WHAT IF Check report

This file was created 2012-01-30 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 pdb3iyn.ent

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

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

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'.

 238 THR   ( 272-)  A  -   OG1
 238 THR   ( 272-)  A  -   CG2
1153 THR   ( 272-)  B  -   OG1
1153 THR   ( 272-)  B  -   CG2
2072 THR   ( 272-)  C  -   OG1
2072 THR   ( 272-)  C  -   CG2
2989 THR   ( 272-)  D  -   OG1
2989 THR   ( 272-)  D  -   CG2
3905 THR   ( 272-)  E  -   OG1
3905 THR   ( 272-)  E  -   CG2
4822 THR   ( 272-)  F  -   OG1
4822 THR   ( 272-)  F  -   CG2
5739 THR   ( 272-)  G  -   OG1
5739 THR   ( 272-)  G  -   CG2
6659 THR   ( 272-)  H  -   OG1
6659 THR   ( 272-)  H  -   CG2
7575 THR   ( 272-)  I  -   OG1
7575 THR   ( 272-)  I  -   CG2
8492 THR   ( 272-)  J  -   OG1
8492 THR   ( 272-)  J  -   CG2
9412 THR   ( 272-)  K  -   OG1
9412 THR   ( 272-)  K  -   CG2
1033  THR  ( 272-) L  -    OG1
1033  THR  ( 272-) L  -    CG2
1185  SER  ( 104-) O  -    OG
1202  SER  ( 104-) P  -    OG

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.

 237 ALA   ( 271-)  A  -   Zero
 238 THR   ( 272-)  A  -   Zero
 239 ALA   ( 273-)  A  -   Zero
 240 GLY   ( 274-)  A  -   Zero
 241 ASN   ( 275-)  A  -   Zero
 242 GLY   ( 276-)  A  -   Zero
 397 LYS   ( 431-)  A  -   Zero
 398 THR   ( 432-)  A  -   Zero
 399 GLY   ( 433-)  A  -   Zero
 400 GLN   ( 434-)  A  -   Zero
 401 GLU   ( 435-)  A  -   Zero
 402 ASN   ( 436-)  A  -   Zero
1152 ALA   ( 271-)  B  -   Zero
1153 THR   ( 272-)  B  -   Zero
1154 ALA   ( 273-)  B  -   Zero
1155 GLY   ( 274-)  B  -   Zero
1156 ASN   ( 275-)  B  -   Zero
1157 GLY   ( 276-)  B  -   Zero
1312 LYS   ( 431-)  B  -   Zero
1313 THR   ( 432-)  B  -   Zero
1314 GLY   ( 433-)  B  -   Zero
1315 GLN   ( 434-)  B  -   Zero
1316 GLU   ( 435-)  B  -   Zero
1317 ASN   ( 436-)  B  -   Zero
2071 ALA   ( 271-)  C  -   Zero
And so on for a total of 144 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. 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:

Temperature not mentioned in PDB file. This most likely means that the temperature record is absent.
Room temperature assumed

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

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: M

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: N

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: O

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: P

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: Q

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: R

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: S

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: T

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.

 295 ARG   ( 329-)  A  -
 435 ARG   ( 469-)  A  -
 519 ARG   ( 553-)  A  -
 768 ARG   ( 802-)  A  -
1210 ARG   ( 329-)  B  -
1350 ARG   ( 469-)  B  -
1434 ARG   ( 553-)  B  -
1683 ARG   ( 802-)  B  -
2129 ARG   ( 329-)  C  -
2269 ARG   ( 469-)  C  -
2353 ARG   ( 553-)  C  -
2602 ARG   ( 802-)  C  -
3046 ARG   ( 329-)  D  -
3186 ARG   ( 469-)  D  -
3270 ARG   ( 553-)  D  -
3519 ARG   ( 802-)  D  -
3962 ARG   ( 329-)  E  -
4102 ARG   ( 469-)  E  -
4186 ARG   ( 553-)  E  -
4435 ARG   ( 802-)  E  -
4879 ARG   ( 329-)  F  -
5019 ARG   ( 469-)  F  -
5103 ARG   ( 553-)  F  -
5352 ARG   ( 802-)  F  -
5796 ARG   ( 329-)  G  -
And so on for a total of 68 lines.

Warning: Tyrosine convention problem

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

  32 TYR   (  37-)  A  -
 115 TYR   ( 120-)  A  -
 160 TYR   ( 194-)  A  -
 335 TYR   ( 369-)  A  -
 359 TYR   ( 393-)  A  -
 378 TYR   ( 412-)  A  -
 439 TYR   ( 473-)  A  -
 445 TYR   ( 479-)  A  -
 452 TYR   ( 486-)  A  -
 466 TYR   ( 500-)  A  -
 468 TYR   ( 502-)  A  -
 510 TYR   ( 544-)  A  -
 546 TYR   ( 580-)  A  -
 581 TYR   ( 615-)  A  -
 660 TYR   ( 694-)  A  -
 663 TYR   ( 697-)  A  -
 664 TYR   ( 698-)  A  -
 672 TYR   ( 706-)  A  -
 796 TYR   ( 830-)  A  -
 859 TYR   ( 893-)  A  -
 882 TYR   ( 916-)  A  -
 905 TYR   ( 939-)  A  -
 947 TYR   (  37-)  B  -
1030 TYR   ( 120-)  B  -
1075 TYR   ( 194-)  B  -
And so on for a total of 285 lines.

Warning: Phenylalanine convention problem

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

  62 PHE   (  67-)  A  -
  95 PHE   ( 100-)  A  -
 165 PHE   ( 199-)  A  -
 232 PHE   ( 266-)  A  -
 298 PHE   ( 332-)  A  -
 349 PHE   ( 383-)  A  -
 532 PHE   ( 566-)  A  -
 575 PHE   ( 609-)  A  -
 677 PHE   ( 711-)  A  -
 690 PHE   ( 724-)  A  -
 844 PHE   ( 878-)  A  -
 977 PHE   (  67-)  B  -
1010 PHE   ( 100-)  B  -
1080 PHE   ( 199-)  B  -
1147 PHE   ( 266-)  B  -
1213 PHE   ( 332-)  B  -
1264 PHE   ( 383-)  B  -
1447 PHE   ( 566-)  B  -
1490 PHE   ( 609-)  B  -
1592 PHE   ( 711-)  B  -
1605 PHE   ( 724-)  B  -
1759 PHE   ( 878-)  B  -
1896 PHE   (  67-)  C  -
1929 PHE   ( 100-)  C  -
1999 PHE   ( 199-)  C  -
And so on for a total of 156 lines.

Warning: Aspartic acid convention problem

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

  49 ASP   (  54-)  A  -
  53 ASP   (  58-)  A  -
  96 ASP   ( 101-)  A  -
 296 ASP   ( 330-)  A  -
 340 ASP   ( 374-)  A  -
 357 ASP   ( 391-)  A  -
 360 ASP   ( 394-)  A  -
 373 ASP   ( 407-)  A  -
 492 ASP   ( 526-)  A  -
 495 ASP   ( 529-)  A  -
 605 ASP   ( 639-)  A  -
 661 ASP   ( 695-)  A  -
 674 ASP   ( 708-)  A  -
 729 ASP   ( 763-)  A  -
 822 ASP   ( 856-)  A  -
 832 ASP   ( 866-)  A  -
 873 ASP   ( 907-)  A  -
 889 ASP   ( 923-)  A  -
 964 ASP   (  54-)  B  -
 968 ASP   (  58-)  B  -
1011 ASP   ( 101-)  B  -
1211 ASP   ( 330-)  B  -
1255 ASP   ( 374-)  B  -
1272 ASP   ( 391-)  B  -
1275 ASP   ( 394-)  B  -
And so on for a total of 241 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.

 374 GLU   ( 408-)  A  -
 389 GLU   ( 423-)  A  -
 426 GLU   ( 460-)  A  -
 707 GLU   ( 741-)  A  -
 871 GLU   ( 905-)  A  -
1289 GLU   ( 408-)  B  -
1304 GLU   ( 423-)  B  -
1341 GLU   ( 460-)  B  -
1622 GLU   ( 741-)  B  -
1786 GLU   ( 905-)  B  -
2208 GLU   ( 408-)  C  -
2223 GLU   ( 423-)  C  -
2260 GLU   ( 460-)  C  -
2541 GLU   ( 741-)  C  -
2705 GLU   ( 905-)  C  -
3125 GLU   ( 408-)  D  -
3140 GLU   ( 423-)  D  -
3177 GLU   ( 460-)  D  -
3458 GLU   ( 741-)  D  -
3622 GLU   ( 905-)  D  -
4041 GLU   ( 408-)  E  -
4056 GLU   ( 423-)  E  -
4093 GLU   ( 460-)  E  -
4374 GLU   ( 741-)  E  -
4538 GLU   ( 905-)  E  -
And so on for a total of 74 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.

1172  HIS  ( 273-) N  -    CB   CG    1.56    4.2

Warning: Directionality in bond lengths and no X-ray cell

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

You have most probably seen symmetry problems earlier. Please correct these and rerun this check to see the possible implications on the X-ray cell axes.

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.

   8 HIS   (  13-)  A  -   CA   CB   CG  109.42   -4.4
  56 GLN   (  61-)  A  -   CG   CD   NE2 126.41    6.7
  56 GLN   (  61-)  A  -   NE2  CD   OE1 112.65   -9.9
 136 GLN   ( 170-)  A  -   CG   CD   NE2 126.69    6.9
 136 GLN   ( 170-)  A  -   NE2  CD   OE1 113.34   -9.3
 150 GLN   ( 184-)  A  -   CG   CD   NE2 126.18    6.5
 150 GLN   ( 184-)  A  -   NE2  CD   OE1 113.08   -9.5
 213 GLY   ( 247-)  A  -   N    CA   C   127.84    5.3
 488 ARG   ( 522-)  A  -   N    CA   C    99.33   -4.2
 570 GLY   ( 604-)  A  -   N    CA   C   124.85    4.3
 704 THR   ( 738-)  A  -   N    CA   C    99.30   -4.2
 821 VAL   ( 855-)  A  -  -C    N    CA  132.64    6.1
 923 HIS   (  13-)  B  -   CA   CB   CG  109.45   -4.4
 971 GLN   (  61-)  B  -   CG   CD   NE2 126.33    6.6
 971 GLN   (  61-)  B  -   NE2  CD   OE1 112.82   -9.8
1051 GLN   ( 170-)  B  -   CG   CD   NE2 126.75    6.9
1051 GLN   ( 170-)  B  -   NE2  CD   OE1 113.27   -9.3
1065 GLN   ( 184-)  B  -   CG   CD   NE2 126.28    6.6
1065 GLN   ( 184-)  B  -   NE2  CD   OE1 113.13   -9.5
1128 GLY   ( 247-)  B  -   N    CA   C   127.89    5.3
1403 ARG   ( 522-)  B  -   N    CA   C    99.26   -4.3
1485 GLY   ( 604-)  B  -   N    CA   C   124.82    4.2
1619 THR   ( 738-)  B  -   N    CA   C    99.32   -4.2
1736 VAL   ( 855-)  B  -  -C    N    CA  132.63    6.1
1842 HIS   (  13-)  C  -   CA   CB   CG  109.43   -4.4
And so on for a total of 197 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.

  49 ASP   (  54-)  A  -
  53 ASP   (  58-)  A  -
  96 ASP   ( 101-)  A  -
 295 ARG   ( 329-)  A  -
 296 ASP   ( 330-)  A  -
 340 ASP   ( 374-)  A  -
 357 ASP   ( 391-)  A  -
 360 ASP   ( 394-)  A  -
 373 ASP   ( 407-)  A  -
 374 GLU   ( 408-)  A  -
 389 GLU   ( 423-)  A  -
 426 GLU   ( 460-)  A  -
 435 ARG   ( 469-)  A  -
 492 ASP   ( 526-)  A  -
 495 ASP   ( 529-)  A  -
 519 ARG   ( 553-)  A  -
 605 ASP   ( 639-)  A  -
 661 ASP   ( 695-)  A  -
 674 ASP   ( 708-)  A  -
 707 GLU   ( 741-)  A  -
 729 ASP   ( 763-)  A  -
 768 ARG   ( 802-)  A  -
 822 ASP   ( 856-)  A  -
 832 ASP   ( 866-)  A  -
 871 GLU   ( 905-)  A  -
And so on for a total of 383 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 158 PRO   ( 192-)  A  -   N     -8.1   -29.14    -2.48
1073 PRO   ( 192-)  B  -   N     -8.1   -29.21    -2.48
1992 PRO   ( 192-)  C  -   N     -8.1   -29.19    -2.48
2909 PRO   ( 192-)  D  -   N     -8.2   -29.28    -2.48
3825 PRO   ( 192-)  E  -   N     -8.2   -29.22    -2.48
4742 PRO   ( 192-)  F  -   N     -8.1   -29.11    -2.48
5659 PRO   ( 192-)  G  -   N     -8.1   -29.10    -2.48
6134 PRO   ( 667-)  G  -   N      8.8    26.40    -2.48
6419 PRO   (   3-)  H  -   N      6.6    19.25    -2.48
6579 PRO   ( 192-)  H  -   N     -8.1   -29.20    -2.48
7495 PRO   ( 192-)  I  -   N     -8.1   -29.12    -2.48
8412 PRO   ( 192-)  J  -   N     -8.2   -29.22    -2.48
9176 PRO   (   7-)  K  -   N     -6.3   -23.06    -2.48
9332 PRO   ( 192-)  K  -   N     -8.1   -29.12    -2.48
9807 PRO   ( 667-)  K  -   N      8.4    25.09    -2.48
1009  PRO  (   3-) L  -    N      8.0    23.71    -2.48
1025  PRO  ( 192-) L  -    N     -8.2   -29.39    -2.48
1112  PRO  ( 153-) M  -    N     -8.1   -29.03    -2.48
1189  PRO  ( 200-) O  -    N      6.0    17.30    -2.48
1190  PRO  ( 209-) O  -    N      9.7    29.22    -2.48
1208  PRO  ( 209-) P  -    N      9.7    29.27    -2.48
1208  PRO  ( 214-) P  -    N      6.5    18.93    -2.48
1215  PRO  (  56-) Q  -    N     -6.7   -24.59    -2.48
1217  PRO  (  84-) Q  -    N     -6.2   -22.79    -2.48
The average deviation= 0.674

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.

2551 GLU   ( 751-)  C  -   5.28
5301 GLU   ( 751-)  F  -   5.27
8971 GLU   ( 751-)  J  -   5.27
1081  GLU  ( 751-) L  -   5.22
7138 GLU   ( 751-)  H  -   5.21
8054 GLU   ( 751-)  I  -   5.20
9891 GLU   ( 751-)  K  -   5.20
 717 GLU   ( 751-)  A  -   5.20
6218 GLU   ( 751-)  G  -   5.20
1632 GLU   ( 751-)  B  -   5.19
4384 GLU   ( 751-)  E  -   5.19
6634 GLY   ( 247-)  H  -   5.16
3880 GLY   ( 247-)  E  -   5.15
9387 GLY   ( 247-)  K  -   5.14
2964 GLY   ( 247-)  D  -   5.14
1128 GLY   ( 247-)  B  -   5.14
8467 GLY   ( 247-)  J  -   5.13
1030  GLY  ( 247-) L  -   5.13
2047 GLY   ( 247-)  C  -   5.13
7550 GLY   ( 247-)  I  -   5.13
 213 GLY   ( 247-)  A  -   5.12
4797 GLY   ( 247-)  F  -   5.11
5714 GLY   ( 247-)  G  -   5.10
6909 ARG   ( 522-)  H  -   4.52
2322 ARG   ( 522-)  C  -   4.52
And so on for a total of 95 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.

4313 THR   ( 680-)  E  -   -3.3
7983 THR   ( 680-)  I  -   -3.3
 646 THR   ( 680-)  A  -   -3.3
3397 THR   ( 680-)  D  -   -3.3
1074  THR  ( 680-) L  -   -3.3
9820 THR   ( 680-)  K  -   -3.3
2480 THR   ( 680-)  C  -   -3.3
5230 THR   ( 680-)  F  -   -3.3
7067 THR   ( 680-)  H  -   -3.3
1561 THR   ( 680-)  B  -   -3.3
8900 THR   ( 680-)  J  -   -3.3
6147 THR   ( 680-)  G  -   -3.2
1190  PRO  ( 209-) O  -   -3.1
1208  PRO  ( 209-) P  -   -3.1
1213  PRO  (  38-) Q  -   -3.1
1235  PRO  (  38-) S  -   -3.1
1243  PRO  (  38-) T  -   -3.1
1226  PRO  (  38-) R  -   -3.1
1215  PRO  (  56-) Q  -   -3.1
1112  PRO  ( 153-) M  -   -3.1
1107  TYR  ( 101-) M  -   -3.0
1189  PHE  ( 192-) O  -   -3.0
1206  PHE  ( 192-) P  -   -3.0
9836 PRO   ( 696-)  K  -   -3.0
3162 PHE   ( 445-)  D  -   -3.0
And so on for a total of 515 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.

   2 PRO   (   7-)  A  - Poor phi/psi
   8 HIS   (  13-)  A  - Poor phi/psi
  30 GLU   (  35-)  A  - Poor phi/psi
  48 HIS   (  53-)  A  - Poor phi/psi
  49 ASP   (  54-)  A  - Poor phi/psi
  83 GLY   (  88-)  A  - Poor phi/psi
 109 PRO   ( 114-)  A  - Poor phi/psi
 110 TYR   ( 115-)  A  - Poor phi/psi
 165 PHE   ( 199-)  A  - Poor phi/psi
 166 GLN   ( 200-)  A  - PRO omega poor
 180 GLU   ( 214-)  A  - Poor phi/psi
 214 ILE   ( 248-)  A  - Poor phi/psi
 215 LEU   ( 249-)  A  - Poor phi/psi
 217 LYS   ( 251-)  A  - Poor phi/psi, omega poor
 220 ASN   ( 254-)  A  - Poor phi/psi
 222 LYS   ( 256-)  A  - omega poor
 223 LEU   ( 257-)  A  - Poor phi/psi, omega poor
 225 SER   ( 259-)  A  - Poor phi/psi
 226 GLN   ( 260-)  A  - Poor phi/psi
 227 VAL   ( 261-)  A  - Poor phi/psi
 235 THR   ( 269-)  A  - Poor phi/psi
 237 ALA   ( 271-)  A  - Poor phi/psi
 241 ASN   ( 275-)  A  - Poor phi/psi
 245 LEU   ( 279-)  A  - Poor phi/psi
 297 ASN   ( 331-)  A  - Poor phi/psi
And so on for a total of 839 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.

 526 GLN   ( 560-)  A  -   0.36
1441 GLN   ( 560-)  B  -   0.36
2360 GLN   ( 560-)  C  -   0.36
3277 GLN   ( 560-)  D  -   0.36
4193 GLN   ( 560-)  E  -   0.36
5110 GLN   ( 560-)  F  -   0.36
6027 GLN   ( 560-)  G  -   0.36
6947 GLN   ( 560-)  H  -   0.36
7863 GLN   ( 560-)  I  -   0.36
8780 GLN   ( 560-)  J  -   0.36
9700 GLN   ( 560-)  K  -   0.36
1062  GLN  ( 560-) L  -   0.36
 593 SER   ( 627-)  A  -   0.38
1508 SER   ( 627-)  B  -   0.38
2427 SER   ( 627-)  C  -   0.38
3344 SER   ( 627-)  D  -   0.38
4260 SER   ( 627-)  E  -   0.38
5177 SER   ( 627-)  F  -   0.38
6094 SER   ( 627-)  G  -   0.38
7014 SER   ( 627-)  H  -   0.38
7930 SER   ( 627-)  I  -   0.38
8847 SER   ( 627-)  J  -   0.38
9767 SER   ( 627-)  K  -   0.38
1068  SER  ( 627-) L  -   0.38
4001 SER   ( 368-)  E  -   0.38
 334 SER   ( 368-)  A  -   0.39
1249 SER   ( 368-)  B  -   0.39
2168 SER   ( 368-)  C  -   0.39
3085 SER   ( 368-)  D  -   0.39
4918 SER   ( 368-)  F  -   0.39
5835 SER   ( 368-)  G  -   0.39
6755 SER   ( 368-)  H  -   0.39
7671 SER   ( 368-)  I  -   0.39
8588 SER   ( 368-)  J  -   0.39
9508 SER   ( 368-)  K  -   0.39
1042  SER  ( 368-) L  -   0.39
ERROR. Too many residues to use DSSP

Warning: Unusual backbone conformations

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

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

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

   7 MET   (  12-)  A  -     0
   8 HIS   (  13-)  A  -     0
   9 ILE   (  14-)  A  -     0
  12 GLN   (  17-)  A  -     0
  17 TYR   (  22-)  A  -     0
  31 THR   (  36-)  A  -     0
  32 TYR   (  37-)  A  -     0
  33 PHE   (  38-)  A  -     0
  35 LEU   (  40-)  A  -     0
  46 PRO   (  51-)  A  -     0
  47 THR   (  52-)  A  -     0
  48 HIS   (  53-)  A  -     0
  49 ASP   (  54-)  A  -     0
  50 VAL   (  55-)  A  -     0
  55 SER   (  60-)  A  -     0
  56 GLN   (  61-)  A  -     0
  58 LEU   (  63-)  A  -     0
  65 VAL   (  70-)  A  -     0
  66 ASP   (  71-)  A  -     0
  70 THR   (  75-)  A  -     0
  72 TYR   (  77-)  A  -     0
  85 ASN   (  90-)  A  -     0
  93 THR   (  98-)  A  -     0
  98 ARG   ( 103-)  A  -     0
 103 ARG   ( 108-)  A  -     0
And so on for a total of 6228 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 : 1.240

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!

2964 GLY   ( 247-)  D  -  3.50   11
8467 GLY   ( 247-)  J  -  3.50   11
4797 GLY   ( 247-)  F  -  3.50   11
3880 GLY   ( 247-)  E  -  3.50   11
7550 GLY   ( 247-)  I  -  3.50   10
6634 GLY   ( 247-)  H  -  3.50   11
1128 GLY   ( 247-)  B  -  3.50   11
2047 GLY   ( 247-)  C  -  3.50   11
9387 GLY   ( 247-)  K  -  3.50   11
 213 GLY   ( 247-)  A  -  3.50   10
1030  GLY  ( 247-) L  -  3.50   10
5714 GLY   ( 247-)  G  -  3.50   10
1116  LEU  ( 193-) M  -  1.98   12
1109  GLY  ( 120-) M  -  1.76   50
1135  GLY  ( 464-) M  -  1.64   32
1198  ALA  (  60-) P  -  1.58   13
1180  ALA  (  60-) O  -  1.58   13
1188  GLY  ( 182-) O  -  1.55   11
1205  GLY  ( 182-) P  -  1.55   11
9416 GLY   ( 276-)  K  -  1.51   18
5743 GLY   ( 276-)  G  -  1.51   18
7579 GLY   ( 276-)  I  -  1.51   18
4826 GLY   ( 276-)  F  -  1.51   17
1033  GLY  ( 276-) L  -  1.51   17
 242 GLY   ( 276-)  A  -  1.51   17
3909 GLY   ( 276-)  E  -  1.51   18
2076 GLY   ( 276-)  C  -  1.51   17
2993 GLY   ( 276-)  D  -  1.51   17
6663 GLY   ( 276-)  H  -  1.51   17
1157 GLY   ( 276-)  B  -  1.51   17
8496 GLY   ( 276-)  J  -  1.51   18

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 832 ASP   ( 866-)  A  -  1.82
1747 ASP   ( 866-)  B  -  1.82
2666 ASP   ( 866-)  C  -  1.81
3583 ASP   ( 866-)  D  -  1.80
4499 ASP   ( 866-)  E  -  1.82
5416 ASP   ( 866-)  F  -  1.81
6333 ASP   ( 866-)  G  -  1.82
7253 ASP   ( 866-)  H  -  1.82
8169 ASP   ( 866-)  I  -  1.81
9086 ASP   ( 866-)  J  -  1.84
1000  ASP  ( 866-) K  -  1.85
1092  ASP  ( 866-) L  -  1.84

Warning: Unusual PRO puckering amplitudes

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

1107  PRO  ( 103-) M  -   0.46 HIGH
1231  PRO  ( 136-) R  -   0.48 HIGH

Warning: Unusual PRO puckering phases

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

1164  PRO  ( 185-) N  -   38.9 envelop C-delta (36 degrees)
1167  PRO  ( 230-) N  -  100.5 envelop C-beta (108 degrees)
1168  PRO  ( 241-) N  -  101.7 envelop C-beta (108 degrees)
1213  PRO  (  38-) Q  -  151.7 envelop C-alpha (144 degrees)
1226  PRO  (  38-) R  -  151.7 envelop C-alpha (144 degrees)
1235  PRO  (  38-) S  -  151.7 envelop C-alpha (144 degrees)
1243  PRO  (  38-) T  -  151.7 envelop C-alpha (144 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

1009  MET  (   5-) L  -    SD   <->  1179  ARG  (  51-) O  -    NH1  1.09    2.21  INTRA BF
3914 PRO   ( 281-)  E  -   CG   <->  4988 TRP   ( 438-)  F  -   CH2  1.00    2.20  INTRA BF
8948 VAL   ( 728-)  J  -   CG1  <->  1210  TYR  ( 226-) P  -    CD2  1.00    2.20  INTRA BF
5158 LYS   ( 608-)  F  -   CD   <->  1245  ASP  (  98-) T  -    CB   0.99    2.21  INTRA BF
4527 ALA   ( 894-)  E  -   CB   <->  4584 MET   (   5-)  F  -   SD   0.98    2.42  INTRA BF
1009  PRO  (   3-) L  -    CB   <->  1180  ILE  (  54-) O  -    CG2  0.95    2.25  INTRA BF
2470 ASN   ( 670-)  C  -   CB   <->  9493 GLN   ( 353-)  K  -   CG   0.95    2.25  INTRA BF
  83 GLY   (  88-)  A  -   CA   <->  3986 GLN   ( 353-)  E  -   CG   0.95    2.25  INTRA BF
5481 HIS   ( 931-)  F  -   CD2  <->  1194  ALA  (  24-) P  -    CB   0.95    2.25  INTRA BF
6668 PRO   ( 281-)  H  -   CG   <->  7741 TRP   ( 438-)  I  -   CH2  0.95    2.25  INTRA BF
1832 PRO   (   3-)  C  -   CB   <->  1108  ASP  ( 115-) M  -    CG   0.94    2.26  INTRA BF
6194 SER   ( 727-)  G  -   CB   <->  1193  PRO  (  15-) P  -    CB   0.93    2.27  INTRA BF
9172 PRO   (   3-)  K  -   CG   <->  9180 TYR   (  11-)  K  -   CE2  0.93    2.27  INTRA BF
6483 PHE   (  67-)  H  -   CE2  <->  8573 GLN   ( 353-)  J  -   CD   0.93    2.27  INTRA BF
  20 PRO   (  25-)  A  -   CG   <->  1190  SER  ( 202-) O  -    CA   0.92    2.28  INTRA BF
8381 CYS   ( 132-)  J  -   SG   <->  8449 MET   ( 229-)  J  -   CE   0.92    2.48  INTRA BF
 127 CYS   ( 132-)  A  -   SG   <->   195 MET   ( 229-)  A  -   CE   0.92    2.48  INTRA BF
2878 CYS   ( 132-)  D  -   SG   <->  2946 MET   ( 229-)  D  -   CE   0.92    2.48  INTRA BF
9301 CYS   ( 132-)  K  -   SG   <->  9369 MET   ( 229-)  K  -   CE   0.92    2.48  INTRA BF
8874 PRO   ( 654-)  J  -   CG   <->  1217  PRO  (  84-) Q  -    CG   0.91    2.29  INTRA BF
7464 CYS   ( 132-)  I  -   SG   <->  7532 MET   ( 229-)  I  -   CE   0.91    2.49  INTRA BF
4711 CYS   ( 132-)  F  -   SG   <->  4779 MET   ( 229-)  F  -   CE   0.91    2.49  INTRA BF
1022  CYS  ( 132-) L  -    SG   <->  1028  MET  ( 229-) L  -    CE   0.91    2.49  INTRA BF
6548 CYS   ( 132-)  H  -   SG   <->  6616 MET   ( 229-)  H  -   CE   0.91    2.49  INTRA BF
5628 CYS   ( 132-)  G  -   SG   <->  5696 MET   ( 229-)  G  -   CE   0.91    2.49  INTRA BF
And so on for a total of 5756 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

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

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.

1187  ARG  ( 179-) O  -     -8.57
1241  ARG  (  18-) T  -     -8.23
1224  ARG  (  18-) R  -     -8.19
1211  ARG  (  18-) Q  -     -8.11
1149  ARG  (  40-) N  -     -8.03
1834 MET   (   5-)  C  -     -7.87
1101  PHE  (  40-) M  -     -7.64
1140  ARG  ( 507-) M  -     -7.53
1165  ARG  ( 193-) N  -     -7.29
6248 TYR   ( 781-)  G  -     -7.16
9393 GLN   ( 253-)  K  -     -7.14
5720 GLN   ( 253-)  G  -     -7.14
6640 GLN   ( 253-)  H  -     -7.13
1031  GLN  ( 253-) L  -     -7.13
 219 GLN   ( 253-)  A  -     -7.13
3886 GLN   ( 253-)  E  -     -7.13
7556 GLN   ( 253-)  I  -     -7.13
2053 GLN   ( 253-)  C  -     -7.13
4414 TYR   ( 781-)  E  -     -7.13
7081 TYR   ( 694-)  H  -     -7.12
8473 GLN   ( 253-)  J  -     -7.12
1134 GLN   ( 253-)  B  -     -7.12
2970 GLN   ( 253-)  D  -     -7.11
4803 GLN   ( 253-)  F  -     -7.11
1224  MET  (  19-) R  -     -7.09
And so on for a total of 486 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.

 218 GLN   ( 252-)  A  -    220 - ASN    254- ( A)  -      -6.14
 271 ILE   ( 305-)  A  -    273 - GLU    307- ( A)  -      -5.51
 400 GLN   ( 434-)  A  -    402 - ASN    436- ( A)  -      -5.21
1133 GLN   ( 252-)  B  -   1135 - ASN    254- ( B)  -      -6.15
1186 ILE   ( 305-)  B  -   1188 - GLU    307- ( B)  -      -5.60
1315 GLN   ( 434-)  B  -   1317 - ASN    436- ( B)  -      -5.22
2052 GLN   ( 252-)  C  -   2054 - ASN    254- ( C)  -      -6.14
2105 ILE   ( 305-)  C  -   2107 - GLU    307- ( C)  -      -5.49
2234 GLN   ( 434-)  C  -   2236 - ASN    436- ( C)  -      -5.20
2969 GLN   ( 252-)  D  -   2971 - ASN    254- ( D)  -      -6.13
3022 ILE   ( 305-)  D  -   3024 - GLU    307- ( D)  -      -5.50
3664 GLY   ( 947-)  D  -   3666 - ALA    949- ( D)  -      -4.88
3885 GLN   ( 252-)  E  -   3887 - ASN    254- ( E)  -      -6.13
3938 ILE   ( 305-)  E  -   3940 - GLU    307- ( E)  -      -5.50
4802 GLN   ( 252-)  F  -   4804 - ASN    254- ( F)  -      -6.13
4855 ILE   ( 305-)  F  -   4857 - GLU    307- ( F)  -      -5.51
5219 ARG   ( 669-)  F  -   5221 - TRP    671- ( F)  -      -4.29
5719 GLN   ( 252-)  G  -   5721 - ASN    254- ( G)  -      -6.16
5772 ILE   ( 305-)  G  -   5774 - GLU    307- ( G)  -      -5.49
6639 GLN   ( 252-)  H  -   6641 - ASN    254- ( H)  -      -6.16
6692 ILE   ( 305-)  H  -   6694 - GLU    307- ( H)  -      -5.50
7555 GLN   ( 252-)  I  -   7557 - ASN    254- ( I)  -      -6.15
7608 ILE   ( 305-)  I  -   7610 - GLU    307- ( I)  -      -5.50
8251 ASN   ( 948-)  I  -   8253 - THR    950- ( I)  -      -4.57
8472 GLN   ( 252-)  J  -   8474 - ASN    254- ( J)  -      -6.14
8525 ILE   ( 305-)  J  -   8527 - GLU    307- ( J)  -      -5.50
8654 GLN   ( 434-)  J  -   8656 - ASN    436- ( J)  -      -5.23
9392 GLN   ( 252-)  K  -   9394 - ASN    254- ( K)  -      -6.17
9445 ILE   ( 305-)  K  -   9447 - GLU    307- ( K)  -      -5.50
9574 GLN   ( 434-)  K  -   9576 - ASN    436- ( K)  -      -5.22
1031  GLN  ( 252-) L  -    1031 -  ASN   254- (L ) -       -6.14
1036  ILE  ( 305-) L  -    1036 -  GLU   307- (L ) -       -5.51
1101  ARG  (  44-) M  -    1102 -  ARG    47- (M ) -       -5.10
1117  GLN  ( 198-) M  -    1117 -  GLY   200- (M ) -       -5.26
1134  PHE  ( 451-) M  -    1134 -  SER   453- (M ) -       -4.86
1144  ARG  ( 547-) M  -    1144 -  THR   550- (M ) -       -4.85
1182  TYR  (  80-) O  -    1182 -  GLU    82- (O ) -       -5.26
1185  GLN  ( 107-) O  -    1185 -  GLY   110- (O ) -       -5.02
1200  TYR  (  80-) P  -    1200 -  GLU    82- (P ) -       -5.24
1210  SER  (  13-) Q  -    1210 -  LEU    15- (Q ) -       -5.02
1212  ILE  (  34-) Q  -    1213 -  ARG    37- (Q ) -       -5.17
1223  SER  (  13-) R  -    1223 -  LEU    15- (R ) -       -5.04
1225  ILE  (  34-) R  -    1225 -  ARG    37- (R ) -       -5.16
1232  SER  (  13-) S  -    1232 -  LEU    15- (S ) -       -4.75
1236  VAL  (  52-) S  -    1236 -  GLY    54- (S ) -       -4.61
1241  SER  (  13-) T  -    1241 -  LEU    15- (T ) -       -5.02
1243  ILE  (  34-) T  -    1243 -  ARG    37- (T ) -       -5.16

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

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

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.

8890 ASN   ( 670-)  J  -  -2.86
8574 LEU   ( 354-)  J  -  -2.86
2470 ASN   ( 670-)  C  -  -2.78
4181 LEU   ( 548-)  E  -  -2.76
7851 LEU   ( 548-)  I  -  -2.76
9111 LEU   ( 891-)  J  -  -2.76
8768 LEU   ( 548-)  J  -  -2.75
2348 LEU   ( 548-)  C  -  -2.75
 514 LEU   ( 548-)  A  -  -2.75
5098 LEU   ( 548-)  F  -  -2.74
6164 TYR   ( 697-)  G  -  -2.71
6935 LEU   ( 548-)  H  -  -2.71
3265 LEU   ( 548-)  D  -  -2.71
1429 LEU   ( 548-)  B  -  -2.71
1060  LEU  ( 548-) L  -  -2.70
6015 LEU   ( 548-)  G  -  -2.70
3987 LEU   ( 354-)  E  -  -2.70
9688 LEU   ( 548-)  K  -  -2.69
9837 TYR   ( 697-)  K  -  -2.69
5220 ASN   ( 670-)  F  -  -2.66
5546 ALA   (  50-)  G  -  -2.66
  45 ALA   (  50-)  A  -  -2.65
9219 ALA   (  50-)  K  -  -2.65
 960 ALA   (  50-)  B  -  -2.64
1013  ALA  (  50-) L  -  -2.64
And so on for a total of 61 lines.

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.

9110 ASN   ( 890-)  J  -  - 9113 TYR   ( 893-)  J  -     -1.95
ERROR. Too many residues to use DSSP

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

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

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.

 297 ASN   ( 331-)  A  -
 305 ASN   ( 339-)  A  -
 321 ASN   ( 355-)  A  -
 336 GLN   ( 370-)  A  -
 369 HIS   ( 403-)  A  -
 415 ASN   ( 449-)  A  -
 436 ASN   ( 470-)  A  -
 505 ASN   ( 539-)  A  -
 589 HIS   ( 623-)  A  -
 636 ASN   ( 670-)  A  -
 738 ASN   ( 772-)  A  -
 740 ASN   ( 774-)  A  -
 764 GLN   ( 798-)  A  -
 856 ASN   ( 890-)  A  -
1212 ASN   ( 331-)  B  -
1220 ASN   ( 339-)  B  -
1236 ASN   ( 355-)  B  -
1251 GLN   ( 370-)  B  -
1284 HIS   ( 403-)  B  -
1330 ASN   ( 449-)  B  -
1351 ASN   ( 470-)  B  -
1420 ASN   ( 539-)  B  -
1551 ASN   ( 670-)  B  -
1653 ASN   ( 772-)  B  -
1655 ASN   ( 774-)  B  -
And so on for a total of 183 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.

  10 SER   (  15-)  A  -   N
  31 THR   (  36-)  A  -   N
  35 LEU   (  40-)  A  -   N
  36 ASN   (  41-)  A  -   N
  50 VAL   (  55-)  A  -   N
  57 ARG   (  62-)  A  -   NE
  59 THR   (  64-)  A  -   N
  61 ARG   (  66-)  A  -   NH1
  72 TYR   (  77-)  A  -   N
  73 SER   (  78-)  A  -   N
  79 THR   (  84-)  A  -   N
  81 ALA   (  86-)  A  -   N
  84 ASP   (  89-)  A  -   N
 106 THR   ( 111-)  A  -   N
 106 THR   ( 111-)  A  -   OG1
 112 GLY   ( 117-)  A  -   N
 128 GLU   ( 133-)  A  -   N
 133 VAL   ( 167-)  A  -   N
 136 GLN   ( 170-)  A  -   NE2
 143 ASN   ( 177-)  A  -   N
 144 ILE   ( 178-)  A  -   N
 154 GLU   ( 188-)  A  -   N
 170 GLN   ( 204-)  A  -   N
 170 GLN   ( 204-)  A  -   NE2
 173 GLU   ( 207-)  A  -   N
And so on for a total of 1939 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.

 125 ASN   ( 130-)  A  -   OD1
 128 GLU   ( 133-)  A  -   OE2
 132 HIS   ( 166-)  A  -   ND1
 170 GLN   ( 204-)  A  -   OE1
 212 GLN   ( 246-)  A  -   OE1
 230 GLN   ( 264-)  A  -   OE1
 415 ASN   ( 449-)  A  -   OD1
 605 ASP   ( 639-)  A  -   OD1
 680 ASN   ( 714-)  A  -   OD1
 720 ASN   ( 754-)  A  -   OD1
1040 ASN   ( 130-)  B  -   OD1
1043 GLU   ( 133-)  B  -   OE2
1047 HIS   ( 166-)  B  -   ND1
1085 GLN   ( 204-)  B  -   OE1
1127 GLN   ( 246-)  B  -   OE1
1145 GLN   ( 264-)  B  -   OE1
1212 ASN   ( 331-)  B  -   OD1
1242 GLN   ( 361-)  B  -   OE1
1330 ASN   ( 449-)  B  -   OD1
1520 ASP   ( 639-)  B  -   OD1
1595 ASN   ( 714-)  B  -   OD1
1635 ASN   ( 754-)  B  -   OD1
1959 ASN   ( 130-)  C  -   OD1
1962 GLU   ( 133-)  C  -   OE2
1966 HIS   ( 166-)  C  -   ND1
And so on for a total of 165 lines.

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

 328 ASP   ( 362-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 605 ASP   ( 639-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 674 ASP   ( 708-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 803 GLU   ( 837-)  A  -  H-bonding suggests Gln
 822 ASP   ( 856-)  A  -  H-bonding suggests Asn
 983 GLU   (  73-)  B  -  H-bonding suggests Gln; but Alt-Rotamer
1520 ASP   ( 639-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
1589 ASP   ( 708-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
1718 GLU   ( 837-)  B  -  H-bonding suggests Gln
1737 ASP   ( 856-)  B  -  H-bonding suggests Asn
2162 ASP   ( 362-)  C  -  H-bonding suggests Asn; but Alt-Rotamer
2439 ASP   ( 639-)  C  -  H-bonding suggests Asn; but Alt-Rotamer
2508 ASP   ( 708-)  C  -  H-bonding suggests Asn; but Alt-Rotamer
2541 GLU   ( 741-)  C  -  H-bonding suggests Gln
2637 GLU   ( 837-)  C  -  H-bonding suggests Gln
2656 ASP   ( 856-)  C  -  H-bonding suggests Asn
2736 GLU   ( 936-)  C  -  H-bonding suggests Gln
3079 ASP   ( 362-)  D  -  H-bonding suggests Asn; but Alt-Rotamer
3356 ASP   ( 639-)  D  -  H-bonding suggests Asn; but Alt-Rotamer
3425 ASP   ( 708-)  D  -  H-bonding suggests Asn; but Alt-Rotamer
3554 GLU   ( 837-)  D  -  H-bonding suggests Gln
3573 ASP   ( 856-)  D  -  H-bonding suggests Asn
3733 ASP   (  71-)  E  -  H-bonding suggests Asn
3995 ASP   ( 362-)  E  -  H-bonding suggests Asn; but Alt-Rotamer
4272 ASP   ( 639-)  E  -  H-bonding suggests Asn; but Alt-Rotamer
And so on for a total of 82 lines.

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 :  -1.995
  2nd generation packing quality :  -2.555
  Ramachandran plot appearance   :  -2.390
  chi-1/chi-2 rotamer normality  :  -1.746
  Backbone conformation          :  -1.384

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.270 (tight)
  Bond angles                    :   0.622 (tight)
  Omega angle restraints         :   0.225 (tight)
  Side chain planarity           :   0.252 (tight)
  Improper dihedral distribution :   0.601
  B-factor distribution          :   0.350
  Inside/Outside distribution    :   1.084

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 : 3.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :   0.6
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.270 (tight)
  Bond angles                    :   0.622 (tight)
  Omega angle restraints         :   0.225 (tight)
  Side chain planarity           :   0.252 (tight)
  Improper dihedral distribution :   0.601
  B-factor distribution          :   0.350
  Inside/Outside distribution    :   1.084
==============

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.