WHAT IF Check report

This file was created 2013-12-10 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 pdb4gkk.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 768685.000
Volume of the Unit Cell V= 28440010.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.625
Vm by authors and this calculated Vm agree remarkably well
Matthews coefficient read from REMARK 280 Vm= 4.600

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.

4120 PAR   (1785-)  A  -

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: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: V

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'.

1507 OADE  (1511-)  A      C3'
1507 OADE  (1511-)  A      O3'
1507 OADE  (1511-)  A      O5'
1507 OADE  (1511-)  A      C5'
1507 OADE  (1511-)  A      C4'
1507 OADE  (1511-)  A      O4'
1507 OADE  (1511-)  A      C1'
1507 OADE  (1511-)  A      C2'
1507 OADE  (1511-)  A      N9
1507 OADE  (1511-)  A      C8
1507 OADE  (1511-)  A      N7
1507 OADE  (1511-)  A      C5
1507 OADE  (1511-)  A      C6
1507 OADE  (1511-)  A      N6
1507 OADE  (1511-)  A      N1
1507 OADE  (1511-)  A      C2
1507 OADE  (1511-)  A      N3
1507 OADE  (1511-)  A      C4
1507 OADE  (1511-)  A      O2'

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.

   1 OURA  (   5-)  A    High
  69 OGUA  (  73-)  A    High
  70 OCYT  (  74-)  A    High
  76 OURA  (  80-)  A    High
  77 OURA  (  81-)  A    High
 136 OGUA  ( 140-)  A    High
 144 OCYT  ( 148-)  A    High
 145 OCYT  ( 149-)  A    High
 146 OGUA  ( 150-)  A    High
 147 OGUA  ( 151-)  A    High
 148 OGUA  ( 152-)  A    High
 149 OGUA  ( 153-)  A    High
 150 OADE  ( 154-)  A    High
 151 OADE  ( 155-)  A    High
 152 OADE  ( 156-)  A    High
 153 OCYT  ( 157-)  A    High
 154 OURA  ( 158-)  A    High
 155 OCYT  ( 159-)  A    High
 156 OGUA  ( 160-)  A    High
 157 OGUA  ( 161-)  A    High
 190 OURA  ( 194-)  A    High
 204 OURA  ( 208-)  A    High
 205 OURA  ( 209-)  A    High
 206 OURA  ( 210-)  A    High
 207 OGUA  ( 211-)  A    High
And so on for a total of 1289 lines.

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 1

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: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: V

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.

2070 ARG   ( 118-)  D

Warning: Tyrosine convention problem

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

1538 TYR   (  31-)  B
1599 TYR   (  92-)  B
1655 TYR   ( 148-)  B
1706 TYR   ( 199-)  B
1743 TYR   ( 236-)  B
1775 TYR   (  29-)  C
1794 TYR   (  48-)  C
1930 TYR   ( 184-)  C
1972 TYR   (  20-)  D
1979 TYR   (  27-)  D
1990 TYR   (  38-)  D
2090 TYR   ( 138-)  D
2159 TYR   ( 207-)  D
2217 TYR   (  60-)  E
2290 TYR   ( 133-)  E
2344 TYR   (  33-)  F
2374 TYR   (  63-)  F
2429 TYR   (  18-)  G
2455 TYR   (  44-)  G
2496 TYR   (  85-)  G
2562 TYR   ( 151-)  G
2565 TYR   ( 154-)  G
2587 TYR   (  20-)  H
2615 TYR   (  48-)  H
2629 TYR   (  62-)  H
2661 TYR   (  94-)  H
2708 TYR   (   4-)  I
2709 TYR   (   5-)  I
2740 TYR   (  36-)  I
2766 TYR   (  62-)  I
2796 TYR   (  92-)  I
2829 TYR   ( 125-)  I
2940 TYR   (  20-)  K
2945 TYR   (  25-)  K
2970 TYR   (  50-)  K
3114 TYR   (  69-)  L
3150 TYR   ( 105-)  L
3165 TYR   ( 120-)  L
3463 TYR   (  17-)  P
3478 TYR   (  32-)  P
3504 TYR   (  58-)  P
3560 TYR   (  32-)  Q
3902 TYR   (  18-)  V
3905 TYR   (  21-)  V

Warning: Phenylalanine convention problem

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

1524 PHE   (  17-)  B
1562 PHE   (  55-)  B
1577 PHE   (  70-)  B
1670 PHE   ( 163-)  B
2045 PHE   (  93-)  D
2183 PHE   (  26-)  E
2371 PHE   (  60-)  F
2408 PHE   (  97-)  F
2722 PHE   (  18-)  I
2741 PHE   (  37-)  I
2763 PHE   (  59-)  I
2805 PHE   ( 101-)  I
2841 PHE   (  11-)  J
2877 PHE   (  47-)  J
2893 PHE   (  63-)  J
3045 PHE   ( 125-)  K
3334 PHE   (  37-)  N
3455 PHE   (   9-)  P
3526 PHE   (  80-)  P
3555 PHE   (  27-)  Q
3599 PHE   (  71-)  Q
3647 PHE   (  29-)  R
3699 PHE   (  81-)  R
3715 PHE   (  10-)  S
3779 PHE   (  74-)  S

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.

1550 ASP   (  43-)  B
1586 ASP   (  79-)  B
1698 ASP   ( 191-)  B
1702 ASP   ( 195-)  B
1705 ASP   ( 198-)  B
1713 ASP   ( 206-)  B
1782 ASP   (  36-)  C
1802 ASP   (  56-)  C
1929 ASP   ( 183-)  C
2005 ASP   (  53-)  D
2054 ASP   ( 102-)  D
2142 ASP   ( 190-)  D
2366 ASP   (  55-)  F
2394 ASP   (  83-)  F
2431 ASP   (  20-)  G
2592 ASP   (  25-)  H
2619 ASP   (  52-)  H
2621 ASP   (  54-)  H
2640 ASP   (  73-)  H
2736 ASP   (  32-)  I
2758 ASP   (  54-)  I
2779 ASP   (  75-)  I
2842 ASP   (  12-)  J
2956 ASP   (  36-)  K
2987 ASP   (  67-)  K
3030 ASP   ( 110-)  K
3031 ASP   ( 111-)  K
3151 ASP   ( 106-)  L
3157 ASP   ( 112-)  L
3378 ASP   (  21-)  O
3475 ASP   (  29-)  P
3486 ASP   (  40-)  P
3493 ASP   (  47-)  P
3574 ASP   (  46-)  Q
3717 ASP   (  12-)  S
3718 ASP   (  13-)  S

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.

1519 GLU   (  12-)  B
1542 GLU   (  35-)  B
1556 GLU   (  49-)  B
1559 GLU   (  52-)  B
1624 GLU   ( 117-)  B
1650 GLU   ( 143-)  B
1677 GLU   ( 170-)  B
1781 GLU   (  35-)  C
1804 GLU   (  58-)  C
1851 GLU   ( 105-)  C
1907 GLU   ( 161-)  C
1912 GLU   ( 166-)  C
1967 GLU   (  15-)  D
1976 GLU   (  24-)  D
2024 GLU   (  72-)  D
2032 GLU   (  80-)  D
2033 GLU   (  81-)  D
2144 GLU   ( 192-)  D
2152 GLU   ( 200-)  D
2157 GLU   ( 205-)  D
2164 GLU   (   7-)  E
2236 GLU   (  79-)  E
2238 GLU   (  81-)  E
2279 GLU   ( 122-)  E
2333 GLU   (  22-)  F
And so on for a total of 56 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.

  12 OADE  (  16-)  A      C6   N1    1.32   -4.1
  28 OADE  (  32-)  A      N9   C4    1.40    4.9
  97 OGUA  ( 101-)  A      N9   C8    1.41    4.6
  97 OGUA  ( 101-)  A      N1   C2    1.41    4.0
 105 OADE  ( 109-)  A      N9   C4    1.35   -4.7
 113 OGUA  ( 117-)  A      C6   O6    1.28    4.3
 114 OURA  ( 118-)  A      C4   O4    1.29    6.8
 171 OGUA  ( 175-)  A      N9   C4    1.41    4.4
 227 OGUA  ( 231-)  A      C6   O6    1.27    4.2
 257 OGUA  ( 261-)  A      N9   C4    1.32   -6.3
 270 OADE  ( 274-)  A      N9   C4    1.33   -6.7
 270 OADE  ( 274-)  A      C5   C6    1.37   -4.5
 299 OCYT  ( 303-)  A      N1   C6    1.34   -5.0
 304 OADE  ( 308-)  A      N9   C4    1.35   -4.2
 344 OADE  ( 348-)  A      N9   C4    1.35   -4.2
 535 OCYT  ( 539-)  A      N1   C6    1.34   -4.1
 547 OGUA  ( 551-)  A      C1'  N9    1.50    4.1
 556 OGUA  ( 560-)  A      C5   C6    1.38   -4.2
 574 OGUA  ( 578-)  A      N7   C5    1.36   -5.2
 590 OADE  ( 594-)  A      N9   C4    1.35   -4.3
 613 OCYT  ( 617-)  A      C4   N3    1.30   -5.1
 655 OADE  ( 659-)  A      N9   C4    1.35   -4.2
 670 OGUA  ( 674-)  A      N7   C5    1.36   -4.2
 709 OGUA  ( 713-)  A      N7   C5    1.36   -4.1
 759 OADE  ( 763-)  A      N9   C4    1.35   -4.2
 790 OCYT  ( 794-)  A      N1   C6    1.34   -5.1
 793 OADE  ( 797-)  A      N7   C5    1.36   -5.4
 793 OADE  ( 797-)  A      C5   C6    1.37   -4.1
 795 OADE  ( 799-)  A      N9   C4    1.34   -6.0
 838 OADE  ( 842-)  A      N3   C4    1.32   -4.0
 858 OGUA  ( 862-)  A      N9   C8    1.34   -4.8
 891 OADE  ( 895-)  A      C6   N1    1.32   -4.0
 892 OADE  ( 896-)  A      N9   C4    1.35   -4.7
 919 OADE  ( 923-)  A      N3   C4    1.32   -4.8
1062 OGUA  (1066-)  A      C5   C4    1.35   -4.5
1204 OADE  (1208-)  A      N9   C4    1.34   -5.9
1276 OADE  (1280-)  A      N3   C4    1.31   -5.2
1373 OCYT  (1377-)  A      N1   C6    1.34   -5.1
1375 OCYT  (1379-)  A      N1   C6    1.40    5.8
1375 OCYT  (1379-)  A      N3   C2    1.39    4.9
1375 OCYT  (1379-)  A      C4   N3    1.37    4.8
1475 OADE  (1479-)  A      C5   C6    1.36   -4.9
1483 OURA  (1487-)  A      N3   C2    1.34   -4.8
1492 OADE  (1496-)  A      N9   C4    1.40    4.8
1496 OGUA  (1500-)  A      N3   C4    1.32   -4.6
1497 OCYT  (1501-)  A      N1   C6    1.34   -4.4
1499 OGUA  (1503-)  A      C5   C4    1.35   -4.1
2887 LYS   (  57-)  J      CB   CG    1.65    4.5
2887 LYS   (  57-)  J      CG   CD    1.65    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

 |  1.002169  0.000195  0.000014|
 |  0.000195  1.001532  0.000124|
 |  0.000014  0.000124  1.001622|
Proposed new scale matrix

 |  0.002480  0.000000  0.000000|
 |  0.000000  0.002481  0.000000|
 |  0.000000  0.000000  0.005685|
With corresponding cell

    A    = 403.287  B   = 403.031  C    = 175.908
    Alpha=  90.003  Beta=  90.003  Gamma=  90.005

The CRYST1 cell dimensions

    A    = 402.370  B   = 402.370  C    = 175.620
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 2723.056
(Under-)estimated Z-score: 38.459

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.

   2 OGUA  (   6-)  A      P   -C3* -O3* 127.62    6.6
   2 OGUA  (   6-)  A      N9   C8   N7  113.64    5.1
   3 OGUA  (   7-)  A      N9   C4   C5  102.32   -7.7
   3 OGUA  (   7-)  A      C8   N9   C4  108.92    6.3
   3 OGUA  (   7-)  A      N7   C5   C6  127.65   -4.6
   3 OGUA  (   7-)  A      N7   C5   C4  113.17    5.9
   3 OGUA  (   7-)  A      C5   C6   O6  125.80   -4.7
   3 OGUA  (   7-)  A      O6   C6   N1  123.87    6.6
   3 OGUA  (   7-)  A      C2   N3   C4  109.90   -4.0
   5 OGUA  (   9-)  A      N9   C8   N7  113.73    5.3
   5 OGUA  (   9-)  A      O6   C6   N1  122.59    4.5
  11 OGUA  (  15-)  A      C1'  N9   C8  121.73   -4.1
  12 OADE  (  16-)  A      N6   C6   N1  116.09   -4.2
  16 OURA  (  20-)  A      C5   C4   O4  123.47   -4.1
  17 OGUA  (  21-)  A      C8   N9   C4  108.13    4.3
  17 OGUA  (  21-)  A      N2   C2   N3  123.30    4.9
  19 OCYT  (  23-)  A      N1   C2   O2  121.36    4.1
  19 OCYT  (  23-)  A      N3   C2   O2  118.77   -4.5
  22 OADE  (  26-)  A      N6   C6   N1  121.14    4.2
  25 OGUA  (  29-)  A      C5   C6   O6  125.92   -4.5
  25 OGUA  (  29-)  A      O6   C6   N1  122.52    4.4
  28 OADE  (  32-)  A      N9   C8   N7  115.90    4.2
  28 OADE  (  32-)  A      C8   N9   C4  103.20   -6.5
  31 OGUA  (  35-)  A      N9   C8   N7  113.84    5.5
  32 OCYT  (  36-)  A      C6   N1   C2  118.69   -4.0
And so on for a total of 960 lines.

Error: Nomenclature error(s)

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

1519 GLU   (  12-)  B
1542 GLU   (  35-)  B
1550 ASP   (  43-)  B
1556 GLU   (  49-)  B
1559 GLU   (  52-)  B
1586 ASP   (  79-)  B
1624 GLU   ( 117-)  B
1650 GLU   ( 143-)  B
1677 GLU   ( 170-)  B
1698 ASP   ( 191-)  B
1702 ASP   ( 195-)  B
1705 ASP   ( 198-)  B
1713 ASP   ( 206-)  B
1781 GLU   (  35-)  C
1782 ASP   (  36-)  C
1802 ASP   (  56-)  C
1804 GLU   (  58-)  C
1851 GLU   ( 105-)  C
1907 GLU   ( 161-)  C
1912 GLU   ( 166-)  C
1929 ASP   ( 183-)  C
1967 GLU   (  15-)  D
1976 GLU   (  24-)  D
2005 ASP   (  53-)  D
2024 GLU   (  72-)  D
And so on for a total of 93 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.

3855 ALA   (  76-)  T    4.99
2208 VAL   (  51-)  E    4.97
1964 CYS   (  12-)  D    4.90
3164 LYS   ( 119-)  L    4.56
2221 ARG   (  64-)  E    4.54
2238 GLU   (  81-)  E    4.51
2545 ALA   ( 134-)  G    4.50
3828 ALA   (  49-)  T    4.45
1718 ILE   ( 211-)  B    4.30
3785 TYR   (  80-)  S    4.13
1750 LYS   (   4-)  C    4.04

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.429

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.

1743 TYR   ( 236-)  B    -3.7
3311 PRO   (  14-)  N    -3.1
2869 PRO   (  39-)  J    -3.0
2834 ILE   (   4-)  J    -3.0
1957 ILE   (   5-)  D    -3.0
2907 PRO   (  77-)  J    -3.0
2658 ARG   (  91-)  H    -2.9
3093 PRO   (  48-)  L    -2.9
3181 ILE   (   9-)  M    -2.9
1813 THR   (  67-)  C    -2.9
1972 TYR   (  20-)  D    -2.8
2504 PRO   (  93-)  G    -2.8
1911 THR   ( 165-)  C    -2.8
2227 PRO   (  70-)  E    -2.8
2465 THR   (  54-)  G    -2.8
3125 HIS   (  80-)  L    -2.8
2836 ILE   (   6-)  J    -2.8
1950 LEU   ( 204-)  C    -2.8
2792 TYR   (  88-)  I    -2.7
2961 THR   (  41-)  K    -2.7
1793 LEU   (  47-)  C    -2.7
1515 LYS   (   8-)  B    -2.7
1528 ARG   (  21-)  B    -2.7
2731 THR   (  27-)  I    -2.7
3558 PRO   (  30-)  Q    -2.7
And so on for a total of 187 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.

1515 LYS   (   8-)  B  Poor phi/psi
1516 GLU   (   9-)  B  Poor phi/psi
1518 LEU   (  11-)  B  omega poor
1519 GLU   (  12-)  B  omega poor
1521 GLY   (  14-)  B  Poor phi/psi
1522 VAL   (  15-)  B  omega poor
1524 PHE   (  17-)  B  Poor phi/psi
1527 GLU   (  20-)  B  Poor phi/psi
1528 ARG   (  21-)  B  Poor phi/psi
1531 TRP   (  24-)  B  omega poor
1544 ASN   (  37-)  B  Poor phi/psi
1584 ALA   (  77-)  B  Poor phi/psi
1600 VAL   (  93-)  B  omega poor
1602 GLN   (  95-)  B  Poor phi/psi
1607 GLY   ( 100-)  B  Poor phi/psi
1637 ARG   ( 130-)  B  Poor phi/psi
1646 LYS   ( 139-)  B  Poor phi/psi
1658 GLY   ( 151-)  B  omega poor
1688 PHE   ( 181-)  B  Poor phi/psi
1696 ASP   ( 189-)  B  Poor phi/psi, omega poor
1707 ILE   ( 200-)  B  omega poor
1714 ALA   ( 207-)  B  Poor phi/psi
1717 SER   ( 210-)  B  Poor phi/psi
1718 ILE   ( 211-)  B  Poor phi/psi
1735 GLY   ( 228-)  B  Poor phi/psi
And so on for a total of 258 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -5.490

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.

3034 VAL   ( 114-)  K    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!

   3 OGUA  (   7-)  A      0
   4 OADE  (   8-)  A      0
   5 OGUA  (   9-)  A      0
   6 OADE  (  10-)  A      0
   7 OGUA  (  11-)  A      0
   8 OURA  (  12-)  A      0
   9 OURA  (  13-)  A      0
  10 OURA  (  14-)  A      0
  11 OGUA  (  15-)  A      0
  12 OADE  (  16-)  A      0
  13 OURA  (  17-)  A      0
  14 OCYT  (  18-)  A      0
  15 OCYT  (  19-)  A      0
  16 OURA  (  20-)  A      0
  17 OGUA  (  21-)  A      0
  18 OGUA  (  22-)  A      0
  19 OCYT  (  23-)  A      0
  20 OURA  (  24-)  A      0
  21 OCYT  (  25-)  A      0
  22 OADE  (  26-)  A      0
  23 OGUA  (  27-)  A      0
  24 OGUA  (  28-)  A      0
  25 OGUA  (  29-)  A      0
  26 OURA  (  30-)  A      0
  27 OGUA  (  31-)  A      0
And so on for a total of 2518 lines.

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!

1891 GLY   ( 145-)  C   3.17   61
1710 GLY   ( 203-)  B   2.68   18
2804 GLY   ( 100-)  I   2.59   21
3198 GLY   (  26-)  M   2.42   10
1734 GLY   ( 227-)  B   2.37   16
1596 GLY   (  89-)  B   1.94   21
2543 GLY   ( 132-)  G   1.80   13
2726 GLY   (  22-)  I   1.70   11
2021 GLY   (  69-)  D   1.62   32
3443 GLY   (  86-)  O   1.54   11
2923 GLY   (  93-)  J   1.51   57

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].

1690 PRO   ( 183-)  B   108.5 envelop C-beta (108 degrees)
1739 PRO   ( 232-)  B   163.9 half-chair C-alpha/N (162 degrees)
1741 PRO   ( 234-)  B  -139.4 envelop C-delta (-144 degrees)
1860 PRO   ( 114-)  C    99.5 envelop C-beta (108 degrees)
1989 PRO   (  37-)  D   -65.8 envelop C-beta (-72 degrees)
2094 PRO   ( 142-)  D    50.0 half-chair C-delta/C-gamma (54 degrees)
2206 PRO   (  49-)  E  -172.8 envelop N (180 degrees)
2209 PRO   (  52-)  E    38.2 envelop C-delta (36 degrees)
2227 PRO   (  70-)  E   -62.7 half-chair C-beta/C-alpha (-54 degrees)
2234 PRO   (  77-)  E  -127.0 half-chair C-delta/C-gamma (-126 degrees)
2469 PRO   (  58-)  G    52.9 half-chair C-delta/C-gamma (54 degrees)
2504 PRO   (  93-)  G  -170.6 half-chair N/C-delta (-162 degrees)
2572 PRO   (   5-)  H    49.3 half-chair C-delta/C-gamma (54 degrees)
2624 PRO   (  57-)  H    19.7 half-chair N/C-delta (18 degrees)
2753 PRO   (  49-)  I  -120.1 half-chair C-delta/C-gamma (-126 degrees)
2869 PRO   (  39-)  J   117.4 half-chair C-beta/C-alpha (126 degrees)
2907 PRO   (  77-)  J   -56.5 half-chair C-beta/C-alpha (-54 degrees)
2921 PRO   (  91-)  J   -63.4 envelop C-beta (-72 degrees)
2978 PRO   (  58-)  K   100.3 envelop C-beta (108 degrees)
3170 PRO   ( 125-)  L   102.0 envelop C-beta (108 degrees)
3269 PRO   (  97-)  M  -167.0 half-chair N/C-delta (-162 degrees)
3285 PRO   ( 113-)  M  -158.1 half-chair N/C-delta (-162 degrees)
3311 PRO   (  14-)  N    -9.4 half-chair C-alpha/N (-18 degrees)
3376 PRO   (  19-)  O  -126.4 half-chair C-delta/C-gamma (-126 degrees)
3558 PRO   (  30-)  Q  -125.0 half-chair C-delta/C-gamma (-126 degrees)
3575 PRO   (  47-)  Q    46.0 half-chair C-delta/C-gamma (54 degrees)
3592 PRO   (  64-)  Q  -113.6 envelop C-gamma (-108 degrees)
3634 PRO   (  16-)  R   101.8 envelop C-beta (108 degrees)
3747 PRO   (  42-)  S   102.7 envelop C-beta (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.

1275 OCYT  (1279-)  A      OP2 <-> 2525 ARG   ( 114-)  G      NH2    0.68    2.02  INTRA BF
3072 LEU   (  27-)  L      O   <-> 3074 GLY   (  29-)  L      N      0.61    2.09  INTRA BL
1782 ASP   (  36-)  C      OD1 <-> 1805 ARG   (  59-)  C      NH2    0.59    2.11  INTRA BF
 418 OURA  ( 422-)  A      OP2 <-> 1988 ARG   (  36-)  D      NH2    0.57    2.13  INTRA BL
2143 ARG   ( 191-)  D      NH1 <-> 2152 GLU   ( 200-)  D      OE1    0.53    2.17  INTRA BF
3910 OADE  (   1-)  W      N1  <-> 3916 OURA  (  36-)  X      N3     0.53    2.47  INTRA BL
1002 OCYT  (1006-)  A      N3  <-> 1012 OGUA  (1016-)  A      N2     0.53    2.47  INTRA BF
1225 OADE  (1229-)  A      N3  <-> 2774 LYS   (  70-)  I      NZ     0.52    2.48  INTRA BF
1760 ILE   (  14-)  C      O   <-> 1762 ARG   (  16-)  C      N      0.51    2.19  INTRA BF
 981 OCYT  ( 985-)  A      N3  <->  996 OGUA  (1000-)  A      N2     0.50    2.50  INTRA BF
1166 OCYT  (1170-)  A      OP1 <-> 2881 ARG   (  51-)  J      NH2    0.50    2.20  INTRA BL
1105 OGUA  (1109-)  A      N1  <-> 1122 OGUA  (1126-)  A      N7     0.50    2.50  INTRA BF
1051 OURA  (1055-)  A      OP2 <-> 2214 LYS   (  57-)  E      NZ     0.49    2.21  INTRA BL
 667 OGUA  ( 671-)  A      N1  <->  678 OCYT  ( 682-)  A      N3     0.48    2.52  INTRA BL
2571 ASP   (   4-)  H      OD2 <-> 2652 ARG   (  85-)  H      NH1    0.47    2.23  INTRA BL
1051 OURA  (1055-)  A      N3  <-> 1080 OADE  (1084-)  A      N1     0.47    2.53  INTRA BL
2804 GLY   ( 100-)  I      O   <-> 2806 LEU   ( 102-)  I      N      0.47    2.23  INTRA BF
 814 OURA  ( 818-)  A      OP1 <-> 3682 ARG   (  64-)  R      NH2    0.46    2.24  INTRA BL
1111 OGUA  (1115-)  A      N2  <-> 1119 OCYT  (1123-)  A      O2     0.46    2.24  INTRA BF
  12 OADE  (  16-)  A      N6  <->  892 OADE  ( 896-)  A      N1     0.45    2.55  INTRA BL
 974 OADE  ( 978-)  A      N1  <->  975 OGUA  ( 979-)  A      N2     0.45    2.55  INTRA BF
3706 LYS   (  88-)  R      NZ  <-> 3930 LYS   (  88-)  R      O''    0.44    2.26  INTRA BF
2117 MET   ( 165-)  D      SD  <-> 2120 ARG   ( 168-)  D      NH1    0.44    2.86  INTRA BF
1900 SER   ( 154-)  C      OG  <-> 1901 GLY   ( 155-)  C      N      0.44    2.16  INTRA BF
 597 OCYT  ( 601-)  A      N3  <->  601 OADE  ( 605-)  A      N6     0.43    2.57  INTRA BL
And so on for a total of 1606 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: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

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.

3708 ARG   (   3-)  S      -8.69
1825 ARG   (  79-)  C      -8.63
3297 ARG   ( 125-)  M      -8.45
3629 ARG   ( 101-)  Q      -8.37
3785 TYR   (  80-)  S      -8.33
2417 ARG   (   6-)  G      -8.31
2001 ARG   (  49-)  D      -8.19
2859 ARG   (  29-)  J      -8.03
3908 ARG   (  24-)  V      -7.91
3783 ARG   (  78-)  S      -7.83
3445 ARG   (  88-)  O      -7.70
3591 ARG   (  63-)  Q      -7.63
3276 ARG   ( 104-)  M      -7.63
2490 ARG   (  79-)  G      -7.61
2828 GLN   ( 124-)  I      -7.55
3309 ARG   (  12-)  N      -7.55
1994 GLN   (  42-)  D      -7.46
2884 PHE   (  54-)  J      -7.42
2566 ARG   ( 155-)  G      -7.41
2415 ARG   (   4-)  G      -7.39
2636 ARG   (  69-)  H      -7.37
2525 ARG   ( 114-)  G      -7.33
1955 ARG   (   3-)  D      -7.30
2443 ARG   (  32-)  G      -7.27
2283 ARG   ( 126-)  E      -7.23
And so on for a total of 172 lines.

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.

1528 ARG   (  21-)  B      1530 - ARG     23- ( B)         -5.02
1749 ASN   (   3-)  C      1751 - ILE      5- ( C)         -5.36
1955 ARG   (   3-)  D      1957 - ILE      5- ( D)         -6.61
1997 GLN   (  45-)  D      1999 - ARG     47- ( D)         -4.97
2036 LYS   (  84-)  D      2038 - LYS     86- ( D)         -5.06
2176 MET   (  19-)  E      2179 - GLY     22- ( E)         -5.10
2309 ARG   ( 152-)  E      2311 - GLY    154- ( E)         -5.05
2414 ARG   (   3-)  G      2417 - ARG      6- ( G)         -7.08
2427 LEU   (  16-)  G      2429 - TYR     18- ( G)         -4.61
2635 ARG   (  68-)  H      2637 - GLN     70- ( H)         -6.46
2671 ARG   ( 104-)  H      2673 - GLY    106- ( H)         -4.95
2713 ARG   (   9-)  I      2715 - LYS     11- ( I)         -4.45
2918 LEU   (  88-)  J      2920 - LEU     90- ( J)         -5.05
3045 PHE   ( 125-)  K      3048 - ALA    128- ( K)         -5.04
3060 ARG   (  15-)  L      3062 - LYS     17- ( L)         -4.75
3064 ARG   (  19-)  L      3066 - LYS     21- ( L)         -4.71
3171 LYS   ( 126-)  L      3173 - ALA    128- ( L)         -5.75
3286 ARG   ( 114-)  M      3289 - VAL    117- ( M)         -4.94
3291 GLY   ( 119-)  M      3294 - LYS    122- ( M)         -5.31
3428 GLN   (  71-)  O      3430 - GLU     73- ( O)         -4.83
3526 PHE   (  80-)  P      3528 - GLN     82- ( P)         -5.53
3628 LYS   ( 100-)  Q      3630 - GLY    102- ( Q)         -6.53
3699 PHE   (  81-)  R      3701 - GLU     83- ( R)         -4.96
3783 ARG   (  78-)  S      3785 - TYR     80- ( S)         -6.77

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 3919 : -1.592

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

Note: Quality value plot

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

Chain identifier: M

Note: Quality value plot

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

Chain identifier: N

Note: Quality value plot

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

Chain identifier: O

Note: Quality value plot

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

Chain identifier: P

Note: Quality value plot

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

Chain identifier: Q

Note: Quality value plot

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

Chain identifier: R

Note: Quality value plot

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

Chain identifier: S

Note: Quality value plot

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

Chain identifier: T

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: V

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.

3136 LYS   (  91-)  L   -3.58
2946 ASN   (  26-)  K   -3.50
2828 GLN   ( 124-)  I   -3.44
2885 LYS   (  55-)  J   -3.37
3783 ARG   (  78-)  S   -3.32
3278 ASN   ( 106-)  M   -3.28
3328 ARG   (  31-)  N   -3.18
1749 ASN   (   3-)  C   -3.15
3711 LYS   (   6-)  S   -3.11
2715 LYS   (  11-)  I   -3.08
2884 PHE   (  54-)  J   -3.06
3091 LYS   (  46-)  L   -3.02
3759 GLY   (  54-)  S   -2.95
1994 GLN   (  42-)  D   -2.92
3720 LEU   (  15-)  S   -2.90
1977 ARG   (  25-)  D   -2.89
3302 ALA   (   5-)  N   -2.88
1758 LEU   (  12-)  C   -2.85
2568 MET   (   1-)  H   -2.83
2808 ARG   ( 104-)  I   -2.83
3488 ARG   (  42-)  P   -2.83
3295 ALA   ( 123-)  M   -2.82
3036 HIS   ( 116-)  K   -2.79
3591 ARG   (  63-)  Q   -2.79
3276 ARG   ( 104-)  M   -2.77
2829 TYR   ( 125-)  I   -2.77
1988 ARG   (  36-)  D   -2.77
2414 ARG   (   3-)  G   -2.73
3038 GLY   ( 118-)  K   -2.70
1955 ARG   (   3-)  D   -2.70
3318 TYR   (  21-)  N   -2.70
2418 ALA   (   7-)  G   -2.69
3076 PRO   (  31-)  L   -2.63
3303 LEU   (   6-)  N   -2.63
2815 ARG   ( 111-)  I   -2.62
2421 ARG   (  10-)  G   -2.62
3040 ARG   ( 120-)  K   -2.60
2361 TYR   (  50-)  F   -2.59
2816 LYS   ( 112-)  I   -2.58
3315 VAL   (  18-)  N   -2.57
3044 LYS   ( 124-)  K   -2.53
3471 ARG   (  25-)  P   -2.53
2682 SER   ( 115-)  H   -2.52
3888 GLY   (   4-)  V   -2.52
3357 SER   (  60-)  N   -2.52

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.

1747 GLN   ( 240-)  B     - 1751 ILE   (   5-)  C        -2.17
1992 PRO   (  40-)  D     - 1995 HIS   (  43-)  D        -1.90
2442 MET   (  31-)  G     - 2445 GLY   (  34-)  G        -1.85
2567 TRP   ( 156-)  G     - 2570 THR   (   3-)  H        -2.27
2809 ASP   ( 105-)  I     - 2813 VAL   ( 109-)  I        -1.93
2814 GLU   ( 110-)  I     - 2818 TYR   ( 114-)  I        -1.81
2883 PRO   (  53-)  J     - 2887 LYS   (  57-)  J        -2.54
3035 PRO   ( 115-)  K     - 3040 ARG   ( 120-)  K        -2.25
3041 PRO   ( 121-)  K     - 3044 LYS   ( 124-)  K        -1.76
3061 GLU   (  16-)  L     - 3066 LYS   (  21-)  L        -1.91
3090 PRO   (  45-)  L     - 3096 ALA   (  51-)  L        -2.11
3161 SER   ( 116-)  L     - 3164 LYS   ( 119-)  L        -1.69
3270 VAL   (  98-)  M     - 3274 ARG   ( 102-)  M        -2.09
3294 LYS   ( 122-)  M     - 3298 LYS   ( 126-)  M        -2.10
3456 GLY   (  10-)  P     - 3459 HIS   (  13-)  P        -1.93

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: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: V

Water, ion, and hydrogenbond related checks

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.

1601 ASN   (  94-)  B
1752 HIS   (   6-)  C
1809 ASN   (  63-)  C
1853 GLN   ( 107-)  C
2230 ASN   (  73-)  E
2384 ASN   (  73-)  F
2559 ASN   ( 148-)  G
2738 ASN   (  34-)  I
2914 GLN   (  84-)  J
3249 ASN   (  77-)  M
3264 HIS   (  92-)  M
3407 HIS   (  50-)  O
3511 GLN   (  65-)  P
3624 GLN   (  96-)  Q
3752 HIS   (  47-)  S
3762 HIS   (  57-)  S
3774 HIS   (  69-)  S
3797 GLN   (  18-)  T

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.

   4 OADE  (   8-)  A      N6
  76 OURA  (  80-)  A      N3
  96 OGUA  ( 100-)  A      N1
  99 OCYT  ( 103-)  A      N4
 101 OGUA  ( 105-)  A      N2
 141 OADE  ( 145-)  A      N6
 150 OADE  ( 154-)  A      N6
 158 OGUA  ( 162-)  A      N2
 159 OCYT  ( 163-)  A      N4
 242 OGUA  ( 246-)  A      N2
 245 OGUA  ( 249-)  A      N2
 251 OGUA  ( 255-)  A      N1
 260 OCYT  ( 264-)  A      N4
 264 OADE  ( 268-)  A      N6
 309 OGUA  ( 313-)  A      N2
 313 OCYT  ( 317-)  A      N4
 318 OADE  ( 322-)  A      N6
 362 OGUA  ( 366-)  A      N2
 398 OGUA  ( 402-)  A      O2'
 402 OADE  ( 406-)  A      N6
 420 OURA  ( 424-)  A      O2'
 453 OADE  ( 457-)  A      O2'
 476 OADE  ( 480-)  A      N6
 501 OCYT  ( 505-)  A      N4
 502 OADE  ( 506-)  A      N6
And so on for a total of 430 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.

1591 GLU   (  84-)  B      OE1
1673 ASP   ( 166-)  B      OD1
1673 ASP   ( 166-)  B      OD2
1696 ASP   ( 189-)  B      OD2
2024 GLU   (  72-)  D      OE1
2318 ASN   (   7-)  F      OD1
2343 ASN   (  32-)  F      OD1
2534 GLU   ( 123-)  G      OE2
2649 HIS   (  82-)  H      ND1
2716 GLU   (  12-)  I      OE1
2716 GLU   (  12-)  I      OE2
2954 ASP   (  34-)  K      OD2
3036 HIS   ( 116-)  K      ND1
3486 ASP   (  40-)  P      OD1
3574 ASP   (  46-)  Q      OD1
3758 ASN   (  53-)  S      OD1
3839 GLU   (  60-)  T      OE2
3854 ASN   (  75-)  T      OD1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

3932  MG   (1601-)  A   -.-  -.-  Too few ligands (3)
3933  MG   (1602-)  A   -.-  -.-  Low probability ion. B= 90.9
3934  MG   (1603-)  A   -.-  -.-  Part of ionic cluster
3934  MG   (1603-)  A   -.-  -.-  Too few ligands (2)
3935  MG   (1604-)  A   -.-  -.-  Low probability ion. B=106.0
3936  MG   (1605-)  A   -.-  -.-  Too few ligands (0)
3937  MG   (1606-)  A   -.-  -.-  Too few ligands (0)
3938  MG   (1607-)  A   -.-  -.-  Too few ligands (2)
3939  MG   (1608-)  A   -.-  -.-  Low probability ion. B= 97.0
3940  MG   (1609-)  A   -.-  -.-  Too few ligands (1)
3941  MG   (1610-)  A   -.-  -.-  Low probability ion. B= 89.8
3942  MG   (1611-)  A   -.-  -.-  Too few ligands (0)
3943  MG   (1612-)  A   -.-  -.-  Too few ligands (0)
3944  MG   (1613-)  A   -.-  -.-  Too few ligands (1)
3945  MG   (1614-)  A   -.-  -.-  Too few ligands (0)
3946  MG   (1615-)  A   -.-  -.-  Too few ligands (0)
3947  MG   (1616-)  A   -.-  -.-  Low probability ion. B= 83.3
3948  MG   (1617-)  A   -.-  -.-  Part of ionic cluster
3948  MG   (1617-)  A   -.-  -.-  Too few ligands (0)
3949  MG   (1618-)  A   -.-  -.-  Too few ligands (2)
3950  MG   (1619-)  A   -.-  -.-  Too few ligands (1)
3951  MG   (1620-)  A   -.-  -.-  Too few ligands (0)
3952  MG   (1621-)  A   -.-  -.-  Too few ligands (2)
3953  MG   (1622-)  A   -.-  -.-  Low probability ion. B= 85.1
3954  MG   (1623-)  A   -.-  -.-  Too few ligands (0)
And so on for a total of 197 lines.

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

1790 GLU   (  44-)  C   H-bonding suggests Gln
1912 GLU   ( 166-)  C   H-bonding suggests Gln; but Alt-Rotamer
2129 ASP   ( 177-)  D   H-bonding suggests Asn
2193 ASP   (  36-)  E   H-bonding suggests Asn
2274 ASP   ( 117-)  E   H-bonding suggests Asn; but Alt-Rotamer
2304 ASP   ( 147-)  E   H-bonding suggests Asn
2456 ASP   (  45-)  G   H-bonding suggests Asn; but Alt-Rotamer
2534 GLU   ( 123-)  G   H-bonding suggests Gln
2716 GLU   (  12-)  I   H-bonding suggests Gln; but Alt-Rotamer
2764 ASP   (  60-)  I   H-bonding suggests Asn; but Alt-Rotamer
2903 ASP   (  73-)  J   H-bonding suggests Asn
2913 GLU   (  83-)  J   H-bonding suggests Gln
2954 ASP   (  34-)  K   H-bonding suggests Asn; but Alt-Rotamer
3172 GLU   ( 127-)  L   H-bonding suggests Gln
3180 GLU   (   8-)  M   H-bonding suggests Gln
3255 ASP   (  83-)  M   H-bonding suggests Asn
3577 GLU   (  49-)  Q   H-bonding suggests Gln
3583 ASP   (  55-)  Q   H-bonding suggests Asn; but Alt-Rotamer
3606 GLU   (  78-)  Q   H-bonding suggests Gln; but Alt-Rotamer
3722 GLU   (  17-)  S   H-bonding suggests Gln

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 :  -2.730
  2nd generation packing quality :  -3.161 (poor)
  Ramachandran plot appearance   :  -4.429 (bad)
  chi-1/chi-2 rotamer normality  :  -5.490 (bad)
  Backbone conformation          :  -0.239

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.776
  Bond angles                    :   1.187
  Omega angle restraints         :   1.186
  Side chain planarity           :   0.273 (tight)
  Improper dihedral distribution :   0.681
  B-factor distribution          :   0.369
  Inside/Outside distribution    :   0.990

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.4
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -1.5
  chi-1/chi-2 rotamer normality  :  -3.0
  Backbone conformation          :   0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.776
  Bond angles                    :   1.187
  Omega angle restraints         :   1.186
  Side chain planarity           :   0.273 (tight)
  Improper dihedral distribution :   0.681
  B-factor distribution          :   0.369
  Inside/Outside distribution    :   0.990
==============

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.