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 pdb3hbx.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.287
CA-only RMS fit for the two chains : 0.097

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.321
CA-only RMS fit for the two chains : 0.106

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.304
CA-only RMS fit for the two chains : 0.119

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.267
CA-only RMS fit for the two chains : 0.078

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and F

All-atom RMS fit for the two chains : 0.277
CA-only RMS fit for the two chains : 0.087

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and F

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 246 PRO   ( 257-)  A  -
 247 GLU   ( 258-)  A  -
 248 LEU   ( 259-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 246 PRO   ( 257-)  A  -
 247 GLU   ( 258-)  A  -
 248 LEU   ( 259-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 266 LLP   ( 277-)  A
 703 LLP   ( 277-)  B
1140 LLP   ( 277-)  C
1577 LLP   ( 277-)  D
2013 LLP   ( 277-)  E
2449 LLP   ( 277-)  F

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 VAL   (  12-)  A    High
  66 MET   (  77-)  A    High
 294 ASN   ( 305-)  A    High
 299 ASP   ( 310-)  A    High
 371 ASP   ( 382-)  A    High
 372 SER   ( 383-)  A    High
 373 SER   ( 384-)  A    High
 374 CYS   ( 385-)  A    High
 431 ARG   ( 442-)  A    High
 435 GLU   ( 446-)  A    High
 436 LEU   ( 447-)  A    High
 437 PRO   ( 448-)  A    High
 503 MET   (  77-)  B    High
 540 GLU   ( 114-)  B    High
 731 ASN   ( 305-)  B    High
 735 ALA   ( 309-)  B    High
 736 ASP   ( 310-)  B    High
 808 ASP   ( 382-)  B    High
 809 SER   ( 383-)  B    High
 810 SER   ( 384-)  B    High
 811 CYS   ( 385-)  B    High
 872 GLU   ( 446-)  B    High
 873 LEU   ( 447-)  B    High
 874 PRO   ( 448-)  B    High
 940 MET   (  77-)  C    High
And so on for a total of 72 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.

2042 TYR   ( 306-)  E    0.53
2043 LEU   ( 307-)  E    0.64
2044 GLY   ( 308-)  E    0.49
2478 TYR   ( 306-)  F    0.62

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: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Nomenclature related problems

Warning: Tyrosine convention problem

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

 176 TYR   ( 187-)  A
 267 TYR   ( 278-)  A
 329 TYR   ( 340-)  A
 613 TYR   ( 187-)  B
 704 TYR   ( 278-)  B
 766 TYR   ( 340-)  B
 831 TYR   ( 405-)  B
1050 TYR   ( 187-)  C
1141 TYR   ( 278-)  C
1169 TYR   ( 306-)  C
1203 TYR   ( 340-)  C
1268 TYR   ( 405-)  C
1487 TYR   ( 187-)  D
1578 TYR   ( 278-)  D
1640 TYR   ( 340-)  D
1705 TYR   ( 405-)  D
1923 TYR   ( 187-)  E
2014 TYR   ( 278-)  E
2076 TYR   ( 340-)  E
2141 TYR   ( 405-)  E
2359 TYR   ( 187-)  F
2450 TYR   ( 278-)  F
2512 TYR   ( 340-)  F

Warning: Phenylalanine convention problem

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

 353 PHE   ( 364-)  A
 790 PHE   ( 364-)  B
1227 PHE   ( 364-)  C
1664 PHE   ( 364-)  D
2100 PHE   ( 364-)  E
2536 PHE   ( 364-)  F

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.

 413 ASP   ( 424-)  A
 736 ASP   ( 310-)  B
 850 ASP   ( 424-)  B
1173 ASP   ( 310-)  C
1287 ASP   ( 424-)  C
1610 ASP   ( 310-)  D
1724 ASP   ( 424-)  D
2046 ASP   ( 310-)  E
2160 ASP   ( 424-)  E
2482 ASP   ( 310-)  F
2596 ASP   ( 424-)  F

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.

 103 GLU   ( 114-)  A
 190 GLU   ( 201-)  A
 219 GLU   ( 230-)  A
 283 GLU   ( 294-)  A
 338 GLU   ( 349-)  A
 435 GLU   ( 446-)  A
 627 GLU   ( 201-)  B
 656 GLU   ( 230-)  B
 720 GLU   ( 294-)  B
 775 GLU   ( 349-)  B
 872 GLU   ( 446-)  B
1064 GLU   ( 201-)  C
1093 GLU   ( 230-)  C
1157 GLU   ( 294-)  C
1212 GLU   ( 349-)  C
1309 GLU   ( 446-)  C
1413 GLU   ( 113-)  D
1501 GLU   ( 201-)  D
1530 GLU   ( 230-)  D
1558 GLU   ( 258-)  D
1594 GLU   ( 294-)  D
1649 GLU   ( 349-)  D
1746 GLU   ( 446-)  D
1850 GLU   ( 114-)  E
1937 GLU   ( 201-)  E
1966 GLU   ( 230-)  E
2030 GLU   ( 294-)  E
2085 GLU   ( 349-)  E
2182 GLU   ( 446-)  E
2285 GLU   ( 113-)  F
2373 GLU   ( 201-)  F
2402 GLU   ( 230-)  F
2466 GLU   ( 294-)  F
2521 GLU   ( 349-)  F
2618 GLU   ( 446-)  F

Geometric checks

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.

 103 GLU   ( 114-)  A
 190 GLU   ( 201-)  A
 219 GLU   ( 230-)  A
 283 GLU   ( 294-)  A
 338 GLU   ( 349-)  A
 413 ASP   ( 424-)  A
 435 GLU   ( 446-)  A
 627 GLU   ( 201-)  B
 656 GLU   ( 230-)  B
 720 GLU   ( 294-)  B
 736 ASP   ( 310-)  B
 775 GLU   ( 349-)  B
 850 ASP   ( 424-)  B
 872 GLU   ( 446-)  B
1064 GLU   ( 201-)  C
1093 GLU   ( 230-)  C
1157 GLU   ( 294-)  C
1173 ASP   ( 310-)  C
1212 GLU   ( 349-)  C
1287 ASP   ( 424-)  C
1309 GLU   ( 446-)  C
1413 GLU   ( 113-)  D
1501 GLU   ( 201-)  D
1530 GLU   ( 230-)  D
1558 GLU   ( 258-)  D
1594 GLU   ( 294-)  D
1610 ASP   ( 310-)  D
1649 GLU   ( 349-)  D
1724 ASP   ( 424-)  D
1746 GLU   ( 446-)  D
1850 GLU   ( 114-)  E
1937 GLU   ( 201-)  E
1966 GLU   ( 230-)  E
2030 GLU   ( 294-)  E
2046 ASP   ( 310-)  E
2085 GLU   ( 349-)  E
2160 ASP   ( 424-)  E
2182 GLU   ( 446-)  E
2285 GLU   ( 113-)  F
2373 GLU   ( 201-)  F
2402 GLU   ( 230-)  F
2466 GLU   ( 294-)  F
2482 ASP   ( 310-)  F
2521 GLU   ( 349-)  F
2596 ASP   ( 424-)  F
2618 GLU   ( 446-)  F

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

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

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

2547 LEU   ( 375-)  F    -2.6
1675 LEU   ( 375-)  D    -2.6
2111 LEU   ( 375-)  E    -2.6
 364 LEU   ( 375-)  A    -2.6
 801 LEU   ( 375-)  B    -2.6
1238 LEU   ( 375-)  C    -2.6
1321 ARG   (  21-)  D    -2.4
  10 ARG   (  21-)  A    -2.4
2193 ARG   (  21-)  F    -2.4
 884 ARG   (  21-)  C    -2.4
 447 ARG   (  21-)  B    -2.4
1757 ARG   (  21-)  E    -2.4
1540 PRO   ( 240-)  D    -2.3
 229 PRO   ( 240-)  A    -2.3
1103 PRO   ( 240-)  C    -2.3
 666 PRO   ( 240-)  B    -2.3
2505 ILE   ( 333-)  F    -2.3
1976 PRO   ( 240-)  E    -2.3
2412 PRO   ( 240-)  F    -2.3
 322 ILE   ( 333-)  A    -2.2
1633 ILE   ( 333-)  D    -2.2
2069 ILE   ( 333-)  E    -2.2
1196 ILE   ( 333-)  C    -2.2
 759 ILE   ( 333-)  B    -2.2
1596 LEU   ( 296-)  D    -2.2
And so on for a total of 76 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.

  98 ASN   ( 109-)  A  Poor phi/psi
 102 GLU   ( 113-)  A  Poor phi/psi
 103 GLU   ( 114-)  A  omega poor
 194 CYS   ( 205-)  A  Poor phi/psi
 250 TRP   ( 261-)  A  Poor phi/psi
 251 ASP   ( 262-)  A  Poor phi/psi
 269 LEU   ( 280-)  A  Poor phi/psi
 273 GLY   ( 284-)  A  Poor phi/psi
 307 PHE   ( 318-)  A  Poor phi/psi
 371 ASP   ( 382-)  A  Poor phi/psi
 373 SER   ( 384-)  A  Poor phi/psi
 398 PRO   ( 409-)  A  omega poor
 535 ASN   ( 109-)  B  Poor phi/psi
 541 ALA   ( 115-)  B  Poor phi/psi
 631 CYS   ( 205-)  B  Poor phi/psi
 687 TRP   ( 261-)  B  Poor phi/psi
 688 ASP   ( 262-)  B  Poor phi/psi
 706 LEU   ( 280-)  B  Poor phi/psi
 710 GLY   ( 284-)  B  Poor phi/psi
 744 PHE   ( 318-)  B  Poor phi/psi
 808 ASP   ( 382-)  B  Poor phi/psi
 810 SER   ( 384-)  B  Poor phi/psi
 835 PRO   ( 409-)  B  omega poor
 972 ASN   ( 109-)  C  Poor phi/psi
 977 GLU   ( 114-)  C  Poor phi/psi
And so on for a total of 68 lines.

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 VAL   (  14-)  A      0
  17 PRO   (  28-)  A      0
  18 ARG   (  29-)  A      0
  19 PHE   (  30-)  A      0
  21 MET   (  32-)  A      0
  24 ASN   (  35-)  A      0
  44 ASN   (  55-)  A      0
  52 PHE   (  63-)  A      0
  68 SER   (  79-)  A      0
  74 VAL   (  85-)  A      0
  76 MET   (  87-)  A      0
  79 TYR   (  90-)  A      0
  97 PHE   ( 108-)  A      0
  99 ALA   ( 110-)  A      0
 100 PRO   ( 111-)  A      0
 103 GLU   ( 114-)  A      0
 104 ALA   ( 115-)  A      0
 105 GLU   ( 116-)  A      0
 108 VAL   ( 119-)  A      0
 113 VAL   ( 124-)  A      0
 137 GLU   ( 148-)  A      0
 140 PRO   ( 151-)  A      0
 141 VAL   ( 152-)  A      0
 142 ASP   ( 153-)  A      0
 143 LYS   ( 154-)  A      0
And so on for a total of 948 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 3.745

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].

 229 PRO   ( 240-)  A    25.2 half-chair N/C-delta (18 degrees)
 301 PRO   ( 312-)  A    51.8 half-chair C-delta/C-gamma (54 degrees)
 392 PRO   ( 403-)  A    29.5 envelop C-delta (36 degrees)
 398 PRO   ( 409-)  A  -112.0 envelop C-gamma (-108 degrees)
 666 PRO   ( 240-)  B    25.3 half-chair N/C-delta (18 degrees)
 829 PRO   ( 403-)  B    29.5 envelop C-delta (36 degrees)
1103 PRO   ( 240-)  C    25.5 half-chair N/C-delta (18 degrees)
1175 PRO   ( 312-)  C    43.0 envelop C-delta (36 degrees)
1266 PRO   ( 403-)  C    29.1 envelop C-delta (36 degrees)
1540 PRO   ( 240-)  D    25.3 half-chair N/C-delta (18 degrees)
1612 PRO   ( 312-)  D    45.5 half-chair C-delta/C-gamma (54 degrees)
1703 PRO   ( 403-)  D    29.2 envelop C-delta (36 degrees)
1709 PRO   ( 409-)  D  -116.0 envelop C-gamma (-108 degrees)
1976 PRO   ( 240-)  E    25.4 half-chair N/C-delta (18 degrees)
2048 PRO   ( 312-)  E    46.5 half-chair C-delta/C-gamma (54 degrees)
2139 PRO   ( 403-)  E    29.4 envelop C-delta (36 degrees)
2145 PRO   ( 409-)  E  -115.2 envelop C-gamma (-108 degrees)
2412 PRO   ( 240-)  F    25.3 half-chair N/C-delta (18 degrees)
2575 PRO   ( 403-)  F    29.6 envelop C-delta (36 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.

1576 HIS   ( 276-)  D      NE2 <-> 1577 LLP   ( 277-)  D      OP1    0.23    2.47  INTRA BL
 266 LLP   ( 277-)  A      OP1 <->  745 SER   ( 319-)  B      CB     0.15    2.65  INTRA BL
 702 HIS   ( 276-)  B      NE2 <->  703 LLP   ( 277-)  B      OP1    0.15    2.55  INTRA BL
 241 ALA   ( 252-)  A      N   <->  242 PRO   ( 253-)  A      CD     0.13    2.87  INTRA BL
1552 ALA   ( 252-)  D      N   <-> 1553 PRO   ( 253-)  D      CD     0.13    2.87  INTRA BL
 678 ALA   ( 252-)  B      N   <->  679 PRO   ( 253-)  B      CD     0.13    2.87  INTRA BL
2424 ALA   ( 252-)  F      N   <-> 2425 PRO   ( 253-)  F      CD     0.13    2.87  INTRA BL
1115 ALA   ( 252-)  C      N   <-> 1116 PRO   ( 253-)  C      CD     0.13    2.87  INTRA BL
1804 MET   (  68-)  E      CE  <-> 1808 CYS   (  72-)  E      SG     0.12    3.28  INTRA BL
  57 MET   (  68-)  A      CE  <->   61 CYS   (  72-)  A      SG     0.12    3.28  INTRA BL
1988 ALA   ( 252-)  E      N   <-> 1989 PRO   ( 253-)  E      CD     0.12    2.88  INTRA BL
2012 HIS   ( 276-)  E      NE2 <-> 2013 LLP   ( 277-)  E      OP1    0.12    2.58  INTRA BL
2448 HIS   ( 276-)  F      NE2 <-> 2449 LLP   ( 277-)  F      OP1    0.12    2.58  INTRA BL
1139 HIS   ( 276-)  C      NE2 <-> 1140 LLP   ( 277-)  C      OP1    0.12    2.58  INTRA BL
1046 LEU   ( 183-)  C      O   <-> 1273 ASN   ( 410-)  C      N      0.11    2.59  INTRA BF
 760 ARG   ( 334-)  B      NH1 <->  877 VAL   (  14-)  C      O      0.11    2.59  INTRA BF
 931 MET   (  68-)  C      CE  <->  935 CYS   (  72-)  C      SG     0.11    3.29  INTRA
2240 MET   (  68-)  F      CE  <-> 2244 CYS   (  72-)  F      SG     0.10    3.30  INTRA BL
 115 SER   ( 126-)  A      N   <->  266 LLP   ( 277-)  A      OP3    0.10    2.60  INTRA BL
1368 MET   (  68-)  D      CE  <-> 1372 CYS   (  72-)  D      SG     0.10    3.30  INTRA BL
 494 MET   (  68-)  B      CE  <->  498 CYS   (  72-)  B      SG     0.09    3.31  INTRA BL
1919 LEU   ( 183-)  E      O   <-> 2146 ASN   ( 410-)  E      N      0.09    2.61  INTRA BF
1483 LEU   ( 183-)  D      O   <-> 1710 ASN   ( 410-)  D      N      0.09    2.61  INTRA BF
 202 THR   ( 213-)  A      O   <->  407 ARG   ( 418-)  A      NH1    0.09    2.61  INTRA BF
1513 THR   ( 213-)  D      O   <-> 1718 ARG   ( 418-)  D      NH1    0.08    2.62  INTRA BF
And so on for a total of 110 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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.

1169 TYR   ( 306-)  C      -6.54
2042 TYR   ( 306-)  E      -6.33
1606 TYR   ( 306-)  D      -6.27
 732 TYR   ( 306-)  B      -6.11
 295 TYR   ( 306-)  A      -6.05
2478 TYR   ( 306-)  F      -6.02
1767 LYS   (  31-)  E      -5.48
1331 LYS   (  31-)  D      -5.46
 894 LYS   (  31-)  C      -5.39
 457 LYS   (  31-)  B      -5.36
  20 LYS   (  31-)  A      -5.35
2203 LYS   (  31-)  F      -5.35
1924 TYR   ( 188-)  E      -5.14
 374 CYS   ( 385-)  A      -5.07
 811 CYS   ( 385-)  B      -5.07
1248 CYS   ( 385-)  C      -5.07
2557 CYS   ( 385-)  F      -5.06
 177 TYR   ( 188-)  A      -5.06
1760 ARG   (  24-)  E      -5.04
  13 ARG   (  24-)  A      -5.04
1685 CYS   ( 385-)  D      -5.04
1324 ARG   (  24-)  D      -5.03
2121 CYS   ( 385-)  E      -5.03
1970 GLU   ( 234-)  E      -5.02
 660 GLU   ( 234-)  B      -5.01
2406 GLU   ( 234-)  F      -5.01
1097 GLU   ( 234-)  C      -5.01
1534 GLU   ( 234-)  D      -5.00
 223 GLU   ( 234-)  A      -5.00

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.

 435 GLU   ( 446-)  A       437 - PRO    448- ( A)         -4.24
 872 GLU   ( 446-)  B       874 - PRO    448- ( B)         -4.25
1309 GLU   ( 446-)  C      1311 - PRO    448- ( C)         -4.26
2618 GLU   ( 446-)  F      2620 - PRO    448- ( F)         -4.25

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

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.

1509 ILE   ( 209-)  D   -2.58
1945 ILE   ( 209-)  E   -2.57
2381 ILE   ( 209-)  F   -2.56
 635 ILE   ( 209-)  B   -2.56
1072 ILE   ( 209-)  C   -2.56
 198 ILE   ( 209-)  A   -2.56

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.

 727 ILE   ( 301-)  B     -  730 ILE   ( 304-)  B        -1.50
1164 ILE   ( 301-)  C     - 1167 ILE   ( 304-)  C        -1.38
1601 ILE   ( 301-)  D     - 1604 ILE   ( 304-)  D        -1.46
2037 ILE   ( 301-)  E     - 2040 ILE   ( 304-)  E        -1.54
2473 ILE   ( 301-)  F     - 2476 ILE   ( 304-)  F        -1.48

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

2624 HOH   ( 553 )  D      O

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.

1166 HIS   ( 303-)  C
2039 HIS   ( 303-)  E

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 SER   (  13-)  A      N
   3 VAL   (  14-)  A      N
   4 HIS   (  15-)  A      N
   6 THR   (  17-)  A      OG1
   7 PHE   (  18-)  A      N
  12 VAL   (  23-)  A      N
  13 ARG   (  24-)  A      N
  29 GLU   (  40-)  A      N
  46 ARG   (  57-)  A      NH2
 115 SER   ( 126-)  A      N
 116 SER   ( 127-)  A      N
 148 THR   ( 159-)  A      OG1
 153 GLN   ( 164-)  A      NE2
 154 VAL   ( 165-)  A      N
 158 LYS   ( 169-)  A      NZ
 178 VAL   ( 189-)  A      N
 194 CYS   ( 205-)  A      N
 201 SER   ( 212-)  A      OG
 251 ASP   ( 262-)  A      N
 263 SER   ( 274-)  A      OG
 265 HIS   ( 276-)  A      NE2
 267 TYR   ( 278-)  A      N
 268 GLY   ( 279-)  A      N
 297 GLY   ( 308-)  A      N
 304 THR   ( 315-)  A      N
And so on for a total of 241 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.

  78 GLU   (  89-)  A      OE2
 103 GLU   ( 114-)  A      OE1
 215 ASP   ( 226-)  A      OD2
 515 GLU   (  89-)  B      OE2
1286 GLU   ( 423-)  C      OE1
1389 GLU   (  89-)  D      OE2
1526 ASP   ( 226-)  D      OD2
1631 GLN   ( 331-)  D      OE1
1825 GLU   (  89-)  E      OE2
2595 GLU   ( 423-)  F      OE1

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.

  78 GLU   (  89-)  A   H-bonding suggests Gln
 215 ASP   ( 226-)  A   H-bonding suggests Asn; but Alt-Rotamer
 223 GLU   ( 234-)  A   H-bonding suggests Gln
 377 GLU   ( 388-)  A   H-bonding suggests Gln
 434 ASP   ( 445-)  A   H-bonding suggests Asn
 435 GLU   ( 446-)  A   H-bonding suggests Gln
 515 GLU   (  89-)  B   H-bonding suggests Gln
 652 ASP   ( 226-)  B   H-bonding suggests Asn; but Alt-Rotamer
 660 GLU   ( 234-)  B   H-bonding suggests Gln
 814 GLU   ( 388-)  B   H-bonding suggests Gln
 871 ASP   ( 445-)  B   H-bonding suggests Asn
 872 GLU   ( 446-)  B   H-bonding suggests Gln
 952 GLU   (  89-)  C   H-bonding suggests Gln
1089 ASP   ( 226-)  C   H-bonding suggests Asn; but Alt-Rotamer
1097 GLU   ( 234-)  C   H-bonding suggests Gln
1251 GLU   ( 388-)  C   H-bonding suggests Gln
1308 ASP   ( 445-)  C   H-bonding suggests Asn
1309 GLU   ( 446-)  C   H-bonding suggests Gln
1389 GLU   (  89-)  D   H-bonding suggests Gln
1414 GLU   ( 114-)  D   H-bonding suggests Gln
1526 ASP   ( 226-)  D   H-bonding suggests Asn; but Alt-Rotamer
1534 GLU   ( 234-)  D   H-bonding suggests Gln
1688 GLU   ( 388-)  D   H-bonding suggests Gln
1745 ASP   ( 445-)  D   H-bonding suggests Asn
1746 GLU   ( 446-)  D   H-bonding suggests Gln
1825 GLU   (  89-)  E   H-bonding suggests Gln
1962 ASP   ( 226-)  E   H-bonding suggests Asn; but Alt-Rotamer
1970 GLU   ( 234-)  E   H-bonding suggests Gln
2124 GLU   ( 388-)  E   H-bonding suggests Gln
2181 ASP   ( 445-)  E   H-bonding suggests Asn
2182 GLU   ( 446-)  E   H-bonding suggests Gln
2261 GLU   (  89-)  F   H-bonding suggests Gln
2398 ASP   ( 226-)  F   H-bonding suggests Asn; but Alt-Rotamer
2406 GLU   ( 234-)  F   H-bonding suggests Gln
2560 GLU   ( 388-)  F   H-bonding suggests Gln
2617 ASP   ( 445-)  F   H-bonding suggests Asn
2618 GLU   ( 446-)  F   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.001
  2nd generation packing quality :  -0.784
  Ramachandran plot appearance   :  -1.116
  chi-1/chi-2 rotamer normality  :  -0.867
  Backbone conformation          :  -0.251

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.153 (tight)
  Bond angles                    :   0.375 (tight)
  Omega angle restraints         :   0.681 (tight)
  Side chain planarity           :   0.140 (tight)
  Improper dihedral distribution :   0.359
  B-factor distribution          :   0.831
  Inside/Outside distribution    :   1.002

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.67


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.2
  2nd generation packing quality :   0.7
  Ramachandran plot appearance   :   1.3
  chi-1/chi-2 rotamer normality  :   1.3
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.153 (tight)
  Bond angles                    :   0.375 (tight)
  Omega angle restraints         :   0.681 (tight)
  Side chain planarity           :   0.140 (tight)
  Improper dihedral distribution :   0.359
  B-factor distribution          :   0.831
  Inside/Outside distribution    :   1.002
==============

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.