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.
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.
215 SER ( 220-) 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.
215 SER ( 220-) 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.
60 HIS ( 64-) A 0.53 156 VAL ( 161-) A 0.96 218 VAL ( 223-) A 0.61
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 9
Crystal temperature (K) :298.000
Warning: More than 2 percent of buried atoms has low B-factor
For protein structures determined at room temperature, no more than
about 1 percent of the B factors of buried atoms is below 5.0.
Percentage of buried atoms with B less than 5 : 3.32
Error: The B-factors of bonded atoms show signs of over-refinement
For each of the bond types in a protein a distribution was derived for the
difference between the square roots of the B-factors of the two atoms. All
bonds in the current protein were scored against these distributions. The
number given below is the RMS Z-score over the structure. For a structure
with completely restrained B-factors within residues, this value will be
around 0.35, for extremely high resolution structures refined with free
isotropic B-factors this number is expected to be near 1.0. Any value over
1.5 is sign of severe over-refinement of B-factors.
RMS Z-score : 1.808 over 1838 bonds
Average difference in B over a bond : 3.89
RMS difference in B over a bond : 5.05
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
Nomenclature related problems
Warning: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
54 ARG ( 58-) A
62 PHE ( 66-) A 255 PHE ( 260-) A
10 GLU ( 14-) A 22 GLU ( 26-) A
10 GLU ( 14-) A 22 GLU ( 26-) A 54 ARG ( 58-) A
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.
79 PRO ( 83-) A -2.5 26 PRO ( 30-) A -2.3 158 VAL ( 163-) A -2.1 197 PRO ( 202-) A -2.0 146 GLY ( 151-) A -2.0 171 PHE ( 176-) 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.
25 SER ( 29-) A PRO omega poor 53 LEU ( 57-) A omega poor 71 ASP ( 75-) A Poor phi/psi 91 PHE ( 95-) A omega poor 107 LYS ( 111-) A Poor phi/psi 173 ASN ( 178-) A Poor phi/psi 192 SER ( 197-) A omega poor 196 PRO ( 201-) A PRO omega poor 198 LEU ( 203-) A Poor phi/psi 202 VAL ( 207-) A omega poor 247 LYS ( 252-) A Poor phi/psi 248 ASN ( 253-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.211
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 TYR ( 7-) A 0 6 HIS ( 10-) A 0 15 ASP ( 19-) A 0 16 PHE ( 20-) A 0 20 LYS ( 24-) A 0 23 ARG ( 27-) A 0 24 GLN ( 28-) A 0 25 SER ( 29-) A 0 46 SER ( 50-) A 0 48 ASP ( 52-) A 0 50 ALA ( 54-) A 0 58 ASN ( 62-) A 0 60 HIS ( 64-) A 0 62 PHE ( 66-) A 0 68 ASP ( 72-) A 0 69 SER ( 73-) A 0 71 ASP ( 75-) A 0 72 LYS ( 76-) A 0 73 ALA ( 77-) A 0 76 LYS ( 80-) A 0 79 PRO ( 83-) A 0 81 ASP ( 85-) A 0 88 GLN ( 92-) A 0 99 GLN ( 103-) A 0 102 GLU ( 106-) A 0And so on for a total of 119 lines.
210 PRO ( 215-) A 51.7 half-chair C-delta/C-gamma (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.
71 ASP ( 75-) A OD1 <-> 85 ARG ( 89-) A NE 0.21 2.49 INTRA 11 HIS ( 15-) A ND1 <-> 14 LYS ( 18-) A NZ 0.18 2.82 INTRA 113 GLU ( 117-) A OE2 <-> 115 HIS ( 119-) A NE2 0.05 2.65 INTRA BL 103 HIS ( 107-) A NE2 <-> 189 TYR ( 194-) A OH 0.04 2.66 INTRA BL 47 TYR ( 51-) A OH <-> 118 HIS ( 122-) A NE2 0.04 2.66 INTRA BL 233 GLU ( 238-) A N <-> 259 HOH ( 315 ) A O 0.04 2.66 INTRA 228 GLY ( 233-) A N <-> 231 GLU ( 236-) A OE1 0.03 2.67 INTRA 23 ARG ( 27-) A CG <-> 200 GLU ( 205-) A CD 0.02 3.18 INTRA 26 PRO ( 30-) A O <-> 244 GLN ( 249-) A N 0.01 2.69 INTRA BL
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.
6 HIS ( 10-) A -6.38 5 LYS ( 9-) A -5.32 131 GLN ( 136-) A -5.11 96 LEU ( 100-) A -5.06
Chain identifier: A
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
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.
259 HOH ( 347 ) A O 8.20 -5.91 -10.40 259 HOH ( 385 ) A O -18.12 20.18 17.76
32 HIS ( 36-) A 49 GLN ( 53-) 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.
27 VAL ( 31-) A N 70 GLN ( 74-) A N 96 LEU ( 100-) A N 172 THR ( 177-) A OG1 199 LEU ( 204-) A N 227 ASN ( 232-) A N 240 TRP ( 245-) A N 255 PHE ( 260-) A N Only metal coordination for 92 HIS ( 96-) A NE2 Only metal coordination for 115 HIS ( 119-) A ND1
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 : -0.241 2nd generation packing quality : 0.596 Ramachandran plot appearance : -0.969 chi-1/chi-2 rotamer normality : 0.211 Backbone conformation : -0.769
Bond lengths : 0.209 (tight) Bond angles : 0.500 (tight) Omega angle restraints : 0.951 Side chain planarity : 0.237 (tight) Improper dihedral distribution : 0.430 B-factor distribution : 1.808 (loose) Inside/Outside distribution : 0.937
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 : 0.2 2nd generation packing quality : 0.6 Ramachandran plot appearance : -0.1 chi-1/chi-2 rotamer normality : 1.0 Backbone conformation : -0.7
Bond lengths : 0.209 (tight) Bond angles : 0.500 (tight) Omega angle restraints : 0.951 Side chain planarity : 0.237 (tight) Improper dihedral distribution : 0.430 B-factor distribution : 1.808 (loose) Inside/Outside distribution : 0.937 ==============
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.