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.
326 DMS ( 321-) A -
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.
120 MET ( 120-) A -
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.
120 MET ( 120-) A -
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
Coordinate problems, unexpected atoms, B-factor and occupancy checks
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.
144 LEU ( 144-) A 0.80 157 TYR ( 157-) A 0.80 161 SER ( 161-) A 1.12 225 GLN ( 225-) A 0.80
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :293.000
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
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.
318 LYS ( 318-) A C O 1.57 17.2
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
| 0.993236 0.001329 -0.002984| | 0.001329 0.999652 -0.000756| | -0.002984 -0.000756 0.996405|Proposed new scale matrix
| 0.010686 0.006121 0.000037| | -0.000016 0.012269 0.000009| | 0.000023 0.000006 0.007625|With corresponding cell
A = 93.508 B = 93.856 C = 131.141 Alpha= 89.904 Beta= 90.344 Gamma= 119.727
The CRYST1 cell dimensions
A = 94.145 B = 94.145 C = 131.616 Alpha= 90.000 Beta= 90.000 Gamma= 120.000
(Under-)estimated Z-score: 9.999
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.
6 THR ( 6-) A CG2 CB OG1 117.67 4.2 11 ARG ( 11-) A CA CB CG 123.74 4.8 11 ARG ( 11-) A CD NE CZ 134.87 7.3 28 TYR ( 28-) A CD1 CG CD2 124.33 4.2 47 ARG ( 47-) A CG CD NE 117.41 4.1 47 ARG ( 47-) A CD NE CZ 130.75 5.0 59 ASP ( 59-) A CA CB CG 118.36 5.8 59 ASP ( 59-) A CB CG OD2 130.56 5.3 62 PHE ( 62-) A -CA -C N 124.79 4.3 74 HIS ( 74-) A N CA CB 103.28 -4.2 74 HIS ( 74-) A CB CG CD2 134.33 4.0 93 TYR ( 93-) A CA C O 113.70 -4.2 97 ASN ( 97-) A ND2 CG OD1 117.31 -5.3 101 ARG ( 101-) A CD NE CZ 130.47 4.9 112 ASN ( 112-) A ND2 CG OD1 118.58 -4.0 114 PHE ( 114-) A CA CB CG 119.82 6.0 116 ASN ( 116-) A CA C O 113.10 -4.5 116 ASN ( 116-) A CA CB CG 117.90 5.3 118 SER ( 118-) A C CA CB 101.95 -4.3 142 HIS ( 142-) A CG ND1 CE1 110.67 5.1 142 HIS ( 142-) A ND1 CE1 NE2 104.22 -5.8 142 HIS ( 142-) A CE1 NE2 CD2 114.70 6.0 142 HIS ( 142-) A NE2 CD2 CG 101.87 -4.6 146 HIS ( 146-) A -CA -C N 124.73 4.3 146 HIS ( 146-) A CA C O 113.85 -4.1 146 HIS ( 146-) A CG ND1 CE1 111.33 5.7 146 HIS ( 146-) A ND1 CE1 NE2 101.82 -7.6 146 HIS ( 146-) A CE1 NE2 CD2 116.68 7.5 146 HIS ( 146-) A NE2 CD2 CG 99.89 -6.6 146 HIS ( 146-) A CD2 CG ND1 110.26 4.2 149 THR ( 149-) A CA CB OG1 102.95 -4.4 160 GLU ( 160-) A CA CB CG 104.74 -4.7 166 GLU ( 166-) A OE2 CD OE1 135.79 5.4 172 PHE ( 172-) A CA CB CG 109.00 -4.8 184 PRO ( 184-) A -CA -C N 123.77 4.6 187 GLU ( 187-) A CA C O 110.97 -5.8 194 THR ( 194-) A -C N CA 129.39 4.3 195 PRO ( 195-) A -O -C N 114.02 -5.7 198 SER ( 198-) A -O -C N 112.48 -6.6 198 SER ( 198-) A -CA -C N 126.78 5.3 202 LEU ( 202-) A N CA CB 103.09 -4.4 231 HIS ( 231-) A CE1 NE2 CD2 112.16 4.0 233 ASN ( 233-) A ND2 CG OD1 128.29 5.7 250 HIS ( 250-) A CG ND1 CE1 112.35 6.7 260 ARG ( 260-) A CG CD NE 117.54 4.1 260 ARG ( 260-) A CD NE CZ 139.52 9.9 267 PHE ( 267-) A CA CB CG 109.17 -4.6 280 ASN ( 280-) A ND2 CG OD1 118.23 -4.4 316 LYS ( 316-) A CA C O 113.39 -4.4
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.
202 LEU ( 202-) A C -6.2 -9.53 0.20 The average deviation= 1.801
68 ALA ( 68-) A 4.35
112 ASN ( 112-) A 5.55 33 ASN ( 33-) A 4.11
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.
6 THR ( 6-) A -2.7 46 TYR ( 46-) A -2.4 107 SER ( 107-) A -2.4 92 SER ( 92-) A -2.3 182 LYS ( 182-) A -2.2 157 TYR ( 157-) A -2.1 51 PRO ( 51-) A -2.0
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.
26 THR ( 26-) A Poor phi/psi 46 TYR ( 46-) A Poor phi/psi 50 LEU ( 50-) A PRO omega poor 60 ASN ( 60-) A Poor phi/psi 89 ASN ( 89-) A Poor phi/psi 92 SER ( 92-) A Poor phi/psi 97 ASN ( 97-) A Poor phi/psi 105 HIS ( 105-) A Poor phi/psi 107 SER ( 107-) A Poor phi/psi 118 SER ( 118-) A Poor phi/psi 132 PRO ( 132-) A omega poor 152 THR ( 152-) A Poor phi/psi 157 TYR ( 157-) A Poor phi/psi 159 ASN ( 159-) A Poor phi/psi 181 ASN ( 181-) A Poor phi/psi 194 THR ( 194-) A Poor phi/psi 227 ASN ( 227-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.152
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!
5 SER ( 5-) A 0 14 LEU ( 14-) A 0 24 TYR ( 24-) A 0 25 SER ( 25-) A 0 26 THR ( 26-) A 0 27 TYR ( 27-) A 0 30 LEU ( 30-) A 0 34 THR ( 34-) A 0 35 ARG ( 35-) A 0 37 ASP ( 37-) A 0 45 LYS ( 45-) A 0 46 TYR ( 46-) A 0 51 PRO ( 51-) A 0 53 SER ( 53-) A 0 55 TRP ( 55-) A 0 58 ALA ( 58-) A 0 60 ASN ( 60-) A 0 61 GLN ( 61-) A 0 62 PHE ( 62-) A 0 63 PHE ( 63-) A 0 91 LEU ( 91-) A 0 92 SER ( 92-) A 0 96 ASN ( 96-) A 0 97 ASN ( 97-) A 0 104 VAL ( 104-) A 0And so on for a total of 125 lines.
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!
277 PRO ( 277-) A 1.75 12
195 PRO ( 195-) A -115.8 envelop C-gamma (-108 degrees)
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.
120 MET ( 120-) A A SD <-> 143 GLU ( 143-) A CB 0.69 2.71 INTRA 120 MET ( 120-) A A CE <-> 143 GLU ( 143-) A CB 0.56 2.64 INTRA 157 TYR ( 157-) A A OH <-> 166 GLU ( 166-) A OE2 0.29 2.11 INTRA 120 MET ( 120-) A A CE <-> 143 GLU ( 143-) A A CG 0.23 2.97 INTRA 112 ASN ( 112-) A ND2 <-> 318 LYS ( 318-) A O 0.12 2.58 INTRA 92 SER ( 92-) A N <-> 327 HOH ( 347 ) A O 0.08 2.62 INTRA BL 262 LYS ( 262-) A NZ <-> 302 GLU ( 302-) A OE2 0.08 2.62 INTRA 68 ALA ( 68-) A N <-> 69 PRO ( 69-) A CD 0.07 2.93 INTRA BL 18 LYS ( 18-) A NZ <-> 72 ASP ( 72-) A OD1 0.06 2.64 INTRA BL 33 ASN ( 33-) A ND2 <-> 327 HOH ( 438 ) A O 0.05 2.65 INTRA 81 TYR ( 81-) A OH <-> 97 ASN ( 97-) A ND2 0.03 2.67 INTRA BL 142 HIS ( 142-) A ND1 <-> 170 ASP ( 170-) A OD1 0.02 2.68 INTRA BL 1 ILE ( 1-) A N <-> 31 GLN ( 31-) A NE2 0.01 2.84 INTRA 16 ASP ( 16-) A OD2 <-> 18 LYS ( 18-) A NZ 0.01 2.69 INTRA
Chain identifier: A
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.
221 TYR ( 221-) A -6.03 108 GLN ( 108-) A -5.95 88 HIS ( 88-) A -5.82 246 GLN ( 246-) A -5.52 157 TYR ( 157-) A -5.47 225 GLN ( 225-) A -5.39 182 LYS ( 182-) A -5.31 251 TYR ( 251-) A -5.28 273 GLN ( 273-) A -5.25 50 LEU ( 50-) A -5.04
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
225 GLN ( 225-) A 228 - GLY 228- ( A) -4.49
Chain identifier: A
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.
44 ALA ( 44-) A -2.77
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
189 GLY ( 189-) A - 192 VAL ( 192-) A -1.56
Chain identifier: A
Water, ion, and hydrogenbond related checks
Warning: Water molecules need moving
The water molecules listed in the table below were found to be significantly
closer to a symmetry related non-water molecule than to the ones given in the
coordinate file. For optimal viewing convenience revised coordinates for
these water molecules should be given.
The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.
327 HOH ( 330 ) A O 32.43 49.45 -20.92
327 HOH ( 431 ) A O Metal-coordinating Histidine residue 142 fixed to 1 Metal-coordinating Histidine residue 146 fixed to 1
19 ASN ( 19-) A 31 GLN ( 31-) A 33 ASN ( 33-) A 273 GLN ( 273-) A 290 GLN ( 290-) A 301 GLN ( 301-) A
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.
35 ARG ( 35-) A N 97 ASN ( 97-) A ND2 112 ASN ( 112-) A N 155 LEU ( 155-) A N 216 HIS ( 216-) A N Only metal coordination for 142 HIS ( 142-) A NE2
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.
238 ASN ( 238-) A OD1
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+.
321 CA ( 323-) A -.- -.- Part of ionic cluster 321 CA ( 323-) A 0.60 0.83 Scores about as good as NA 322 CA ( 324-) A -.- -.- Part of ionic cluster 322 CA ( 324-) A 0.73 0.96 Scores about as good as NA 323 CA ( 325-) A 0.73 0.97 Scores about as good as NA 324 CA ( 326-) A 0.69 0.92 Scores about as good as NA
The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.
327 HOH ( 376 ) A O 0.90 K 4
37 ASP ( 37-) A H-bonding suggests Asn 119 GLU ( 119-) A H-bonding suggests Gln 143 GLU ( 143-) A H-bonding suggests Gln 294 ASP ( 294-) A H-bonding suggests Asn; but Alt-Rotamer
The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.
Structure Z-scores, positive is better than average:
1st generation packing quality : -1.017 2nd generation packing quality : -1.250 Ramachandran plot appearance : 0.127 chi-1/chi-2 rotamer normality : -0.152 Backbone conformation : -0.730
Bond lengths : 0.745 Bond angles : 1.459 Omega angle restraints : 0.788 Side chain planarity : 1.280 Improper dihedral distribution : 1.512 (loose) B-factor distribution : 0.983 Inside/Outside distribution : 1.017
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 : 1.65
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.8 2nd generation packing quality : -1.3 Ramachandran plot appearance : -0.1 chi-1/chi-2 rotamer normality : -0.4 Backbone conformation : -1.0
Bond lengths : 0.745 Bond angles : 1.459 Omega angle restraints : 0.788 Side chain planarity : 1.280 Improper dihedral distribution : 1.512 (loose) B-factor distribution : 0.983 Inside/Outside distribution : 1.017 ==============
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.