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 (1000-) 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 - 144 LEU ( 144-) 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 - 144 LEU ( 144-) 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.
157 TYR ( 157-) A 0.80 225 GLN ( 225-) A 0.50
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.
88 HIS ( 88-) A CG CD2 1.40 4.0 231 HIS ( 231-) A CG CD2 1.40 4.2
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
| 0.996186 0.000425 -0.001093| | 0.000425 0.997972 -0.000583| | -0.001093 -0.000583 0.997437|Proposed new scale matrix
| 0.010686 0.006156 0.000015| | -0.000005 0.012321 0.000007| | 0.000008 0.000004 0.007644|With corresponding cell
A = 93.556 B = 93.643 C = 130.829 Alpha= 89.995 Beta= 90.126 Gamma= 119.920
The CRYST1 cell dimensions
A = 93.910 B = 93.910 C = 131.170 Alpha= 90.000 Beta= 90.000 Gamma= 120.000
(Under-)estimated Z-score: 6.874
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.
5 SER ( 5-) A CA CB OG 101.53 -4.8 11 ARG ( 11-) A CD NE CZ 132.61 6.1 14 LEU ( 14-) A -O -C N 116.48 -4.1 18 LYS ( 18-) A CG CD CE 122.05 4.7 21 ASN ( 21-) A ND2 CG OD1 118.07 -4.5 26 THR ( 26-) A CA C O 112.70 -4.8 32 ASP ( 32-) A CA CB CG 116.60 4.0 41 THR ( 41-) A CA CB OG1 103.00 -4.4 47 ARG ( 47-) A CD NE CZ 138.03 9.1 53 SER ( 53-) A C CA CB 100.40 -5.1 57 ASP ( 57-) A CA CB CG 107.03 -5.6 59 ASP ( 59-) A CB CG OD2 129.67 4.9 61 GLN ( 61-) A -O -C N 105.36 -11.0 61 GLN ( 61-) A -CA -C N 132.26 8.0 61 GLN ( 61-) A -C N CA 140.48 10.4 62 PHE ( 62-) A -O -C N 114.08 -5.6 62 PHE ( 62-) A -C N CA 113.52 -4.5 67 ASP ( 67-) A C CA CB 102.32 -4.1 69 PRO ( 69-) A N CA CB 108.44 4.9 74 HIS ( 74-) A CA CB CG 109.17 -4.6 86 ASN ( 86-) A CA CB CG 108.56 -4.0 109 GLY ( 109-) A -O -C N 114.53 -5.3 114 PHE ( 114-) A CA CB CG 118.05 4.2 117 GLY ( 117-) A -O -C N 116.01 -4.4 118 SER ( 118-) A C CA CB 102.47 -4.0And so on for a total of 65 lines.
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.
25 SER ( 25-) A C -7.9 -12.73 0.37 61 GLN ( 61-) A C -11.6 -18.00 0.15 89 ASN ( 89-) A C 9.3 14.88 0.27 189 GLY ( 189-) A C 7.9 10.43 0.06 225 GLN ( 225-) A C 6.2 9.79 0.15 259 GLY ( 259-) A C 6.6 8.80 0.06 The average deviation= 1.907
216 HIS ( 216-) A 4.77
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.
157 TYR ( 157-) A -2.7 6 THR ( 6-) A -2.7 182 LYS ( 182-) A -2.5 46 TYR ( 46-) A -2.5 20 ILE ( 20-) A -2.4 107 SER ( 107-) A -2.4 92 SER ( 92-) A -2.4
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 45 LYS ( 45-) 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 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 130 PHE ( 130-) A omega poor 132 PRO ( 132-) A omega poor 152 THR ( 152-) A Poor phi/psi 159 ASN ( 159-) A Poor phi/psi 199 GLY ( 199-) A Poor phi/psi 227 ASN ( 227-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.937
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.
291 SER ( 291-) A 0.38
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 19 ASN ( 19-) 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 49 THR ( 49-) 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 0And so on for a total of 127 lines.
208 PRO ( 208-) A 0.20 LOW 277 PRO ( 277-) A 0.47 HIGH
51 PRO ( 51-) A -59.6 half-chair C-beta/C-alpha (-54 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 0.48 2.92 INTRA BL 231 HIS ( 231-) A NE2 <-> 327 HOH (1001 ) A O 0.31 2.39 INTRA BF 157 TYR ( 157-) A A OH <-> 166 GLU ( 166-) A OE2 0.30 2.10 INTRA 120 MET ( 120-) A A CE <-> 143 GLU ( 143-) A CB 0.27 2.93 INTRA BL 226 ASP ( 226-) A OD1 <-> 231 HIS ( 231-) A ND1 0.21 2.49 INTRA 9 VAL ( 9-) A O <-> 62 PHE ( 62-) A N 0.20 2.50 INTRA BL 206 SER ( 206-) A O <-> 239 LYS ( 239-) A NZ 0.14 2.56 INTRA 129 THR ( 129-) A O <-> 194 THR ( 194-) A N 0.13 2.57 INTRA 16 ASP ( 16-) A OD2 <-> 18 LYS ( 18-) A NZ 0.12 2.58 INTRA 280 ASN ( 280-) A N <-> 283 GLN ( 283-) A OE1 0.10 2.60 INTRA 262 LYS ( 262-) A NZ <-> 302 GLU ( 302-) A OE2 0.08 2.62 INTRA 149 THR ( 149-) A O <-> 154 GLY ( 154-) A N 0.06 2.64 INTRA BL 68 ALA ( 68-) A N <-> 69 PRO ( 69-) A CD 0.06 2.94 INTRA BL 41 THR ( 41-) A OG1 <-> 74 HIS ( 74-) A ND1 0.05 2.65 INTRA BL 308 GLN ( 308-) A O <-> 312 ALA ( 312-) A N 0.05 2.65 INTRA BL 126 ASP ( 126-) A OD1 <-> 128 GLN ( 128-) A N 0.05 2.65 INTRA 243 LEU ( 243-) A O <-> 247 GLY ( 247-) A N 0.05 2.65 INTRA 4 THR ( 4-) A O <-> 24 TYR ( 24-) A N 0.03 2.67 INTRA BL 25 SER ( 25-) A O <-> 27 TYR ( 27-) A N 0.03 2.67 INTRA 217 TYR ( 217-) A N <-> 313 VAL ( 313-) A O 0.03 2.67 INTRA BL 226 ASP ( 226-) A OD2 <-> 231 HIS ( 231-) A N 0.02 2.68 INTRA 131 ILE ( 131-) A CB <-> 132 PRO ( 132-) A CD 0.02 3.08 INTRA 215 ASP ( 215-) A N <-> 216 HIS ( 216-) A N 0.01 2.59 INTRA BL 269 ARG ( 269-) A NE <-> 294 ASP ( 294-) A OD2 0.01 2.69 INTRA 46 TYR ( 46-) A N <-> 105 HIS ( 105-) A O 0.01 2.69 INTRA BL 222 THR ( 222-) A N <-> 327 HOH (1139 ) A O 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.
108 GLN ( 108-) A -5.89 221 TYR ( 221-) A -5.87 88 HIS ( 88-) A -5.71 251 TYR ( 251-) A -5.60 246 GLN ( 246-) A -5.54 157 TYR ( 157-) A -5.52 182 LYS ( 182-) A -5.50 273 GLN ( 273-) A -5.27 225 GLN ( 225-) A -5.21
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 -2.76 185 ASP ( 185-) A -2.53
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 -1.52
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 (1125 ) A O 60.42 49.34 -2.12
327 HOH (1106 ) 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 290 GLN ( 290-) A 301 GLN ( 301-) A 308 GLN ( 308-) 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 138 ASP ( 138-) A N 155 LEU ( 155-) A N 190 GLU ( 190-) A N 209 ALA ( 209-) A N 216 HIS ( 216-) A N Only metal coordination for 142 HIS ( 142-) A NE2 Only metal coordination for 146 HIS ( 146-) A NE2 Only metal coordination for 166 GLU ( 166-) A OE1 Only metal coordination for 190 GLU ( 190-) A OE1
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 ( 402-) A -.- -.- Part of ionic cluster 321 CA ( 402-) A 0.49 1.44 Is perhaps K 322 CA ( 403-) A -.- -.- Part of ionic cluster 322 CA ( 403-) A 0.63 0.86 Scores about as good as NA 323 CA ( 404-) A 0.55 0.77 Scores about as good as NA 324 CA ( 405-) A 0.47 1.32 Is perhaps K
37 ASP ( 37-) A H-bonding suggests Asn 119 GLU ( 119-) 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 : -0.937 2nd generation packing quality : -1.285 Ramachandran plot appearance : -0.173 chi-1/chi-2 rotamer normality : -0.937 Backbone conformation : -0.461
Bond lengths : 0.717 Bond angles : 1.475 Omega angle restraints : 0.888 Side chain planarity : 1.185 Improper dihedral distribution : 1.716 (loose) B-factor distribution : 1.167 Inside/Outside distribution : 1.019
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 : 2.10
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.5 2nd generation packing quality : -0.8 Ramachandran plot appearance : 0.6 chi-1/chi-2 rotamer normality : 0.0 Backbone conformation : -0.4
Bond lengths : 0.717 Bond angles : 1.475 Omega angle restraints : 0.888 Side chain planarity : 1.185 Improper dihedral distribution : 1.716 (loose) B-factor distribution : 1.167 Inside/Outside distribution : 1.019 ==============
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.