (-126 degrees)
2531 PRO   (  91-)  I   102.7 envelop C-beta (108 degrees)
3020 PRO   ( 120-)  J  -113.2 envelop C-gamma (-108 degrees)
3753 PRO   (  91-)  M   103.4 envelop C-beta (108 degrees)
4323 PRO   (  50-)  O  -117.3 half-chair C-delta/C-gamma (-126 degrees)
4364 PRO   (  91-)  O   104.8 envelop C-beta (108 degrees)
4853 PRO   ( 120-)  P  -115.0 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

2766 HIS   ( 327-)  I      NE2 <-> 4913 HOH   (4147 )  I      O      0.47    2.23  INTRA
4432 ARG   ( 159-)  O      NH1 <-> 4669 ASP   ( 397-)  O      OD1    0.46    2.24  INTRA BL
3800 MET   ( 138-)  M      CE  <-> 3978 TRP   ( 317-)  M      NE1    0.42    2.68  INTRA BL
 766 ARG   ( 159-)  C      NH2 <->  774 ARG   ( 167-)  C      O      0.38    2.32  INTRA BL
3973 ARG   ( 312-)  M      NE  <-> 4917 HOH   (4091 )  M      O      0.38    2.32  INTRA BL
1358 LEU   ( 140-)  E      CD1 <-> 1537 MET   ( 320-)  E      SD     0.37    3.03  INTRA BL
 155 ARG   ( 159-)  A      NH2 <->  163 ARG   ( 167-)  A      O      0.36    2.34  INTRA BL
1299 ARG   (  81-)  E      NH1 <-> 4909 HOH   (4072 )  E      O      0.36    2.34  INTRA BL
2363 ASP   (  76-)  H      N   <-> 4912 HOH   ( 209 )  H      O      0.35    2.35  INTRA
 183 ARG   ( 187-)  A      NH2 <-> 4187 TRP   (  67-)  N      O      0.34    2.36  INTRA BL
 765 GLU   ( 158-)  C      OE2 <->  931 HIS   ( 325-)  C      NE2    0.33    2.37  INTRA BL
1377 ARG   ( 159-)  E      NH2 <-> 1385 ARG   ( 167-)  E      O      0.33    2.37  INTRA BL
1988 ARG   ( 159-)  G      NH2 <-> 1996 ARG   ( 167-)  G      O      0.33    2.37  INTRA BL
1969 LEU   ( 140-)  G      CD1 <-> 2148 MET   ( 320-)  G      SD     0.32    3.08  INTRA BL
3197 LYS   ( 146-)  K      NZ  <-> 4915 HOH   (4078 )  K      O      0.32    2.38  INTRA BL
2580 LEU   ( 140-)  I      CD1 <-> 2759 MET   ( 320-)  I      SD     0.31    3.09  INTRA BL
 612 THR   (   6-)  C      N   <-> 4907 HOH   (4126 )  C      O      0.31    2.39  INTRA BF
3344 HIS   ( 294-)  K      ND1 <-> 3346 ALA   ( 296-)  K      N      0.31    2.69  INTRA
3210 ARG   ( 159-)  K      NH2 <-> 3218 ARG   ( 167-)  K      O      0.31    2.39  INTRA BL
 325 THR   ( 330-)  A      O   <->  327 VAL   ( 332-)  A      N      0.31    2.39  INTRA BF
3821 ARG   ( 159-)  M      NH2 <-> 3829 ARG   ( 167-)  M      O      0.31    2.39  INTRA BL
2766 HIS   ( 327-)  I      ND1 <-> 4913 HOH   (4055 )  I      O      0.31    2.39  INTRA
1377 ARG   ( 159-)  E      NH1 <-> 1614 ASP   ( 397-)  E      OD1    0.30    2.40  INTRA BL
 521 TRP   (  67-)  B      O   <-> 2627 ARG   ( 187-)  I      NH2    0.30    2.40  INTRA
 155 ARG   ( 159-)  A      NH1 <->  392 ASP   ( 397-)  A      OD1    0.30    2.40  INTRA BL
And so on for a total of 963 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

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.

4244 HIS   ( 122-)  N      -6.23
1189 HIS   ( 122-)  D      -6.21
4855 HIS   ( 122-)  P      -6.17
3022 HIS   ( 122-)  J      -6.16
 578 HIS   ( 122-)  B      -6.13
2410 LYS   ( 121-)  H      -6.10
2446 ARG   (   7-)  I      -6.07
1835 ARG   (   7-)  G      -6.06
3633 HIS   ( 122-)  L      -6.05
3668 ARG   (   7-)  M      -6.04
1800 HIS   ( 122-)  F      -6.02
2411 HIS   ( 122-)  H      -6.02
 577 LYS   ( 121-)  B      -5.93
3057 ARG   (   7-)  K      -5.91
4243 LYS   ( 121-)  N      -5.89
   2 ARG   (   7-)  A      -5.79
4854 LYS   ( 121-)  P      -5.79
3143 ASN   (  92-)  K      -5.73
4279 ARG   (   7-)  O      -5.70
 613 ARG   (   7-)  C      -5.68
1188 LYS   ( 121-)  D      -5.68
1921 ASN   (  92-)  G      -5.46
1224 ARG   (   7-)  E      -5.43
1225 ILE   (   8-)  E      -5.43
 699 ASN   (  92-)  C      -5.42
1836 ILE   (   8-)  G      -5.33
1310 ASN   (  92-)  E      -5.33
3754 ASN   (  92-)  M      -5.28
3021 LYS   ( 121-)  J      -5.27
  88 ASN   (  92-)  A      -5.23
2447 ILE   (   8-)  I      -5.23
1799 LYS   ( 121-)  F      -5.23
3632 LYS   ( 121-)  L      -5.21
3062 ARG   (  12-)  K      -5.20
3683 LYS   (  22-)  M      -5.18
4365 ASN   (  92-)  O      -5.16
4280 ILE   (   8-)  O      -5.13
1367 GLN   ( 149-)  E      -5.08
   5 ASN   (  10-)  A      -5.07
1838 ASN   (  10-)  G      -5.06
4282 ASN   (  10-)  O      -5.05
 517 ARG   (  51-)  B      -5.02

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 577 LYS   ( 121-)  B       579 - GLU    123- ( B)         -5.48
1188 LYS   ( 121-)  D      1190 - GLU    123- ( D)         -5.36
1220 GLU   ( 153-)  D      1222 - TYR    155- ( D)         -4.29
1799 LYS   ( 121-)  F      1801 - GLU    123- ( F)         -5.20
1835 ARG   (   7-)  G      1838 - ASN     10- ( G)         -5.22
2410 LYS   ( 121-)  H      2412 - GLU    123- ( H)         -5.47
2446 ARG   (   7-)  I      2449 - ASN     10- ( I)         -5.25
3021 LYS   ( 121-)  J      3023 - GLU    123- ( J)         -5.31
3057 ARG   (   7-)  K      3060 - ASN     10- ( K)         -5.10
3632 LYS   ( 121-)  L      3634 - GLU    123- ( L)         -5.20
3668 ARG   (   7-)  M      3671 - ASN     10- ( M)         -5.16
4243 LYS   ( 121-)  N      4245 - GLU    123- ( N)         -5.56
4279 ARG   (   7-)  O      4282 - ASN     10- ( O)         -5.10
4854 LYS   ( 121-)  P      4856 - GLU    123- ( P)         -5.42

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: C

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: D

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: E

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: F

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: G

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: H

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: I

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: J

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: K

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: L

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: M

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: N

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: O

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: P

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.

   4 LYS   (   9-)  A   -2.90
4303 GLN   (  30-)  O   -2.87
1859 GLN   (  30-)  G   -2.85
2190 LEU   ( 362-)  G   -2.77
 968 LEU   ( 362-)  C   -2.76
2801 LEU   ( 362-)  I   -2.76
1579 LEU   ( 362-)  E   -2.76
4023 LEU   ( 362-)  M   -2.76
1323 LEU   ( 105-)  E   -2.74
3412 LEU   ( 362-)  K   -2.73
4634 LEU   ( 362-)  O   -2.73
1934 LEU   ( 105-)  G   -2.70
1748 LEU   (  72-)  F   -2.70
 357 LEU   ( 362-)  A   -2.69
 526 LEU   (  72-)  B   -2.68
4378 LEU   ( 105-)  O   -2.67
4192 LEU   (  72-)  N   -2.67
 956 LEU   ( 350-)  C   -2.66
3767 LEU   ( 105-)  M   -2.64
2545 LEU   ( 105-)  I   -2.63
4803 LEU   (  72-)  P   -2.63
 519 ALA   (  65-)  B   -2.62
1130 ALA   (  65-)  D   -2.60
1837 LYS   (   9-)  G   -2.58
3581 LEU   (  72-)  L   -2.57
 712 LEU   ( 105-)  C   -2.57
3156 LEU   ( 105-)  K   -2.57
1226 LYS   (   9-)  E   -2.55
1936 LEU   ( 107-)  G   -2.53

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.

3782 ILE   ( 120-)  M     - 3786 VAL   ( 124-)  M        -1.65

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Water, ion, and hydrogenbond related checks

Error: Water clusters without contacts with non-water atoms

The water molecules listed in the table below are part of water molecule clusters that do not make contacts with non-waters. These water molecules are part of clusters that have a distance at least 1 Angstrom larger than the sum of the Van der Waals radii to the nearest non-solvent atom. Because these kinds of water clusters usually are not observed with X-ray diffraction their presence could indicate a refinement artifact. The number in brackets is the identifier of the water molecule in the input file.

4908 HOH   ( 256 )  D      O
4909 HOH   (4247 )  E      O
4916 HOH   ( 166 )  L      O
4916 HOH   ( 288 )  L      O
4918 HOH   (2988 )  N      O

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.

4906 HOH   ( 239 )  B      O     86.47    6.14   85.40
4907 HOH   (4226 )  C      O     75.32   23.93    1.65
4907 HOH   (4256 )  C      O     71.51   42.94   14.19
4907 HOH   (4257 )  C      O     72.51   41.65   19.17
4907 HOH   (4285 )  C      O     69.12   34.39    9.58
4907 HOH   (4291 )  C      O     54.70   30.56    3.07
4907 HOH   (4302 )  C      O     76.55   15.19   -0.99
4907 HOH   (4304 )  C      O     45.79   10.31  -18.08
4908 HOH   ( 256 )  D      O      0.30   54.10   53.93
4909 HOH   (4254 )  E      O     61.47  -26.57    1.63
4909 HOH   (4273 )  E      O     42.03  -36.29   -8.10
4911 HOH   (4187 )  G      O     39.01  -47.46  101.79
4911 HOH   (4192 )  G      O     21.74  -46.83   91.32
4911 HOH   (4193 )  G      O     17.41  -48.03   92.33
4916 HOH   ( 222 )  L      O    103.47  -37.70   37.65
4917 HOH   (4244 )  M      O     21.36   39.84   -0.39
4917 HOH   (4276 )  M      O     48.23  -45.99    2.78
4917 HOH   (4285 )  M      O      1.96   45.23   41.35
4917 HOH   (4286 )  M      O      1.31   48.21   39.02
4918 HOH   (2988 )  N      O     93.71   26.23   43.51
4919 HOH   (4271 )  O      O    107.99   13.33   31.79
4920 HOH   ( 250 )  P      O     77.79  -57.19   72.58
4920 HOH   ( 253 )  P      O     79.64  -57.94   47.51
4920 HOH   ( 275 )  P      O     96.08  -36.59   31.98
4920 HOH   ( 282 )  P      O     79.48  -61.52   46.51
4920 HOH   ( 285 )  P      O     94.20  -39.83   38.04

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.

4905 HOH   (4073 )  A      O
4905 HOH   (4094 )  A      O
4905 HOH   (4201 )  A      O
4905 HOH   (4221 )  A      O
4905 HOH   (4223 )  A      O
4905 HOH   (4224 )  A      O
4905 HOH   (4227 )  A      O
4905 HOH   (4231 )  A      O
4905 HOH   (4236 )  A      O
4905 HOH   (4239 )  A      O
4905 HOH   (4240 )  A      O
4905 HOH   (4253 )  A      O
4905 HOH   (4254 )  A      O
4905 HOH   (4255 )  A      O
4905 HOH   (4256 )  A      O
4905 HOH   (4257 )  A      O
4905 HOH   (4265 )  A      O
4905 HOH   (4271 )  A      O
4905 HOH   (4274 )  A      O
4905 HOH   (4279 )  A      O
4906 HOH   ( 231 )  B      O
4906 HOH   ( 232 )  B      O
4906 HOH   ( 239 )  B      O
4906 HOH   ( 240 )  B      O
4906 HOH   ( 246 )  B      O
And so on for a total of 170 lines.

Error: HIS, ASN, GLN side chain flips

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

 237 ASN   ( 241-)  A
 251 ASN   ( 255-)  A
 463 ASN   ( 468-)  A
 478 GLN   (  12-)  B
 542 ASN   (  88-)  B
 574 ASN   ( 118-)  B
 599 HIS   ( 143-)  B
 848 ASN   ( 241-)  C
 904 ASN   ( 298-)  C
1089 GLN   (  12-)  D
1153 ASN   (  88-)  D
1185 ASN   ( 118-)  D
1189 HIS   ( 122-)  D
1210 HIS   ( 143-)  D
1459 ASN   ( 241-)  E
1700 GLN   (  12-)  F
1764 ASN   (  88-)  F
1796 ASN   ( 118-)  F
1821 HIS   ( 143-)  F
2070 ASN   ( 241-)  G
2084 ASN   ( 255-)  G
2216 HIS   ( 388-)  G
2296 ASN   ( 468-)  G
2311 GLN   (  12-)  H
2348 HIS   (  49-)  H
And so on for a total of 60 lines.

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

   2 ARG   (   7-)  A      N
  13 ILE   (  18-)  A      N
  61 THR   (  65-)  A      OG1
  63 THR   (  67-)  A      N
  88 ASN   (  92-)  A      N
 130 ARG   ( 134-)  A      NH2
 155 ARG   ( 159-)  A      NH2
 163 ARG   ( 167-)  A      N
 170 THR   ( 174-)  A      OG1
 171 LYS   ( 175-)  A      N
 174 LEU   ( 178-)  A      N
 175 GLY   ( 179-)  A      N
 177 SER   ( 181-)  A      N
 177 SER   ( 181-)  A      OG
 183 ARG   ( 187-)  A      NH2
 201 ASN   ( 205-)  A      ND2
 213 ARG   ( 217-)  A      NE
 213 ARG   ( 217-)  A      NH1
 240 ALA   ( 244-)  A      N
 266 VAL   ( 271-)  A      N
 290 ARG   ( 295-)  A      N
 295 THR   ( 300-)  A      N
 295 THR   ( 300-)  A      OG1
 298 ARG   ( 303-)  A      NH2
 299 GLN   ( 304-)  A      NE2
And so on for a total of 415 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.

 234 HIS   ( 238-)  A      ND1
 264 ASP   ( 268-)  A      OD2
 355 GLU   ( 360-)  A      OE1
 845 HIS   ( 238-)  C      ND1
 875 ASP   ( 268-)  C      OD2
1434 GLU   ( 216-)  E      OE2
1456 HIS   ( 238-)  E      ND1
1486 ASP   ( 268-)  E      OD2
1987 GLU   ( 158-)  G      OE1
2067 HIS   ( 238-)  G      ND1
2097 ASP   ( 268-)  G      OD2
2211 HIS   ( 383-)  G      ND1
2220 HIS   ( 392-)  G      ND1
2348 HIS   (  49-)  H      NE2
2678 HIS   ( 238-)  I      ND1
2708 ASP   ( 268-)  I      OD1
3209 GLU   ( 158-)  K      OE2
3255 GLU   ( 204-)  K      OE2
3256 ASN   ( 205-)  K      OD1
3289 HIS   ( 238-)  K      ND1
3319 ASP   ( 268-)  K      OD2
3433 HIS   ( 383-)  K      NE2
3442 HIS   ( 392-)  K      ND1
3654 HIS   ( 143-)  L      ND1
3900 HIS   ( 238-)  M      ND1
3930 ASP   ( 268-)  M      OD1
4265 HIS   ( 143-)  N      ND1
4511 HIS   ( 238-)  O      ND1
4541 ASP   ( 268-)  O      OD1
4664 HIS   ( 392-)  O      ND1

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.

4905 HOH   (4129 )  A      O  1.06  K  4
4906 HOH   ( 181 )  B      O  1.12  K  5
4906 HOH   ( 207 )  B      O  0.88  K  4 Ion-B
4907 HOH   (4005 )  C      O  0.95  K  4
4907 HOH   (4072 )  C      O  0.88 NA  5
4907 HOH   (4125 )  C      O  0.89  K  4
4907 HOH   (4130 )  C      O  0.97  K  4 Ion-B
4907 HOH   (4162 )  C      O  0.95  K  4
4907 HOH   (4188 )  C      O  0.85  K  4 Ion-B
4908 HOH   ( 164 )  D      O  1.00  K  4
4908 HOH   ( 197 )  D      O  0.91  K  5
4909 HOH   (4053 )  E      O  1.11  K  4
4909 HOH   (4123 )  E      O  0.89  K  4
4909 HOH   (4153 )  E      O  0.88  K  4
4909 HOH   (4163 )  E      O  1.03  K  4 Ion-B
4910 HOH   ( 158 )  F      O  0.87  K  4 Ion-B
4910 HOH   ( 214 )  F      O  0.92  K  4 Ion-B
4910 HOH   ( 227 )  F      O  0.93  K  5 Ion-B
4912 HOH   ( 183 )  H      O  0.97  K  5
4913 HOH   (4012 )  I      O  0.93  K  4
4913 HOH   (4051 )  I      O  1.02  K  4 Ion-B
4913 HOH   (4097 )  I      O  0.95  K  4 Ion-B
4913 HOH   (4116 )  I      O  1.09  K  4
4914 HOH   ( 408 )  J      O  0.93  K  5
4915 HOH   (4090 )  K      O  1.09  K  4
4915 HOH   (4109 )  K      O  1.05  K  5
4915 HOH   (4133 )  K      O  1.07  K  5
4915 HOH   (4136 )  K      O  1.08  K  4
4916 HOH   ( 177 )  L      O  0.90  K  5 Ion-B
4916 HOH   ( 238 )  L      O  0.97  K  4
4918 HOH   (1151 )  N      O  1.07  K  6
4919 HOH   (4154 )  O      O  1.11  K  6
4919 HOH   (4155 )  O      O  0.89  K  6
4920 HOH   ( 206 )  P      O  0.97 CA  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.

  84 ASP   (  88-)  A   H-bonding suggests Asn; but Alt-Rotamer
 264 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 420 GLU   ( 425-)  A   H-bonding suggests Gln
 455 ASP   ( 460-)  A   H-bonding suggests Asn; but Alt-Rotamer
 565 GLU   ( 109-)  B   H-bonding suggests Gln; but Alt-Rotamer
 695 ASP   (  88-)  C   H-bonding suggests Asn; but Alt-Rotamer
 875 ASP   ( 268-)  C   H-bonding suggests Asn; but Alt-Rotamer
1031 GLU   ( 425-)  C   H-bonding suggests Gln
1066 ASP   ( 460-)  C   H-bonding suggests Asn
1176 GLU   ( 109-)  D   H-bonding suggests Gln; but Alt-Rotamer
1246 ASP   (  28-)  E   H-bonding suggests Asn; but Alt-Rotamer
1306 ASP   (  88-)  E   H-bonding suggests Asn; but Alt-Rotamer
1486 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
1642 GLU   ( 425-)  E   H-bonding suggests Gln
1677 ASP   ( 460-)  E   H-bonding suggests Asn
1787 GLU   ( 109-)  F   H-bonding suggests Gln
1842 GLU   (  14-)  G   H-bonding suggests Gln
1901 ASP   (  72-)  G   H-bonding suggests Asn; but Alt-Rotamer
1917 ASP   (  88-)  G   H-bonding suggests Asn; but Alt-Rotamer
2097 ASP   ( 268-)  G   H-bonding suggests Asn; but Alt-Rotamer
2239 ASP   ( 411-)  G   H-bonding suggests Asn
2253 GLU   ( 425-)  G   H-bonding suggests Gln
2288 ASP   ( 460-)  G   H-bonding suggests Asn
2398 GLU   ( 109-)  H   H-bonding suggests Gln; but Alt-Rotamer
2528 ASP   (  88-)  I   H-bonding suggests Asn; but Alt-Rotamer
2708 ASP   ( 268-)  I   H-bonding suggests Asn
2899 ASP   ( 460-)  I   H-bonding suggests Asn
3009 GLU   ( 109-)  J   H-bonding suggests Gln; but Alt-Rotamer
3123 ASP   (  72-)  K   H-bonding suggests Asn
3139 ASP   (  88-)  K   H-bonding suggests Asn; but Alt-Rotamer
3319 ASP   ( 268-)  K   H-bonding suggests Asn; but Alt-Rotamer
3510 ASP   ( 460-)  K   H-bonding suggests Asn
3620 GLU   ( 109-)  L   H-bonding suggests Gln; but Alt-Rotamer
3675 GLU   (  14-)  M   H-bonding suggests Gln
3690 ASP   (  28-)  M   H-bonding suggests Asn
3734 ASP   (  72-)  M   H-bonding suggests Asn; but Alt-Rotamer
3750 ASP   (  88-)  M   H-bonding suggests Asn; but Alt-Rotamer
3930 ASP   ( 268-)  M   H-bonding suggests Asn; but Alt-Rotamer
4121 ASP   ( 460-)  M   H-bonding suggests Asn
4231 GLU   ( 109-)  N   H-bonding suggests Gln; but Alt-Rotamer
4345 ASP   (  72-)  O   H-bonding suggests Asn; but Alt-Rotamer
4361 ASP   (  88-)  O   H-bonding suggests Asn; but Alt-Rotamer
4541 ASP   ( 268-)  O   H-bonding suggests Asn
4697 GLU   ( 425-)  O   H-bonding suggests Gln
4842 GLU   ( 109-)  P   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 :  -0.318
  2nd generation packing quality :  -1.249
  Ramachandran plot appearance   :  -2.072
  chi-1/chi-2 rotamer normality  :  -2.571
  Backbone conformation          :  -0.335

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.279 (tight)
  Bond angles                    :   0.626 (tight)
  Omega angle restraints         :   0.232 (tight)
  Side chain planarity           :   0.229 (tight)
  Improper dihedral distribution :   0.577
  B-factor distribution          :   0.542
  Inside/Outside distribution    :   1.067

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 : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -0.4
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.279 (tight)
  Bond angles                    :   0.626 (tight)
  Omega angle restraints         :   0.232 (tight)
  Side chain planarity           :   0.229 (tight)
  Improper dihedral distribution :   0.577
  B-factor distribution          :   0.542
  Inside/Outside distribution    :   1.067
==============

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.