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.
262 BE0 ( 503-) A - 263 BE7 ( 505-) A - 264 BE0 ( 504-) 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.
218 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.
218 SER ( 220-) A -
For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.
63 HIS ( 64-) A - NE2 bound to 261 ZN ( 502-) A - ZN
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: Missing atoms
The atoms listed in the table below are missing from the entry. If many atoms
are missing, the other checks can become less sensitive. Be aware that it
often happens that groups at the termini of DNA or RNA are really missing,
so that the absence of these atoms normally is neither an error nor the
result of poor electron density. Some of the atoms listed here might also be
listed by other checks, most noticeably by the options in the previous
section that list missing atoms in several categories. The plausible atoms
with zero occupancy are not listed here, as they already got assigned a
non-zero occupancy, and thus are no longer 'missing'.
8 LYS ( 9-) A CG 8 LYS ( 9-) A CD 8 LYS ( 9-) A CE 8 LYS ( 9-) A NZ 44 LYS ( 45-) A CG 44 LYS ( 45-) A CD 44 LYS ( 45-) A CE 44 LYS ( 45-) A NZ 75 LYS ( 76-) A CG 75 LYS ( 76-) A CD 75 LYS ( 76-) A CE 75 LYS ( 76-) A NZ
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.
63 HIS ( 64-) A 0.62
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :110.000
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: Phenylalanine convention problem
The phenylalanine residues listed in the table below have their chi-2 not
between -90.0 and 90.0.
129 PHE ( 131-) A
128 ASP ( 130-) A
25 GLU ( 26-) A 219 GLU ( 221-) A
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.
95 HIS ( 96-) A CG CD2 1.41 5.0 95 HIS ( 96-) A ND1 CE1 1.40 5.9
3 HIS ( 4-) A CG ND1 CE1 109.63 4.0 14 HIS ( 15-) A CG ND1 CE1 119.60 14.0 14 HIS ( 15-) A ND1 CE1 NE2 100.39 -8.7 14 HIS ( 15-) A CE1 NE2 CD2 112.42 4.2 14 HIS ( 15-) A CD2 CG ND1 101.21 -4.9 14 HIS ( 15-) A CB CG CD2 134.51 4.2 18 ASP ( 19-) A CA CB CG 107.13 -5.5 26 ARG ( 27-) A CA CB CG 128.22 7.1 26 ARG ( 27-) A CG CD NE 100.19 -6.1 35 HIS ( 36-) A CG ND1 CE1 109.84 4.2 73 GLN ( 74-) A CA C O 113.46 -4.3 73 GLN ( 74-) A NE2 CD OE1 128.53 5.9 84 ASP ( 85-) A CA CB CG 118.10 5.5 100 ASP ( 101-) A CA CB CG 117.06 4.5 102 GLN ( 103-) A NE2 CD OE1 116.45 -6.2 106 HIS ( 107-) A CA CB CG 109.65 -4.2 106 HIS ( 107-) A CG ND1 CE1 109.60 4.0 106 HIS ( 107-) A NE2 CD2 CG 111.26 4.8 121 HIS ( 122-) A CG ND1 CE1 109.60 4.0 121 HIS ( 122-) A NE2 CD2 CG 110.53 4.0 128 ASP ( 130-) A CA CB CG 117.51 4.9 128 ASP ( 130-) A OD2 CG OD1 109.28 -5.7 160 ASP ( 162-) A CA CB CG 106.17 -6.4 163 ASP ( 165-) A CA CB CG 119.11 6.5 177 PHE ( 179-) A CA CB CG 109.70 -4.1 188 ASP ( 190-) A -O -C N 114.22 -5.5 188 ASP ( 190-) A -C N CA 129.12 4.1 188 ASP ( 190-) A CA CB CG 116.70 4.1 223 LYS ( 225-) A CB CG CD 121.70 4.5 224 PHE ( 226-) A CA CB CG 119.87 6.1 228 ASN ( 230-) A CA CB CG 117.12 4.5 229 PHE ( 231-) A CA CB CG 119.83 6.0 251 ASN ( 253-) A CA CB CG 117.11 4.5 252 ARG ( 254-) A -O -C N 130.63 4.8
25 GLU ( 26-) A 128 ASP ( 130-) A 219 GLU ( 221-) 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.
174 PHE ( 176-) A -2.4 200 PRO ( 202-) A -2.3 161 VAL ( 163-) A -2.2 149 GLY ( 151-) 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.
28 SER ( 29-) A PRO omega poor 56 LEU ( 57-) A omega poor 91 GLN ( 92-) A omega poor 110 LYS ( 111-) A Poor phi/psi 176 ASN ( 178-) A Poor phi/psi 189 TYR ( 191-) A omega poor 195 SER ( 197-) A omega poor 199 PRO ( 201-) A PRO omega poor 201 LEU ( 203-) A Poor phi/psi 204 CYS ( 206-) A omega poor 205 VAL ( 207-) A omega poor 213 PRO ( 215-) A omega poor 241 ASP ( 243-) A Poor phi/psi 250 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.329
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!
4 TRP ( 5-) A 0 6 TYR ( 7-) A 0 9 HIS ( 10-) A 0 18 ASP ( 19-) A 0 19 PHE ( 20-) A 0 23 LYS ( 24-) A 0 26 ARG ( 27-) A 0 27 GLN ( 28-) A 0 28 SER ( 29-) A 0 37 ALA ( 38-) A 0 44 LYS ( 45-) A 0 49 SER ( 50-) A 0 53 ALA ( 54-) A 0 61 ASN ( 62-) A 0 63 HIS ( 64-) A 0 71 ASP ( 72-) A 0 72 SER ( 73-) A 0 74 ASP ( 75-) A 0 75 LYS ( 76-) A 0 76 ALA ( 77-) A 0 79 LYS ( 80-) A 0 82 PRO ( 83-) A 0 84 ASP ( 85-) A 0 91 GLN ( 92-) A 0 98 SER ( 99-) A 0And so on for a total of 116 lines.
235 PRO ( 237-) A 0.45 HIGH 245 PRO ( 247-) A 0.18 LOW
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.
260 HG ( 501-) A HG <-> 263 BE7 ( 505-) A C5 0.86 2.34 INTRA 26 ARG ( 27-) A NH2 <-> 265 HOH (1262 ) A O 0.21 2.49 INTRA 35 HIS ( 36-) A ND1 <-> 265 HOH (1087 ) A O 0.21 2.49 INTRA 253 GLN ( 255-) A NE2 <-> 265 HOH (1166 ) A O 0.20 2.50 INTRA 255 LYS ( 257-) A NZ <-> 265 HOH (1160 ) A O 0.14 2.56 INTRA 173 ASP ( 175-) A OD1 <-> 265 HOH (1159 ) A O 0.11 2.29 INTRA 106 HIS ( 107-) A NE2 <-> 192 TYR ( 194-) A OH 0.11 2.59 INTRA BL 260 HG ( 501-) A HG <-> 263 BE7 ( 505-) A C4 0.08 3.12 INTRA 88 ARG ( 89-) A NH1 <-> 265 HOH (1256 ) A O 0.07 2.63 INTRA 250 LYS ( 252-) A NZ <-> 265 HOH (1241 ) A O 0.06 2.64 INTRA BF 212 GLU ( 214-) A OE2 <-> 265 HOH (1078 ) A O 0.04 2.36 INTRA 157 LYS ( 159-) A NZ <-> 265 HOH (1194 ) A O 0.04 2.66 INTRA 63 HIS ( 64-) A ND1 <-> 265 HOH (1258 ) A O 0.04 2.66 INTRA BL 86 THR ( 87-) A OG1 <-> 265 HOH (1216 ) A O 0.02 2.38 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.
9 HIS ( 10-) A -6.61 73 GLN ( 74-) A -6.55 2 HIS ( 3-) A -6.38 99 LEU ( 100-) A -5.20 3 HIS ( 4-) A -5.04
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.
75 LYS ( 76-) A -3.66 125 LYS ( 127-) A -3.08 17 LYS ( 18-) A -2.61 44 LYS ( 45-) A -2.56
Chain identifier: A
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.
265 HOH (1243 ) A O Metal-coordinating Histidine residue 93 fixed to 1 Metal-coordinating Histidine residue 95 fixed to 1 Metal-coordinating Histidine residue 118 fixed to 1 Metal-coordinating Histidine residue 63 fixed to 1
2 HIS ( 3-) A 3 HIS ( 4-) A 52 GLN ( 53-) A 134 GLN ( 136-) A Atom is not a donor 63 HIS ( 64-) A NE2
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.
28 SER ( 29-) A OG 30 VAL ( 31-) A N 39 TYR ( 40-) A N 99 LEU ( 100-) A N 202 LEU ( 204-) A N 228 ASN ( 230-) A ND2 242 ASN ( 244-) A ND2 243 TRP ( 245-) A N Only metal coordination for 95 HIS ( 96-) A NE2 Only metal coordination for 118 HIS ( 119-) A ND1
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.
265 HOH (1094 ) A O 0.89 K 4 ION-B 265 HOH (1128 ) A O 1.10 K 4 Ion-B 265 HOH (1165 ) A O 0.93 K 4 265 HOH (1172 ) A O 1.06 K 5 Ion-B
163 ASP ( 165-) 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 : -0.059 2nd generation packing quality : 0.453 Ramachandran plot appearance : -0.991 chi-1/chi-2 rotamer normality : 0.329 Backbone conformation : -1.129
Bond lengths : 0.671 Bond angles : 1.234 Omega angle restraints : 1.186 Side chain planarity : 0.881 Improper dihedral distribution : 0.823 B-factor distribution : 0.941 Inside/Outside distribution : 0.962
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 : 1.17
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.2 2nd generation packing quality : -0.4 Ramachandran plot appearance : -1.3 chi-1/chi-2 rotamer normality : -0.2 Backbone conformation : -1.3
Bond lengths : 0.671 Bond angles : 1.234 Omega angle restraints : 1.186 Side chain planarity : 0.881 Improper dihedral distribution : 0.823 B-factor distribution : 0.941 Inside/Outside distribution : 0.962 ==============
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.