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 pdb2nvz.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: C 1 2 1
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity

Error: Matthews Coefficient (Vm) very 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.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 414556.000
Volume of the Unit Cell V= 7176687.5
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 8.656
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.820 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)

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.

3578 UTP   (3000-)  A  -

Non-validating, descriptive output paragraph

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

3577  MG   (2002-)  B  -

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: E

Note: Ramachandran plot

Chain identifier: F

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

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'.

  10 OADE  (  10-)  R      O3'

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 OADE  (   1-)  R    High
   2 OURA  (   2-)  R    High
   3 OCYT  (   3-)  R    High
   4 OGUA  (   4-)  R    High
   5 OADE  (   5-)  R    High
   6 OGUA  (   6-)  R    High
   7 OADE  (   7-)  R    High
   8 OGUA  (   8-)  R    High
  11 DCYT  (   1-)  T    High
  12 DTHY  (   2-)  T    High
  13 DADE  (   3-)  T    High
  14 DCYT  (   4-)  T    High
  15 DCYT  (   5-)  T    High
  16 DGUA  (   6-)  T    High
  17 DADE  (   7-)  T    High
  18 DTHY  (   8-)  T    High
  19 DADE  (   9-)  T    High
  20 DADE  (  10-)  T    High
  21 DGUA  (  11-)  T    High
  22 DCYT  (  12-)  T    High
  23 DADE  (  13-)  T    High
  24 DGUA  (  14-)  T    High
  25 DADE  (  15-)  T    High
  26 DCYT  (  16-)  T    High
  27 DGUA  (  17-)  T    High
And so on for a total of 3108 lines.

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  11 DCYT  (   1-)  T    0.50

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: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

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

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.

 740 ARG   ( 711-)  A
1188 ARG   (1159-)  A
3205 ARG   ( 130-)  H
3265 ARG   (  45-)  I

Warning: Tyrosine convention problem

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

 412 TYR   ( 383-)  A
 433 TYR   ( 404-)  A
 457 TYR   ( 428-)  A
 507 TYR   ( 478-)  A
 833 TYR   ( 804-)  A
 881 TYR   ( 852-)  A
 897 TYR   ( 868-)  A
 926 TYR   ( 897-)  A
 962 TYR   ( 933-)  A
1064 TYR   (1035-)  A
1148 TYR   (1119-)  A
1182 TYR   (1153-)  A
1183 TYR   (1154-)  A
1303 TYR   (1298-)  A
1354 TYR   (1349-)  A
1358 TYR   (1353-)  A
1508 TYR   (  96-)  B
1525 TYR   ( 113-)  B
1571 TYR   ( 190-)  B
1654 TYR   ( 275-)  B
1682 TYR   ( 303-)  B
1801 TYR   ( 431-)  B
1821 TYR   ( 459-)  B
1990 TYR   ( 634-)  B
2039 TYR   ( 692-)  B
2123 TYR   ( 785-)  B
2317 TYR   ( 994-)  B
2396 TYR   (1073-)  B
2414 TYR   (1091-)  B
2626 TYR   (  82-)  C
2658 TYR   ( 114-)  C
2735 TYR   ( 191-)  C
2753 TYR   ( 209-)  C
2838 TYR   (  28-)  E
2856 TYR   (  46-)  E
2958 TYR   ( 168-)  E
3022 TYR   (  88-)  F
3107 TYR   (  20-)  H
3168 TYR   (  93-)  H
3170 TYR   (  95-)  H
3177 TYR   ( 102-)  H
3190 TYR   ( 115-)  H
3191 TYR   ( 116-)  H
3204 TYR   ( 129-)  H
3235 TYR   (  15-)  I
3254 TYR   (  34-)  I
3384 TYR   (  44-)  J
3466 TYR   (  61-)  K
3524 TYR   (  29-)  L

Warning: Phenylalanine convention problem

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

  70 PHE   (  19-)  A
  73 PHE   (  22-)  A
  88 PHE   (  37-)  A
 146 PHE   (  95-)  A
 252 PHE   ( 219-)  A
 257 PHE   ( 224-)  A
 261 PHE   ( 228-)  A
 285 PHE   ( 252-)  A
 297 PHE   ( 264-)  A
 331 PHE   ( 298-)  A
 376 PHE   ( 347-)  A
 497 PHE   ( 468-)  A
 511 PHE   ( 482-)  A
 569 PHE   ( 540-)  A
 620 PHE   ( 591-)  A
 675 PHE   ( 646-)  A
 743 PHE   ( 714-)  A
 750 PHE   ( 721-)  A
 784 PHE   ( 755-)  A
 806 PHE   ( 777-)  A
 808 PHE   ( 779-)  A
 816 PHE   ( 787-)  A
 842 PHE   ( 813-)  A
 844 PHE   ( 815-)  A
 895 PHE   ( 866-)  A
And so on for a total of 80 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.

 167 ASP   ( 116-)  A
 202 ASP   ( 151-)  A
 293 ASP   ( 260-)  A
 301 ASP   ( 268-)  A
 391 ASP   ( 362-)  A
 510 ASP   ( 481-)  A
 512 ASP   ( 483-)  A
 555 ASP   ( 526-)  A
 567 ASP   ( 538-)  A
 573 ASP   ( 544-)  A
 745 ASP   ( 716-)  A
 819 ASP   ( 790-)  A
 882 ASP   ( 853-)  A
 903 ASP   ( 874-)  A
 913 ASP   ( 884-)  A
 934 ASP   ( 905-)  A
 938 ASP   ( 909-)  A
 959 ASP   ( 930-)  A
1003 ASP   ( 974-)  A
1195 ASP   (1166-)  A
1225 ASP   (1206-)  A
1242 ASP   (1223-)  A
1262 ASP   (1257-)  A
1293 ASP   (1288-)  A
1339 ASP   (1334-)  A
And so on for a total of 61 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.

  76 GLU   (  25-)  A
 123 GLU   (  72-)  A
 171 GLU   ( 120-)  A
 238 GLU   ( 205-)  A
 265 GLU   ( 232-)  A
 313 GLU   ( 280-)  A
 323 GLU   ( 290-)  A
 389 GLU   ( 360-)  A
 462 GLU   ( 433-)  A
 524 GLU   ( 495-)  A
 525 GLU   ( 496-)  A
 529 GLU   ( 500-)  A
 622 GLU   ( 593-)  A
 665 GLU   ( 636-)  A
 714 GLU   ( 685-)  A
 741 GLU   ( 712-)  A
 800 GLU   ( 771-)  A
 824 GLU   ( 795-)  A
 830 GLU   ( 801-)  A
 841 GLU   ( 812-)  A
 851 GLU   ( 822-)  A
 875 GLU   ( 846-)  A
 908 GLU   ( 879-)  A
 923 GLU   ( 894-)  A
 947 GLU   ( 918-)  A
And so on for a total of 91 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.

   2 OURA  (   2-)  R      C1'  N1    1.53    6.4
   3 OCYT  (   3-)  R      C1'  N1    1.54    5.4
  22 DCYT  (  12-)  T      C1'  N1    1.52    4.3
  26 DCYT  (  16-)  T      C1'  N1    1.54    5.7
  33 DCYT  (  23-)  T      C1'  N1    1.55    6.5
  35 DCYT  (  25-)  T      C1'  N1    1.52    4.4
  39 DCYT  (   1-)  N      C1'  N1    1.52    4.4
1187 PRO   (1158-)  A      CG   CD    1.70    5.7
3385 CYS   (  45-)  J      SG  -SG*   2.29    6.2

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.996899 -0.000089  0.000044|
 | -0.000089  0.997220 -0.000014|
 |  0.000044 -0.000014  0.996839|
Proposed new scale matrix

 |  0.005913  0.000000  0.001221|
 |  0.000000  0.004511  0.000000|
 |  0.000000  0.000000  0.005272|
With corresponding cell

    A    = 169.112  B   = 221.703  C    = 193.693
    Alpha=  90.002  Beta= 101.664  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 169.647  B   = 222.338  C    = 194.316
    Alpha=  90.000  Beta= 101.670  Gamma=  90.000

Variance: 1302.448
(Under-)estimated Z-score: 26.598

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.

   3 OCYT  (   3-)  R      C6   N1   C2  118.49   -4.5
   4 OGUA  (   4-)  R      N9   C8   N7  114.33    6.5
   6 OGUA  (   6-)  R      N9   C8   N7  114.14    6.1
   8 OGUA  (   8-)  R      C3'  C4'  O4'  99.07   -4.6
   9 OGUA  (   9-)  R      N9   C8   N7  113.35    4.5
  14 DCYT  (   4-)  T      O4'  C1'  N1  111.88    5.1
  15 DCYT  (   5-)  T      O4'  C1'  N1  111.64    4.8
  16 DGUA  (   6-)  T      N9   C8   N7  113.66    5.1
  18 DTHY  (   8-)  T      O4'  C1'  N1  111.36    4.5
  21 DGUA  (  11-)  T      O4'  C1'  N9  114.23    8.0
  21 DGUA  (  11-)  T      N9   C8   N7  113.88    5.6
  24 DGUA  (  14-)  T      N9   C8   N7  113.72    5.2
  25 DADE  (  15-)  T      C2   N3   C4  112.64    4.1
  26 DCYT  (  16-)  T      P   -C3* -O3* 128.96    7.7
  26 DCYT  (  16-)  T      O4'  C1'  N1  114.50    8.4
  27 DGUA  (  17-)  T      N9   C8   N7  114.53    6.9
  29 DTHY  (  19-)  T      C6   C5   C7  118.46   -7.4
  29 DTHY  (  19-)  T      C4   C5   C7  123.86    8.1
  30 DCYT  (  20-)  T      C3'  C4'  O4' 101.11   -4.5
  30 DCYT  (  20-)  T      C4'  C3'  C2'  97.53   -5.7
  32 DTHY  (  22-)  T      C5   C4   O4  121.79   -4.4
  33 DCYT  (  23-)  T      C3'  C4'  O4' 100.42   -5.2
  33 DCYT  (  23-)  T      C4'  C3'  C2'  97.66   -5.5
  33 DCYT  (  23-)  T      O4'  C1'  N1  113.77    7.5
  34 DTHY  (  24-)  T      C5   C4   O4  121.52   -4.8
And so on for a total of 82 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.

  76 GLU   (  25-)  A
 123 GLU   (  72-)  A
 167 ASP   ( 116-)  A
 171 GLU   ( 120-)  A
 202 ASP   ( 151-)  A
 238 GLU   ( 205-)  A
 265 GLU   ( 232-)  A
 293 ASP   ( 260-)  A
 301 ASP   ( 268-)  A
 313 GLU   ( 280-)  A
 323 GLU   ( 290-)  A
 389 GLU   ( 360-)  A
 391 ASP   ( 362-)  A
 462 GLU   ( 433-)  A
 510 ASP   ( 481-)  A
 512 ASP   ( 483-)  A
 524 GLU   ( 495-)  A
 525 GLU   ( 496-)  A
 529 GLU   ( 500-)  A
 555 ASP   ( 526-)  A
 567 ASP   ( 538-)  A
 573 ASP   ( 544-)  A
 622 GLU   ( 593-)  A
 665 GLU   ( 636-)  A
 714 GLU   ( 685-)  A
And so on for a total of 156 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.

1004 HIS   ( 975-)  A      CA    -6.7    21.72    34.11
1005 THR   ( 976-)  A      CA    -7.9    20.69    33.84
1123 VAL   (1094-)  A      CA    -7.0    23.07    33.23
1247 TRP   (1228-)  A      CA    -7.0    22.23    34.04
2057 LEU   ( 710-)  B      CA    -6.7    23.98    34.19
The average deviation= 0.736

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.

1099 GLN   (1070-)  A    6.45
1098 ALA   (1069-)  A    6.20
1220 ALA   (1201-)  A    5.30
1908 MET   ( 552-)  B    4.73
1100 SER   (1071-)  A    4.66
1565 ALA   ( 184-)  B    4.29
1192 ILE   (1163-)  A    4.29
2712 ALA   ( 168-)  C    4.28
 417 LEU   ( 388-)  A    4.26
1612 PRO   ( 231-)  B    4.12

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 : -5.061

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.

2074 THR   ( 736-)  B    -3.7
1045 THR   (1016-)  A    -3.6
3224 PHE   (   4-)  I    -3.5
 120 THR   (  69-)  A    -3.5
2345 THR   (1022-)  B    -3.4
3521 THR   (  26-)  L    -3.4
3538 THR   (  43-)  L    -3.3
  95 THR   (  44-)  A    -3.3
3119 THR   (  32-)  H    -3.2
 675 PHE   ( 646-)  A    -3.2
1185 PRO   (1156-)  A    -3.1
1187 PRO   (1158-)  A    -3.1
2771 THR   ( 227-)  C    -3.1
2218 THR   ( 880-)  B    -3.1
1653 PRO   ( 274-)  B    -3.1
1612 PRO   ( 231-)  B    -3.1
 732 THR   ( 703-)  A    -3.1
2075 THR   ( 737-)  B    -3.0
  61 PRO   (  10-)  A    -3.0
2915 PRO   ( 125-)  E    -3.0
1927 PRO   ( 571-)  B    -3.0
3177 TYR   ( 102-)  H    -3.0
 480 HIS   ( 451-)  A    -3.0
1992 PRO   ( 636-)  B    -3.0
1001 HIS   ( 972-)  A    -3.0
And so on for a total of 312 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.

  54 GLY   (   3-)  A  omega poor
  59 SER   (   8-)  A  omega poor
  88 PHE   (  37-)  A  PRO omega poor
  89 PRO   (  38-)  A  omega poor
  90 GLU   (  39-)  A  Poor phi/psi
  92 MET   (  41-)  A  Poor phi/psi
  95 THR   (  44-)  A  Poor phi/psi, omega poor
  99 ALA   (  48-)  A  Poor phi/psi
 103 GLY   (  52-)  A  Poor phi/psi
 105 ASN   (  54-)  A  Poor phi/psi
 107 PRO   (  56-)  A  omega poor
 114 ARG   (  63-)  A  Poor phi/psi
 120 THR   (  69-)  A  omega poor
 122 GLN   (  71-)  A  Poor phi/psi
 123 GLU   (  72-)  A  Poor phi/psi, omega poor
 159 MET   ( 108-)  A  Poor phi/psi
 178 ALA   ( 127-)  A  Poor phi/psi
 181 ASP   ( 130-)  A  Poor phi/psi
 193 CYS   ( 142-)  A  Poor phi/psi
 246 HIS   ( 213-)  A  Poor phi/psi
 247 ILE   ( 214-)  A  Poor phi/psi
 256 GLY   ( 223-)  A  Poor phi/psi
 281 PRO   ( 248-)  A  Poor phi/psi
 282 SER   ( 249-)  A  Poor phi/psi
 283 ILE   ( 250-)  A  Poor phi/psi
And so on for a total of 483 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 : -5.662

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.

1076 SER   (1047-)  A    0.36
1817 SER   ( 455-)  B    0.36
2182 SER   ( 844-)  B    0.37
1851 SER   ( 489-)  B    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 OCYT  (   3-)  R      0
   4 OGUA  (   4-)  R      0
   5 OADE  (   5-)  R      0
   6 OGUA  (   6-)  R      0
   7 OADE  (   7-)  R      0
   8 OGUA  (   8-)  R      0
   9 OGUA  (   9-)  R      0
  10 OADE  (  10-)  R      0
  11 DCYT  (   1-)  T      0
  12 DTHY  (   2-)  T      0
  13 DADE  (   3-)  T      0
  14 DCYT  (   4-)  T      0
  15 DCYT  (   5-)  T      0
  16 DGUA  (   6-)  T      0
  17 DADE  (   7-)  T      0
  18 DTHY  (   8-)  T      0
  19 DADE  (   9-)  T      0
  20 DADE  (  10-)  T      0
  21 DGUA  (  11-)  T      0
  22 DCYT  (  12-)  T      0
  23 DADE  (  13-)  T      0
  24 DGUA  (  14-)  T      0
  25 DADE  (  15-)  T      0
  26 DCYT  (  16-)  T      0
  27 DGUA  (  17-)  T      0
And so on for a total of 1806 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!

3105 GLY   (  18-)  H   3.29   12
2685 GLY   ( 141-)  C   3.21   11
 950 GLY   ( 921-)  A   3.04   14
1031 GLY   (1002-)  A   2.17   12
3075 GLY   ( 141-)  F   2.10   54
 702 GLY   ( 673-)  A   1.99   10
2311 GLY   ( 988-)  B   1.94   35
 623 GLY   ( 594-)  A   1.94   52
1749 GLY   ( 379-)  B   1.81   80
2117 GLY   ( 779-)  B   1.68   21
2362 GLY   (1039-)  B   1.66   80
 394 GLY   ( 365-)  A   1.63   13
2579 ARG   (  35-)  C   1.60   14
 836 GLY   ( 807-)  A   1.58   18
 901 GLY   ( 872-)  A   1.58   51
1473 GLY   (  42-)  B   1.57   18
 229 GLY   ( 183-)  A   1.51   78
1726 LEU   ( 356-)  B   1.50   11

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...

 734 LYS   ( 705-)  A   1.69
1654 TYR   ( 275-)  B   1.67
1655 ILE   ( 276-)  B   1.69
2188 LEU   ( 850-)  B   1.51

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]

1187 PRO   (1158-)  A    0.51 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].

  61 PRO   (  10-)  A     0.8 envelop N (0 degrees)
  89 PRO   (  38-)  A    19.8 half-chair N/C-delta (18 degrees)
 107 PRO   (  56-)  A   -23.4 half-chair C-alpha/N (-18 degrees)
 129 PRO   (  78-)  A   -38.2 envelop C-alpha (-36 degrees)
 204 PRO   ( 153-)  A   102.9 envelop C-beta (108 degrees)
 218 PRO   ( 172-)  A   -57.2 half-chair C-beta/C-alpha (-54 degrees)
 277 PRO   ( 244-)  A  -138.0 envelop C-delta (-144 degrees)
 281 PRO   ( 248-)  A    48.6 half-chair C-delta/C-gamma (54 degrees)
 350 PRO   ( 321-)  A   -41.0 envelop C-alpha (-36 degrees)
 406 PRO   ( 377-)  A   107.8 envelop C-beta (108 degrees)
 411 PRO   ( 382-)  A  -114.9 envelop C-gamma (-108 degrees)
 429 PRO   ( 400-)  A    49.9 half-chair C-delta/C-gamma (54 degrees)
 470 PRO   ( 441-)  A    40.0 envelop C-delta (36 degrees)
 521 PRO   ( 492-)  A  -115.8 envelop C-gamma (-108 degrees)
 592 PRO   ( 563-)  A  -119.8 half-chair C-delta/C-gamma (-126 degrees)
 597 PRO   ( 568-)  A   145.4 envelop C-alpha (144 degrees)
 629 PRO   ( 600-)  A  -118.4 half-chair C-delta/C-gamma (-126 degrees)
 668 PRO   ( 639-)  A    40.2 envelop C-delta (36 degrees)
 839 PRO   ( 810-)  A  -157.5 half-chair N/C-delta (-162 degrees)
1007 PRO   ( 978-)  A    15.9 half-chair N/C-delta (18 degrees)
1143 PRO   (1114-)  A     3.7 envelop N (0 degrees)
1185 PRO   (1156-)  A   150.2 envelop C-alpha (144 degrees)
1187 PRO   (1158-)  A   137.6 envelop C-alpha (144 degrees)
1193 PRO   (1164-)  A  -151.3 envelop C-delta (-144 degrees)
1307 PRO   (1302-)  A   -47.0 half-chair C-beta/C-alpha (-54 degrees)
And so on for a total of 65 lines.

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.

1109 THR   (1080-)  A      O   <-> 1111 ASN   (1082-)  A      N      0.84    1.86  INTRA BL
3323 CYS   ( 103-)  I      SG  <-> 3326 CYS   ( 106-)  I      SG     0.78    2.67  INTRA BF
2636 CYS   (  92-)  C      SG  <-> 2639 CYS   (  95-)  C      SG     0.60    2.85  INTRA BL
2728 ASN   ( 184-)  C      ND2 <-> 2733 THR   ( 189-)  C      O      0.57    2.13  INTRA BL
1536 TYR   ( 124-)  B      OH  <-> 1560 CYS   ( 179-)  B      SG     0.51    2.49  INTRA BL
 118 CYS   (  67-)  A      SG  <->  128 CYS   (  77-)  A      SG     0.50    3.10  INTRA BF
 736 GLY   ( 707-)  A      CA  <->  738 THR   ( 709-)  A      N      0.48    2.62  INTRA BF
1104 PRO   (1075-)  A      O   <-> 1108 MET   (1079-)  A      N      0.46    2.24  INTRA BL
1093 VAL   (1064-)  A      O   <-> 1097 ALA   (1068-)  A      N      0.44    2.26  INTRA BL
 317 ALA   ( 284-)  A      N   <->  318 PRO   ( 285-)  A      CD     0.44    2.56  INTRA BF
1112 THR   (1083-)  A      N   <-> 1113 PHE   (1084-)  A      C      0.43    2.47  INTRA BL
2068 ARG   ( 728-)  B      NH1 <-> 2098 ASP   ( 760-)  B      OD2    0.42    2.28  INTRA BF
 730 LEU   ( 701-)  A      CA  <->  731 LEU   ( 702-)  A      CB     0.42    2.58  INTRA BF
1666 ARG   ( 287-)  B      NH1 <-> 1703 ILE   ( 324-)  B      O      0.42    2.28  INTRA BF
 452 ASP   ( 423-)  A      CG  <->  453 ILE   ( 424-)  A      N      0.41    2.59  INTRA BL
1991 ARG   ( 635-)  B      CB  <-> 1992 PRO   ( 636-)  B      CD     0.41    2.69  INTRA BL
 811 ARG   ( 782-)  A      NH2 <-> 2046 GLU   ( 699-)  B      O      0.41    2.29  INTRA BL
2186 ARG   ( 848-)  B      NH1 <-> 3348 PHE   (   8-)  J      O      0.40    2.30  INTRA BL
3323 CYS   ( 103-)  I      SG  <-> 3326 CYS   ( 106-)  I      CB     0.40    3.00  INTRA BF
2836 ARG   (  26-)  E      NH2 <-> 2923 GLU   ( 133-)  E      OE1    0.39    2.31  INTRA BF
 128 CYS   (  77-)  A      SG  <->  131 HIS   (  80-)  A      NE2    0.39    2.91  INTRA BF
1196 GLU   (1167-)  A      CB  <-> 1197 GLU   (1168-)  A      CA     0.38    2.62  INTRA BF
 519 HIS   ( 490-)  A      ND1 <-> 2473 ARG   (1150-)  B      NH1    0.37    2.63  INTRA BL
 741 GLU   ( 712-)  A      N   <->  742 SER   ( 713-)  A      CB     0.37    2.53  INTRA BF
2215 PRO   ( 877-)  B      CA  <-> 2216 GLN   ( 878-)  B      CB     0.37    2.63  INTRA BF
And so on for a total of 724 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: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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

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.

2753 TYR   ( 209-)  C      -8.19
  57 TYR   (   6-)  A      -7.99
2545 ARG   (1222-)  B      -7.91
3155 ARG   (  80-)  H      -7.84
 290 ARG   ( 257-)  A      -7.73
 349 ARG   ( 320-)  A      -7.70
1838 ARG   ( 476-)  B      -7.67
1188 ARG   (1159-)  A      -7.66
3250 ARG   (  30-)  I      -7.64
3162 ARG   (  87-)  H      -7.61
1654 TYR   ( 275-)  B      -7.59
2206 MET   ( 868-)  B      -7.56
2431 ARG   (1108-)  B      -7.55
3158 GLN   (  83-)  H      -7.39
3537 ARG   (  42-)  L      -7.32
2882 MET   (  75-)  E      -7.27
3106 ARG   (  19-)  H      -7.19
3290 ARG   (  70-)  I      -7.14
2543 ARG   (1220-)  B      -7.08
 114 ARG   (  63-)  A      -7.06
1207 GLN   (1188-)  A      -7.04
1929 GLN   ( 573-)  B      -7.00
 285 PHE   ( 252-)  A      -7.00
2002 LEU   ( 646-)  B      -6.99
3152 ARG   (  77-)  H      -6.92
And so on for a total of 157 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.

  53 VAL   (   2-)  A        55 - GLN      4- ( A)         -4.58
 158 CYS   ( 107-)  A       161 - CYS    110- ( A)         -5.06
 285 PHE   ( 252-)  A       287 - GLU    254- ( A)         -5.16
 366 ARG   ( 337-)  A       368 - ASN    339- ( A)         -4.63
 618 GLN   ( 589-)  A       620 - PHE    591- ( A)         -4.86
1002 ILE   ( 973-)  A      1006 - LYS    977- ( A)         -4.58
1139 ASN   (1110-)  A      1141 - LYS   1112- ( A)         -4.89
1625 LEU   ( 244-)  B      1629 - SER    248- ( B)         -5.08
1654 TYR   ( 275-)  B      1656 - LYS    277- ( B)         -5.71
1804 ARG   ( 434-)  B      1806 - VAL    436- ( B)         -4.02
1830 GLU   ( 468-)  B      1832 - LYS    470- ( B)         -4.78
2069 ILE   ( 729-)  B      2071 - VAL    731- ( B)         -4.65
2202 LYS   ( 864-)  B      2204 - TYR    866- ( B)         -5.84
2222 ARG   ( 884-)  B      2225 - HIS    887- ( B)         -5.43
3334 GLN   ( 114-)  I      3339 - THR    119- ( I)         -5.16

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

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

Average for range 1 - 3565 : -1.720

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: 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: 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

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.

 476 GLN   ( 447-)  A   -3.21
2498 LEU   (1175-)  B   -3.07
3240 LYS   (  20-)  I   -2.96
 477 PRO   ( 448-)  A   -2.96
2456 MET   (1133-)  B   -2.90
2072 SER   ( 732-)  B   -2.86
2445 ARG   (1122-)  B   -2.86
1976 ARG   ( 620-)  B   -2.79
 165 LEU   ( 114-)  A   -2.77
1185 PRO   (1156-)  A   -2.76
  81 ILE   (  30-)  A   -2.74
1004 HIS   ( 975-)  A   -2.74
2978 LEU   ( 188-)  E   -2.73
 857 ALA   ( 828-)  A   -2.72
2437 LEU   (1114-)  B   -2.70
1632 THR   ( 253-)  B   -2.68
1682 TYR   ( 303-)  B   -2.67
3212 GLN   ( 137-)  H   -2.66
1927 PRO   ( 571-)  B   -2.61
2004 HIS   ( 648-)  B   -2.60
2897 GLU   ( 102-)  E   -2.60
2475 MET   (1152-)  B   -2.59
1114 HIS   (1085-)  A   -2.59
1977 GLU   ( 621-)  B   -2.58
3389 MET   (  49-)  J   -2.56
 647 GLU   ( 618-)  A   -2.55
 587 GLY   ( 558-)  A   -2.53
1122 LYS   (1093-)  A   -2.53
2032 LEU   ( 685-)  B   -2.52
1113 PHE   (1084-)  A   -2.52
 194 LYS   ( 143-)  A   -2.51
 481 LYS   ( 452-)  A   -2.50

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.

 284 SER   ( 251-)  A     -  287 GLU   ( 254-)  A        -1.92
 348 GLY   ( 319-)  A     -  352 LYS   ( 323-)  A        -1.70
 478 SER   ( 449-)  A     -  481 LYS   ( 452-)  A        -1.95
 728 ALA   ( 699-)  A     -  731 LEU   ( 702-)  A        -1.86
1111 ASN   (1082-)  A     - 1114 HIS   (1085-)  A        -2.03
1183 TYR   (1154-)  A     - 1186 ASP   (1157-)  A        -1.99
1243 LEU   (1224-)  A     - 1247 TRP   (1228-)  A        -1.83
1652 LEU   ( 273-)  B     - 1655 ILE   ( 276-)  B        -1.61
1974 ASP   ( 618-)  B     - 1977 GLU   ( 621-)  B        -2.02
2480 ALA   (1157-)  B     - 2483 VAL   (1160-)  B        -1.55
2494 VAL   (1171-)  B     - 2499 ASN   (1176-)  B        -1.95
3232 ASN   (  12-)  I     - 3235 TYR   (  15-)  I        -2.07
3243 ASN   (  23-)  I     - 3246 LEU   (  26-)  I        -1.87
3261 PRO   (  41-)  I     - 3264 TYR   (  44-)  I        -1.59
3554 ALA   (  59-)  L     - 3558 ARG   (  63-)  L        -1.82

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: E

Note: Second generation quality Z-score plot

Chain identifier: F

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

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.

 105 ASN   (  54-)  A
 119 GLN   (  68-)  A
 134 HIS   (  83-)  A
 258 ASN   ( 225-)  A
 346 GLN   ( 313-)  A
 368 ASN   ( 339-)  A
 517 ASN   ( 488-)  A
 519 HIS   ( 490-)  A
 574 GLN   ( 545-)  A
 613 ASN   ( 584-)  A
 660 HIS   ( 631-)  A
 770 ASN   ( 741-)  A
 786 ASN   ( 757-)  A
 831 ASN   ( 802-)  A
 887 ASN   ( 858-)  A
 955 GLN   ( 926-)  A
1001 HIS   ( 972-)  A
1206 GLN   (1187-)  A
1437 GLN   (1432-)  A
1527 GLN   ( 115-)  B
1596 GLN   ( 215-)  B
1605 GLN   ( 224-)  B
1720 GLN   ( 350-)  B
1736 GLN   ( 366-)  B
1827 ASN   ( 465-)  B
1871 HIS   ( 515-)  B
2082 HIS   ( 744-)  B
2108 GLN   ( 770-)  B
2416 GLN   (1093-)  B
2464 HIS   (1141-)  B
2500 HIS   (1177-)  B
2561 ASN   (  17-)  C
2675 HIS   ( 131-)  C
2815 ASN   (   5-)  E
3209 ASN   ( 134-)  H
3303 ASN   (  83-)  I
3310 GLN   (  90-)  I
3393 HIS   (  53-)  J
3434 ASN   (  29-)  K

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

   4 OGUA  (   4-)  R      N1
  34 DTHY  (  24-)  T      N3
  36 DGUA  (  26-)  T      N1
  44 DTHY  (   6-)  N      N3
  48 DGUA  (  10-)  N      N1
  50 DTHY  (  12-)  N      N3
  56 GLN   (   5-)  A      N
  58 SER   (   7-)  A      N
  73 PHE   (  22-)  A      N
  74 SER   (  23-)  A      N
  84 ALA   (  33-)  A      N
 100 LYS   (  49-)  A      N
 101 ILE   (  50-)  A      N
 103 GLY   (  52-)  A      N
 108 ARG   (  57-)  A      N
 109 LEU   (  58-)  A      N
 110 GLY   (  59-)  A      N
 112 ILE   (  61-)  A      N
 113 ASP   (  62-)  A      N
 115 ASN   (  64-)  A      N
 117 LYS   (  66-)  A      N
 121 CYS   (  70-)  A      N
 131 HIS   (  80-)  A      N
 131 HIS   (  80-)  A      ND1
 139 LYS   (  88-)  A      N
And so on for a total of 826 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.

  69 GLN   (  18-)  A      OE1
 119 GLN   (  68-)  A      OE1
 200 GLU   ( 149-)  A      OE1
 217 GLN   ( 171-)  A      OE1
 339 ASN   ( 306-)  A      OD1
 462 GLU   ( 433-)  A      OE2
 469 ASP   ( 440-)  A      OD1
 474 ASN   ( 445-)  A      OD1
 487 HIS   ( 458-)  A      ND1
 512 ASP   ( 483-)  A      OD1
 524 GLU   ( 495-)  A      OE1
 555 ASP   ( 526-)  A      OD2
 660 HIS   ( 631-)  A      NE2
 665 GLU   ( 636-)  A      OE1
 677 ASN   ( 648-)  A      OD1
 883 ASN   ( 854-)  A      OD1
 913 ASP   ( 884-)  A      OD1
 961 GLU   ( 932-)  A      OE1
1132 GLU   (1103-)  A      OE2
1169 HIS   (1140-)  A      ND1
1184 ASP   (1155-)  A      OD1
1372 HIS   (1367-)  A      ND1
1408 GLU   (1403-)  A      OE2
1422 GLU   (1417-)  A      OE2
1424 ASP   (1419-)  A      OD2
And so on for a total of 63 lines.

Warning: Unusual ion packing

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

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

3576  MG   (2001-)  A   -.-  -.-  Low probability ion. B= 97.5
3577  MG   (2002-)  B   -.-  -.-  Low probability ion. B=102.4
Since there are no waters, the water check has been skipped.

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.

  93 ASP   (  42-)  A   H-bonding suggests Asn
  94 GLU   (  43-)  A   H-bonding suggests Gln; but Alt-Rotamer
 106 ASP   (  55-)  A   H-bonding suggests Asn
 127 GLU   (  76-)  A   H-bonding suggests Gln
 202 ASP   ( 151-)  A   H-bonding suggests Asn
 293 ASP   ( 260-)  A   H-bonding suggests Asn; but Alt-Rotamer
 313 GLU   ( 280-)  A   H-bonding suggests Gln
 340 ASP   ( 307-)  A   H-bonding suggests Asn; but Alt-Rotamer
 452 ASP   ( 423-)  A   H-bonding suggests Asn; but Alt-Rotamer
 469 ASP   ( 440-)  A   H-bonding suggests Asn
 567 ASP   ( 538-)  A   H-bonding suggests Asn
 665 GLU   ( 636-)  A   H-bonding suggests Gln
 725 GLU   ( 696-)  A   H-bonding suggests Gln
 855 ASP   ( 826-)  A   H-bonding suggests Asn
 919 ASP   ( 890-)  A   H-bonding suggests Asn
 929 ASP   ( 900-)  A   H-bonding suggests Asn
 959 ASP   ( 930-)  A   H-bonding suggests Asn; but Alt-Rotamer
 960 GLU   ( 931-)  A   H-bonding suggests Gln
1042 ASP   (1013-)  A   H-bonding suggests Asn; but Alt-Rotamer
1079 GLU   (1050-)  A   H-bonding suggests Gln; but Alt-Rotamer
1132 GLU   (1103-)  A   H-bonding suggests Gln; but Alt-Rotamer
1184 ASP   (1155-)  A   H-bonding suggests Asn; but Alt-Rotamer
1196 GLU   (1167-)  A   H-bonding suggests Gln; but Alt-Rotamer
1217 ASP   (1198-)  A   H-bonding suggests Asn
1233 GLU   (1214-)  A   H-bonding suggests Gln
And so on for a total of 57 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 :  -3.049
  2nd generation packing quality :  -3.606 (poor)
  Ramachandran plot appearance   :  -5.061 (bad)
  chi-1/chi-2 rotamer normality  :  -5.662 (bad)
  Backbone conformation          :  -1.272

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.479 (tight)
  Bond angles                    :   0.746
  Omega angle restraints         :   1.257
  Side chain planarity           :   0.326 (tight)
  Improper dihedral distribution :   0.684
  B-factor distribution          :   0.344
  Inside/Outside distribution    :   1.067

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 4.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.3
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :  -1.7
  chi-1/chi-2 rotamer normality  :  -3.1 (poor)
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.479 (tight)
  Bond angles                    :   0.746
  Omega angle restraints         :   1.257
  Side chain planarity           :   0.326 (tight)
  Improper dihedral distribution :   0.684
  B-factor distribution          :   0.344
  Inside/Outside distribution    :   1.067
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.