WHAT IF Check report

This file was created 2011-12-17 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 pdb3rko.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: 429139.563
Volume of the Unit Cell V= 1889496.4
Space group multiplicity: 1
No NCS symmetry matrices (MTRIX records) found in PDB file
but the number of MTRIX matrices flagged as `do not use` = 6
which, by the way, seems inconsistent with the SEQRES multiplicity
Matthews coefficient for observed atoms and Z high: Vm= 4.403
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.250

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.

3905 LFA   ( 614-)  L  -
3906 CA7   ( 510-)  M  -
3907 LFA   ( 512-)  M  -
3908 LFA   ( 486-)  M  -
3909 LFA   ( 488-)  N  -
3910 LFA   ( 489-)  N  -
3911 LFA   ( 614-)  B  -
3912 LFA   ( 512-)  C  -
3913 LFA   ( 513-)  C  -
3914 LFA   ( 487-)  D  -
3915 LFA   ( 488-)  D  -
3916 A17   ( 486-)  D  -
3917 A16   ( 511-)  C  -
3918 CA7   ( 510-)  C  -
3919 A15   ( 616-)  B  -
3920 A14   ( 615-)  B  -
3921 A13   ( 487-)  N  -
3922 A12   ( 511-)  M  -
3923 A11   ( 616-)  L  -
3924 A10   ( 615-)  L  -

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: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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

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 MET   (   1-)  L    High
   2 ASN   (   2-)  L    High
   3 MET   (   3-)  L    High
   4 LEU   (   4-)  L    High
   5 ALA   (   5-)  L    High
   6 LEU   (   6-)  L    High
   9 ILE   (   9-)  L    High
  10 LEU   (  10-)  L    High
  11 PRO   (  11-)  L    High
  12 LEU   (  12-)  L    High
  16 VAL   (  16-)  L    High
  18 LEU   (  18-)  L    High
  20 PHE   (  20-)  L    High
  21 SER   (  21-)  L    High
  22 ARG   (  22-)  L    High
  23 GLY   (  23-)  L    High
  24 ARG   (  24-)  L    High
  25 TRP   (  25-)  L    High
  26 SER   (  26-)  L    High
  27 GLU   (  27-)  L    High
  28 ASN   (  28-)  L    High
  30 SER   (  30-)  L    High
  32 ILE   (  32-)  L    High
  33 VAL   (  33-)  L    High
  36 GLY   (  36-)  L    High
And so on for a total of 2426 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: 46

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 7.559 over 17339 bonds
Average difference in B over a bond : 23.30
RMS difference in B over a bond : 29.57

Note: B-factor plot

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

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: A

Note: B-factor plot

Chain identifier: J

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: G

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

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.

 198 ARG   ( 198-)  L
 268 ARG   ( 268-)  L
 431 ARG   ( 431-)  L
 592 ARG   ( 592-)  L
 779 ARG   ( 167-)  M
1184 ARG   (  68-)  N
1478 ARG   ( 369-)  N
1615 ARG   (  26-)  K
1675 ARG   (  86-)  K
1715 ARG   (  40-)  A
1717 ARG   (  42-)  A
1721 ARG   (  63-)  A
2150 ARG   ( 198-)  B
2220 ARG   ( 268-)  B
2383 ARG   ( 431-)  B
2544 ARG   ( 592-)  B
2731 ARG   ( 167-)  C
3136 ARG   (  68-)  D
3430 ARG   ( 369-)  D
3567 ARG   (  26-)  G
3627 ARG   (  86-)  G
3667 ARG   (  40-)  E
3669 ARG   (  42-)  E
3673 ARG   (  63-)  E

Warning: Tyrosine convention problem

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

 102 TYR   ( 102-)  L
 594 TYR   ( 594-)  L
 664 TYR   (  52-)  M
 763 TYR   ( 151-)  M
 789 TYR   ( 177-)  M
 809 TYR   ( 197-)  M
 929 TYR   ( 317-)  M
 975 TYR   ( 363-)  M
1294 TYR   ( 178-)  N
1340 TYR   ( 231-)  N
1409 TYR   ( 300-)  N
1438 TYR   ( 329-)  N
1442 TYR   ( 333-)  N
1532 TYR   ( 423-)  N
1533 TYR   ( 424-)  N
1534 TYR   ( 425-)  N
1542 TYR   ( 433-)  N
1651 TYR   (  62-)  K
1843 TYR   (  59-)  J
2054 TYR   ( 102-)  B
2103 TYR   ( 151-)  B
2546 TYR   ( 594-)  B
2616 TYR   (  52-)  C
2715 TYR   ( 151-)  C
2741 TYR   ( 177-)  C
2761 TYR   ( 197-)  C
2881 TYR   ( 317-)  C
2927 TYR   ( 363-)  C
3246 TYR   ( 178-)  D
3292 TYR   ( 231-)  D
3361 TYR   ( 300-)  D
3390 TYR   ( 329-)  D
3394 TYR   ( 333-)  D
3484 TYR   ( 423-)  D
3485 TYR   ( 424-)  D
3486 TYR   ( 425-)  D
3494 TYR   ( 433-)  D
3603 TYR   (  62-)  G
3795 TYR   (  59-)  F

Warning: Phenylalanine convention problem

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

  52 PHE   (  52-)  L
  73 PHE   (  73-)  L
  77 PHE   (  77-)  L
 116 PHE   ( 116-)  L
 117 PHE   ( 117-)  L
 156 PHE   ( 156-)  L
 180 PHE   ( 180-)  L
 186 PHE   ( 186-)  L
 296 PHE   ( 296-)  L
 340 PHE   ( 340-)  L
 363 PHE   ( 363-)  L
 430 PHE   ( 430-)  L
 466 PHE   ( 466-)  L
 541 PHE   ( 541-)  L
 549 PHE   ( 549-)  L
 623 PHE   (  11-)  M
 679 PHE   (  67-)  M
 687 PHE   (  75-)  M
 728 PHE   ( 116-)  M
 743 PHE   ( 131-)  M
 754 PHE   ( 142-)  M
 764 PHE   ( 152-)  M
 817 PHE   ( 205-)  M
 843 PHE   ( 231-)  M
 886 PHE   ( 274-)  M
And so on for a total of 96 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.

  51 ASP   (  51-)  L
 160 ASP   ( 160-)  L
1178 ASP   (  62-)  N
1186 ASP   (  70-)  N
1216 ASP   ( 100-)  N
1219 ASP   ( 103-)  N
1299 ASP   ( 183-)  N
2003 ASP   (  51-)  B
2112 ASP   ( 160-)  B
3130 ASP   (  62-)  D
3138 ASP   (  70-)  D
3168 ASP   ( 100-)  D
3171 ASP   ( 103-)  D
3251 ASP   ( 183-)  D

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.

 144 GLU   ( 144-)  L
 359 GLU   ( 359-)  L
 441 GLU   ( 441-)  L
 756 GLU   ( 144-)  M
 821 GLU   ( 209-)  M
1739 GLU   (  81-)  A
1786 GLU   (   2-)  J
1946 GLU   ( 162-)  J
2096 GLU   ( 144-)  B
2311 GLU   ( 359-)  B
2393 GLU   ( 441-)  B
2708 GLU   ( 144-)  C
2773 GLU   ( 209-)  C
3691 GLU   (  81-)  E
3738 GLU   (   2-)  F
3898 GLU   ( 162-)  F

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.998578 -0.000092  0.000121|
 | -0.000092  0.998700  0.000044|
 |  0.000121  0.000044  0.999661|
Proposed new scale matrix

 |  0.010544  0.003530  0.003614|
 |  0.000000  0.009059  0.002285|
 |  0.000000  0.000000  0.005558|
With corresponding cell

    A    =  94.843  B   = 116.416  C    = 191.294
    Alpha=  98.505  Beta= 104.060  Gamma= 108.512

The CRYST1 cell dimensions

    A    =  94.980  B   = 116.570  C    = 191.370
    Alpha=  98.510  Beta= 104.080  Gamma= 108.510

Variance: 147.965
(Under-)estimated Z-score: 8.965

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.

 860 HIS   ( 248-)  M      CG   ND1  CE1 109.95    4.3
2812 HIS   ( 248-)  C      CG   ND1  CE1 109.86    4.3

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.

  51 ASP   (  51-)  L
 144 GLU   ( 144-)  L
 160 ASP   ( 160-)  L
 198 ARG   ( 198-)  L
 268 ARG   ( 268-)  L
 359 GLU   ( 359-)  L
 431 ARG   ( 431-)  L
 441 GLU   ( 441-)  L
 592 ARG   ( 592-)  L
 756 GLU   ( 144-)  M
 779 ARG   ( 167-)  M
 821 GLU   ( 209-)  M
1178 ASP   (  62-)  N
1184 ARG   (  68-)  N
1186 ASP   (  70-)  N
1216 ASP   ( 100-)  N
1219 ASP   ( 103-)  N
1299 ASP   ( 183-)  N
1478 ARG   ( 369-)  N
1615 ARG   (  26-)  K
1675 ARG   (  86-)  K
1715 ARG   (  40-)  A
1717 ARG   (  42-)  A
1721 ARG   (  63-)  A
1739 GLU   (  81-)  A
And so on for a total of 54 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.

 851 PRO   ( 239-)  M      N     10.1    30.50    -2.48
2803 PRO   ( 239-)  C      N     10.1    30.48    -2.48
The average deviation= 0.603

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.

1398 LEU   ( 289-)  N    4.76
3350 LEU   ( 289-)  D    4.76
3425 GLY   ( 364-)  D    4.49
1473 GLY   ( 364-)  N    4.33
2591 VAL   (  27-)  C    4.24
 639 VAL   (  27-)  M    4.22
 431 ARG   ( 431-)  L    4.21
2383 ARG   ( 431-)  B    4.03

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 : -5.316

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.

1349 THR   ( 240-)  N    -3.2
3301 THR   ( 240-)  D    -3.2
2186 PRO   ( 234-)  B    -3.1
 234 PRO   ( 234-)  L    -3.1
1007 THR   ( 395-)  M    -2.9
2741 TYR   ( 177-)  C    -2.8
 789 TYR   ( 177-)  M    -2.8
3529 PRO   ( 473-)  D    -2.8
1403 ILE   ( 294-)  N    -2.8
3355 ILE   ( 294-)  D    -2.8
1577 PRO   ( 473-)  N    -2.8
2959 THR   ( 395-)  C    -2.8
 252 LEU   ( 252-)  L    -2.7
2204 LEU   ( 252-)  B    -2.7
3283 PRO   ( 222-)  D    -2.7
1331 PRO   ( 222-)  N    -2.7
2147 LEU   ( 195-)  B    -2.7
 195 LEU   ( 195-)  L    -2.7
2417 THR   ( 465-)  B    -2.6
3203 ILE   ( 135-)  D    -2.6
1251 ILE   ( 135-)  N    -2.6
 465 THR   ( 465-)  L    -2.6
2199 THR   ( 247-)  B    -2.5
 247 THR   ( 247-)  L    -2.5
 616 PRO   (   4-)  M    -2.5
And so on for a total of 177 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 ASN   (   2-)  L  Poor phi/psi
  14 GLY   (  14-)  L  Poor phi/psi
  23 GLY   (  23-)  L  Poor phi/psi
  57 GLU   (  57-)  L  Poor phi/psi
  65 TRP   (  65-)  L  Poor phi/psi
  68 MET   (  68-)  L  Poor phi/psi
  82 ASP   (  82-)  L  Poor phi/psi
 135 ASN   ( 135-)  L  Poor phi/psi
 157 TYR   ( 157-)  L  Poor phi/psi
 194 THR   ( 194-)  L  Poor phi/psi
 196 ASN   ( 196-)  L  omega poor
 212 ASN   ( 212-)  L  Poor phi/psi
 213 ASN   ( 213-)  L  Poor phi/psi
 224 GLY   ( 224-)  L  Poor phi/psi
 231 ALA   ( 231-)  L  Poor phi/psi
 233 LEU   ( 233-)  L  PRO omega poor
 257 THR   ( 257-)  L  Poor phi/psi, omega poor
 357 HIS   ( 357-)  L  Poor phi/psi
 358 HIS   ( 358-)  L  Poor phi/psi
 360 GLN   ( 360-)  L  Poor phi/psi
 367 GLY   ( 367-)  L  Poor phi/psi
 383 GLY   ( 383-)  L  Poor phi/psi
 388 ALA   ( 388-)  L  Poor phi/psi
 392 VAL   ( 392-)  L  Poor phi/psi
 400 ASP   ( 400-)  L  Poor phi/psi
And so on for a total of 165 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 : -5.003

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.

 351 SER   ( 351-)  L    0.33
1580 SER   ( 476-)  N    0.33
2303 SER   ( 351-)  B    0.33
3532 SER   ( 476-)  D    0.33
1157 SER   (  41-)  N    0.34
  85 SER   (  85-)  L    0.34
3109 SER   (  41-)  D    0.35
2037 SER   (  85-)  B    0.35
1564 SER   ( 460-)  N    0.35
 655 SER   (  43-)  M    0.35
3516 SER   ( 460-)  D    0.36
2885 SER   ( 321-)  C    0.36
 933 SER   ( 321-)  M    0.36
1279 SER   ( 163-)  N    0.36
1446 SER   ( 337-)  N    0.36
2473 SER   ( 521-)  B    0.36
3231 SER   ( 163-)  D    0.36
3398 SER   ( 337-)  D    0.36
 250 SER   ( 250-)  L    0.37
2202 SER   ( 250-)  B    0.37
2607 SER   (  43-)  C    0.37
 114 SER   ( 114-)  L    0.37
1272 SER   ( 156-)  N    0.37
2066 SER   ( 114-)  B    0.37
3224 SER   ( 156-)  D    0.37
 349 SER   ( 349-)  L    0.38
2301 SER   ( 349-)  B    0.38
1640 SER   (  51-)  K    0.38
 532 SER   ( 532-)  L    0.39
2484 SER   ( 532-)  B    0.39
1283 SER   ( 167-)  N    0.39
3235 SER   ( 167-)  D    0.39
1884 SER   ( 100-)  J    0.39
3836 SER   ( 100-)  F    0.39
1048 SER   ( 436-)  M    0.39
3000 SER   ( 436-)  C    0.39
 567 SER   ( 567-)  L    0.39
2519 SER   ( 567-)  B    0.39
3236 SER   ( 168-)  D    0.39

Warning: Unusual backbone conformations

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

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

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

   3 MET   (   3-)  L      0
   4 LEU   (   4-)  L      0
  22 ARG   (  22-)  L      0
  24 ARG   (  24-)  L      0
  25 TRP   (  25-)  L      0
  57 GLU   (  57-)  L      0
  58 GLN   (  58-)  L      0
  63 PRO   (  63-)  L      0
  65 TRP   (  65-)  L      0
  67 TRP   (  67-)  L      0
  68 MET   (  68-)  L      0
  70 VAL   (  70-)  L      0
  72 ASP   (  72-)  L      0
  77 PHE   (  77-)  L      0
 107 MET   ( 107-)  L      0
 108 ARG   ( 108-)  L      0
 111 GLU   ( 111-)  L      0
 113 TYR   ( 113-)  L      0
 132 LEU   ( 132-)  L      0
 133 ALA   ( 133-)  L      0
 135 ASN   ( 135-)  L      0
 136 LEU   ( 136-)  L      0
 156 PHE   ( 156-)  L      0
 157 TYR   ( 157-)  L      0
 158 TYR   ( 158-)  L      0
And so on for a total of 869 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!

2061 GLY   ( 109-)  B   2.01   80
 109 GLY   ( 109-)  L   2.00   80
 945 GLY   ( 333-)  M   1.74   52
2897 GLY   ( 333-)  C   1.73   52
1959 THR   (   7-)  B   1.70   15
   7 THR   (   7-)  L   1.69   16
2722 GLY   ( 158-)  C   1.67   12
 770 GLY   ( 158-)  M   1.66   12

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].

 161 PRO   ( 161-)  L   100.4 envelop C-beta (108 degrees)
 234 PRO   ( 234-)  L   -62.6 half-chair C-beta/C-alpha (-54 degrees)
 248 PRO   ( 248-)  L   102.2 envelop C-beta (108 degrees)
 390 PRO   ( 390-)  L    99.8 envelop C-beta (108 degrees)
 616 PRO   (   4-)  M   106.7 envelop C-beta (108 degrees)
 685 PRO   (  73-)  M    99.3 envelop C-beta (108 degrees)
 848 PRO   ( 236-)  M   -59.9 half-chair C-beta/C-alpha (-54 degrees)
 851 PRO   ( 239-)  M   163.1 half-chair C-alpha/N (162 degrees)
 997 PRO   ( 385-)  M  -123.2 half-chair C-delta/C-gamma (-126 degrees)
1011 PRO   ( 399-)  M   108.4 envelop C-beta (108 degrees)
1121 PRO   (   5-)  N   106.6 envelop C-beta (108 degrees)
1331 PRO   ( 222-)  N    30.0 envelop C-delta (36 degrees)
1346 PRO   ( 237-)  N  -123.9 half-chair C-delta/C-gamma (-126 degrees)
1371 PRO   ( 262-)  N  -113.4 envelop C-gamma (-108 degrees)
1459 PRO   ( 350-)  N   105.6 envelop C-beta (108 degrees)
1546 PRO   ( 437-)  N   -11.9 half-chair C-alpha/N (-18 degrees)
1549 PRO   ( 445-)  N   106.3 envelop C-beta (108 degrees)
1575 PRO   ( 471-)  N  -115.0 envelop C-gamma (-108 degrees)
1577 PRO   ( 473-)  N   110.1 envelop C-beta (108 degrees)
1907 PRO   ( 123-)  J   110.0 envelop C-beta (108 degrees)
2113 PRO   ( 161-)  B   101.3 envelop C-beta (108 degrees)
2186 PRO   ( 234-)  B   -62.4 half-chair C-beta/C-alpha (-54 degrees)
2200 PRO   ( 248-)  B   101.5 envelop C-beta (108 degrees)
2342 PRO   ( 390-)  B    99.9 envelop C-beta (108 degrees)
2568 PRO   (   4-)  C   106.8 envelop C-beta (108 degrees)
2637 PRO   (  73-)  C    99.3 envelop C-beta (108 degrees)
2800 PRO   ( 236-)  C   -59.3 half-chair C-beta/C-alpha (-54 degrees)
2803 PRO   ( 239-)  C   164.3 half-chair C-alpha/N (162 degrees)
2949 PRO   ( 385-)  C  -122.8 half-chair C-delta/C-gamma (-126 degrees)
2963 PRO   ( 399-)  C   106.9 envelop C-beta (108 degrees)
3073 PRO   (   5-)  D   107.8 envelop C-beta (108 degrees)
3283 PRO   ( 222-)  D    29.5 envelop C-delta (36 degrees)
3298 PRO   ( 237-)  D  -124.0 half-chair C-delta/C-gamma (-126 degrees)
3323 PRO   ( 262-)  D  -114.0 envelop C-gamma (-108 degrees)
3411 PRO   ( 350-)  D   105.3 envelop C-beta (108 degrees)
3498 PRO   ( 437-)  D   -13.0 half-chair C-alpha/N (-18 degrees)
3501 PRO   ( 445-)  D   105.6 envelop C-beta (108 degrees)
3527 PRO   ( 471-)  D  -115.3 envelop C-gamma (-108 degrees)
3529 PRO   ( 473-)  D   110.5 envelop C-beta (108 degrees)
3859 PRO   ( 123-)  F   109.9 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.

2356 ALA   ( 404-)  B      O   <-> 2360 ALA   ( 408-)  B      CB     0.53    2.27  INTRA BF
 404 ALA   ( 404-)  L      O   <->  408 ALA   ( 408-)  L      CB     0.52    2.28  INTRA BF
 487 HIS   ( 487-)  L      ND1 <->  488 GLY   ( 488-)  L      N      0.45    2.45  INTRA BF
2439 HIS   ( 487-)  B      ND1 <-> 2440 GLY   ( 488-)  B      N      0.44    2.46  INTRA BF
2792 PHE   ( 228-)  C      O   <-> 2795 PHE   ( 231-)  C      N      0.41    2.29  INTRA BL
 840 PHE   ( 228-)  M      O   <->  843 PHE   ( 231-)  M      N      0.41    2.29  INTRA BL
1047 TYR   ( 435-)  M      CD1 <-> 1048 SER   ( 436-)  M      N      0.40    2.60  INTRA BL
2550 MET   ( 598-)  B      SD  <-> 3277 PHE   ( 216-)  D      CD2    0.39    3.01  INTRA BL
 598 MET   ( 598-)  L      SD  <-> 1325 PHE   ( 216-)  N      CD2    0.39    3.01  INTRA BL
2999 TYR   ( 435-)  C      CD1 <-> 3000 SER   ( 436-)  C      N      0.38    2.62  INTRA BL
2708 GLU   ( 144-)  C      CD  <-> 2743 GLN   ( 179-)  C      NE2    0.38    2.72  INTRA BL
1726 PHE   (  68-)  A      CE1 <-> 1784 THR   ( 126-)  A      C      0.36    2.84  INTRA BF
1186 ASP   (  70-)  N      OD2 <-> 1365 ARG   ( 256-)  N      NH2    0.36    2.34  INTRA BF
3678 PHE   (  68-)  E      CE1 <-> 3736 THR   ( 126-)  E      C      0.36    2.84  INTRA BF
 756 GLU   ( 144-)  M      CD  <->  791 GLN   ( 179-)  M      NE2    0.36    2.74  INTRA BL
3138 ASP   (  70-)  D      OD2 <-> 3317 ARG   ( 256-)  D      NH2    0.35    2.35  INTRA BF
 200 MET   ( 200-)  L      O   <->  204 ALA   ( 204-)  L      CB     0.34    2.46  INTRA BF
1473 GLY   ( 364-)  N      C   <-> 1475 PHE   ( 366-)  N      N      0.34    2.56  INTRA BF
2544 ARG   ( 592-)  B      NH2 <-> 3823 TRP   (  87-)  F      CZ2    0.34    2.76  INTRA BF
1211 LEU   (  95-)  N      O   <-> 1214 TYR   (  98-)  N      N      0.34    2.36  INTRA BL
2152 MET   ( 200-)  B      O   <-> 2156 ALA   ( 204-)  B      CB     0.34    2.46  INTRA BF
3169 ASN   ( 101-)  D      ND2 <-> 3896 ARG   ( 160-)  F      NH2    0.34    2.51  INTRA BF
3005 HIS   ( 441-)  C      ND1 <-> 3009 PHE   ( 445-)  C      CD2    0.33    2.77  INTRA BL
3163 LEU   (  95-)  D      O   <-> 3166 TYR   (  98-)  D      N      0.33    2.37  INTRA BL
 874 ILE   ( 262-)  M      O   <->  877 LYS   ( 265-)  M      N      0.32    2.38  INTRA BF
And so on for a total of 961 lines.

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.176

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: 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: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

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: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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.

3413 ARG   ( 352-)  D      -8.28
1461 ARG   ( 352-)  N      -8.22
2514 ARG   ( 562-)  B      -7.75
 562 ARG   ( 562-)  L      -7.75
1947 ARG   ( 163-)  J      -6.71
3899 ARG   ( 163-)  F      -6.70
1460 TYR   ( 351-)  N      -6.57
3412 TYR   ( 351-)  D      -6.53
3640 ARG   (  99-)  G      -6.40
1688 ARG   (  99-)  K      -6.39
3540 LEU   ( 484-)  D      -6.27
1588 LEU   ( 484-)  N      -6.26
 485 LEU   ( 485-)  L      -6.15
2437 LEU   ( 485-)  B      -6.14
1146 TRP   (  30-)  N      -6.14
3098 TRP   (  30-)  D      -6.14
1547 GLU   ( 438-)  N      -5.99
 449 LYS   ( 449-)  L      -5.93
2401 LYS   ( 449-)  B      -5.92
1976 ARG   (  24-)  B      -5.90
  24 ARG   (  24-)  L      -5.90
 108 ARG   ( 108-)  L      -5.87
2060 ARG   ( 108-)  B      -5.87
3496 HIS   ( 435-)  D      -5.87
1544 HIS   ( 435-)  N      -5.84
And so on for a total of 76 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.

 470 LEU   ( 470-)  L       472 - VAL    472- ( L)         -4.74
1146 TRP   (  30-)  N      1148 - ARG     32- ( N)         -4.92
2422 LEU   ( 470-)  B      2424 - VAL    472- ( B)         -4.74
3098 TRP   (  30-)  D      3100 - ARG     32- ( D)         -4.93

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: 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: 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: 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: 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: 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: 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

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.

3216 ARG   ( 148-)  D   -3.04
1264 ARG   ( 148-)  N   -2.99
 768 LEU   ( 156-)  M   -2.87
2720 LEU   ( 156-)  C   -2.86
 585 LEU   ( 585-)  L   -2.71
2537 LEU   ( 585-)  B   -2.71
3414 GLY   ( 353-)  D   -2.66
1462 GLY   ( 353-)  N   -2.65
2192 ALA   ( 240-)  B   -2.60
3382 MET   ( 321-)  D   -2.58
 240 ALA   ( 240-)  L   -2.58
2500 VAL   ( 548-)  B   -2.56
1515 HIS   ( 406-)  N   -2.56
1430 MET   ( 321-)  N   -2.56
3467 HIS   ( 406-)  D   -2.55
 548 VAL   ( 548-)  L   -2.55

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.

1459 PRO   ( 350-)  N     - 1463 PRO   ( 354-)  N        -1.74
3411 PRO   ( 350-)  D     - 3414 GLY   ( 353-)  D        -1.70

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: 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: K

Note: Second generation quality Z-score plot

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: J

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: G

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

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.

 100 HIS   ( 100-)  L
 121 ASN   ( 121-)  L
 232 GLN   ( 232-)  L
 270 HIS   ( 270-)  L
 409 ASN   ( 409-)  L
 570 ASN   ( 570-)  L
 808 HIS   ( 196-)  M
 818 ASN   ( 206-)  M
 956 GLN   ( 344-)  M
1053 HIS   ( 441-)  M
1867 GLN   (  83-)  J
2052 HIS   ( 100-)  B
2073 ASN   ( 121-)  B
2184 GLN   ( 232-)  B
2222 HIS   ( 270-)  B
2361 ASN   ( 409-)  B
2522 ASN   ( 570-)  B
2760 HIS   ( 196-)  C
2770 ASN   ( 206-)  C
2814 GLN   ( 250-)  C
2908 GLN   ( 344-)  C
3005 HIS   ( 441-)  C
3217 GLN   ( 149-)  D
3819 GLN   (  83-)  F

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

   2 ASN   (   2-)  L      N
   3 MET   (   3-)  L      N
   4 LEU   (   4-)  L      N
   5 ALA   (   5-)  L      N
   7 THR   (   7-)  L      N
  25 TRP   (  25-)  L      N
  28 ASN   (  28-)  L      N
  58 GLN   (  58-)  L      N
  65 TRP   (  65-)  L      NE1
  69 SER   (  69-)  L      N
  73 PHE   (  73-)  L      N
 102 TYR   ( 102-)  L      OH
 121 ASN   ( 121-)  L      ND2
 135 ASN   ( 135-)  L      N
 135 ASN   ( 135-)  L      ND2
 137 LEU   ( 137-)  L      N
 138 LEU   ( 138-)  L      N
 139 MET   ( 139-)  L      N
 143 TRP   ( 143-)  L      NE1
 157 TYR   ( 157-)  L      N
 163 ASN   ( 163-)  L      ND2
 175 ARG   ( 175-)  L      NH2
 194 THR   ( 194-)  L      N
 195 LEU   ( 195-)  L      N
 196 ASN   ( 196-)  L      N
And so on for a total of 435 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.

  62 GLN   (  62-)  L      OE1
 100 HIS   ( 100-)  L      NE2
 111 GLU   ( 111-)  L      OE2
 121 ASN   ( 121-)  L      OD1
 144 GLU   ( 144-)  L      OE2
 232 GLN   ( 232-)  L      OE1
 334 HIS   ( 334-)  L      NE2
 400 ASP   ( 400-)  L      OD1
 411 HIS   ( 411-)  L      ND1
 484 GLU   ( 484-)  L      OE1
 587 GLU   ( 587-)  L      OE1
 587 GLU   ( 587-)  L      OE2
 725 GLN   ( 113-)  M      OE1
 729 HIS   ( 117-)  M      ND1
 747 ASP   ( 135-)  M      OD2
 756 GLU   ( 144-)  M      OE1
 791 GLN   ( 179-)  M      OE1
 860 HIS   ( 248-)  M      ND1
 870 ASP   ( 258-)  M      OD1
 870 ASP   ( 258-)  M      OD2
 973 GLN   ( 361-)  M      OE1
1076 GLU   ( 464-)  M      OE1
1178 ASP   (  62-)  N      OD2
1219 ASP   ( 103-)  N      OD1
1249 GLU   ( 133-)  N      OE2
And so on for a total of 62 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.

 178 ASP   ( 178-)  L   H-bonding suggests Asn; but Alt-Rotamer
 400 ASP   ( 400-)  L   H-bonding suggests Asn
 441 GLU   ( 441-)  L   H-bonding suggests Gln; but Alt-Rotamer
 546 ASP   ( 546-)  L   H-bonding suggests Asn; but Alt-Rotamer
 587 GLU   ( 587-)  L   H-bonding suggests Gln
 747 ASP   ( 135-)  M   H-bonding suggests Asn; but Alt-Rotamer
 756 GLU   ( 144-)  M   H-bonding suggests Gln
 832 GLU   ( 220-)  M   H-bonding suggests Gln
1178 ASP   (  62-)  N   H-bonding suggests Asn; but Alt-Rotamer
1625 GLU   (  36-)  K   H-bonding suggests Gln; but Alt-Rotamer
2130 ASP   ( 178-)  B   H-bonding suggests Asn; but Alt-Rotamer
2352 ASP   ( 400-)  B   H-bonding suggests Asn
2393 GLU   ( 441-)  B   H-bonding suggests Gln; but Alt-Rotamer
2498 ASP   ( 546-)  B   H-bonding suggests Asn; but Alt-Rotamer
2539 GLU   ( 587-)  B   H-bonding suggests Gln
2699 ASP   ( 135-)  C   H-bonding suggests Asn; but Alt-Rotamer
2708 GLU   ( 144-)  C   H-bonding suggests Gln
2784 GLU   ( 220-)  C   H-bonding suggests Gln; but Alt-Rotamer
3130 ASP   (  62-)  D   H-bonding suggests Asn; but Alt-Rotamer
3577 GLU   (  36-)  G   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.680
  2nd generation packing quality :  -1.382
  Ramachandran plot appearance   :  -5.316 (bad)
  chi-1/chi-2 rotamer normality  :  -5.003 (bad)
  Backbone conformation          :   1.188

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.297 (tight)
  Bond angles                    :   0.540 (tight)
  Omega angle restraints         :   0.857
  Side chain planarity           :   0.264 (tight)
  Improper dihedral distribution :   0.553
  B-factor distribution          :   7.559 (loose)
  Inside/Outside distribution    :   1.176 (unusual)

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 : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :  -2.6
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :   1.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.297 (tight)
  Bond angles                    :   0.540 (tight)
  Omega angle restraints         :   0.857
  Side chain planarity           :   0.264 (tight)
  Improper dihedral distribution :   0.553
  B-factor distribution          :   7.559 (loose)
  Inside/Outside distribution    :   1.176 (unusual)
==============

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.