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.
390 MRD (2000-) A - 391 03W ( 400-) 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.
9 ARG ( 10-) A - 75 ARG ( 76-) A - 185 GLU ( 186-) A - 254 ASP ( 255-) A - 388 MG ( 501-) 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.
9 ARG ( 10-) A - 75 ARG ( 76-) A - 185 GLU ( 186-) A - 254 ASP ( 255-) A -
Plausible side chain atoms were detected with (near) zero occupancy
When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.
68 GLU ( 69-) A - CD 68 GLU ( 69-) A - OE1 68 GLU ( 69-) A - OE2
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: 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
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
9 ARG ( 10-) A 204 ARG ( 205-) A 265 ARG ( 266-) A 283 ARG ( 284-) A 339 ARG ( 340-) A 367 ARG ( 368-) A
336 GLU ( 337-) A 372 GLU ( 373-) A
RMS Z-score for bond lengths: 0.337
RMS-deviation in bond distances: 0.008
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.
219 HIS ( 220-) A CG ND1 CE1 110.00 4.4 367 ARG ( 368-) A CB CG CD 105.87 -4.1
9 ARG ( 10-) A 204 ARG ( 205-) A 265 ARG ( 266-) A 283 ARG ( 284-) A 336 GLU ( 337-) A 339 ARG ( 340-) A 367 ARG ( 368-) A 372 GLU ( 373-) 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.
186 PRO ( 187-) A -2.5 89 THR ( 90-) A -2.5 287 PHE ( 288-) A -2.3 185 GLU ( 186-) 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.
2 TYR ( 3-) A Poor phi/psi 9 ARG ( 10-) A Poor phi/psi 16 THR ( 17-) A Poor phi/psi 52 PHE ( 53-) A omega poor 93 PHE ( 94-) A Poor phi/psi 185 GLU ( 186-) A Poor phi/psi, PRO omega poor 192 LEU ( 193-) A Poor phi/psi 256 ASP ( 257-) A Poor phi/psi 333 ARG ( 334-) A Poor phi/psi 370 ALA ( 371-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.829
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.
301 SER ( 302-) A 0.36
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!
10 PHE ( 11-) A 0 19 TRP ( 20-) A 0 20 GLN ( 21-) A 0 22 ARG ( 23-) A 0 23 ASP ( 24-) A 0 25 PHE ( 26-) A 0 28 ALA ( 29-) A 0 30 ARG ( 31-) A 0 45 LEU ( 46-) A 0 48 HIS ( 49-) A 0 60 PHE ( 61-) A 0 83 MET ( 84-) A 0 86 PRO ( 87-) A 0 87 MET ( 88-) A 0 92 LEU ( 93-) A 0 93 PHE ( 94-) A 0 94 THR ( 95-) A 0 98 PHE ( 99-) A 0 100 ASP ( 101-) A 0 103 PHE ( 104-) A 0 105 ALA ( 106-) A 0 106 ASN ( 107-) A 0 108 ARG ( 109-) A 0 128 LEU ( 129-) A 0 130 ALA ( 131-) A 0And so on for a total of 116 lines.
181 PRO ( 182-) A 0.16 LOW
96 PRO ( 97-) A -117.2 half-chair C-delta/C-gamma (-126 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.
389 FMT ( 401-) A B O1 <-> 391 03W ( 400-) A O1 1.59 0.81 INTRA 389 FMT ( 401-) A B C <-> 391 03W ( 400-) A O1 1.29 1.51 INTRA 389 FMT ( 401-) A B C <-> 391 03W ( 400-) A C1 0.86 2.34 INTRA 389 FMT ( 401-) A B O1 <-> 391 03W ( 400-) A C1 0.65 2.15 INTRA 207 ARG ( 208-) A NH1 <-> 392 HOH (1341 ) A O 0.39 2.31 INTRA 204 ARG ( 205-) A A NH2 <-> 392 HOH ( 439 ) A O 0.33 2.37 INTRA 40 ARG ( 41-) A NH2 <-> 392 HOH (1360 ) A O 0.28 2.42 INTRA 288 LYS ( 289-) A NZ <-> 392 HOH (1326 ) A O 0.24 2.46 INTRA 165 GLY ( 166-) A C <-> 207 ARG ( 208-) A NH2 0.21 2.89 INTRA 165 GLY ( 166-) A O <-> 207 ARG ( 208-) A NH2 0.17 2.53 INTRA 73 ARG ( 74-) A CZ <-> 392 HOH (1256 ) A O 0.16 2.64 INTRA 60 PHE ( 61-) A CD2 <-> 392 HOH ( 512 ) A O 0.16 2.64 INTRA 73 ARG ( 74-) A NH1 <-> 392 HOH (1256 ) A O 0.14 2.56 INTRA 207 ARG ( 208-) A CZ <-> 392 HOH (1341 ) A O 0.12 2.68 INTRA 169 THR ( 170-) A OG1 <-> 207 ARG ( 208-) A NH2 0.12 2.58 INTRA 367 ARG ( 368-) A NE <-> 392 HOH (1366 ) A O 0.11 2.59 INTRA 254 ASP ( 255-) A A OD1 <-> 392 HOH (1329 ) A O 0.10 2.30 INTRA BL 22 ARG ( 23-) A NE <-> 392 HOH (1148 ) A O 0.10 2.60 INTRA 353 ARG ( 354-) A NE <-> 358 GLU ( 359-) A OE2 0.07 2.63 INTRA 95 HIS ( 96-) A ND1 <-> 97 VAL ( 98-) A N 0.07 2.93 INTRA BL 53 HIS ( 54-) A NE2 <-> 391 03W ( 400-) A O3 0.05 2.65 INTRA 176 ARG ( 177-) A NH1 <-> 392 HOH ( 522 ) A O 0.04 2.66 INTRA 204 ARG ( 205-) A A CZ <-> 392 HOH ( 439 ) A O 0.03 2.77 INTRA 41 ARG ( 42-) A NH2 <-> 392 HOH (1306 ) A O 0.03 2.67 INTRA 100 ASP ( 101-) A OD2 <-> 148 LYS ( 149-) A NZ 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.
25 PHE ( 26-) A -7.01 60 PHE ( 61-) A -6.74 22 ARG ( 23-) A -6.57 236 TRP ( 237-) A -6.25 253 TYR ( 254-) A -6.06 171 GLN ( 172-) A -5.54 139 ARG ( 140-) A -5.44 143 GLU ( 144-) A -5.42 99 LYS ( 100-) A -5.39 367 ARG ( 368-) A -5.05
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.
223 ALA ( 224-) A -2.60
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.
392 HOH ( 415 ) A O 16.09 110.87 69.71 392 HOH ( 424 ) A O 27.37 112.21 75.93 392 HOH ( 444 ) A O 20.87 52.96 72.75 392 HOH ( 475 ) A O 11.65 117.09 60.82 392 HOH ( 481 ) A O 48.93 95.79 61.53 392 HOH ( 516 ) A O 16.13 100.57 64.97 392 HOH (1325 ) A O 41.55 82.15 43.50 392 HOH (1327 ) A O 50.84 95.36 60.06 392 HOH (1328 ) A O 18.20 101.93 64.05 392 HOH (1333 ) A O 40.21 131.07 67.68
392 HOH ( 445 ) A O 392 HOH (1341 ) A O Metal-coordinating Histidine residue 219 fixed to 1
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.
15 TRP ( 16-) A N 21 GLY ( 22-) A N 52 PHE ( 53-) A N 87 MET ( 88-) A N 121 ASN ( 122-) A ND2 136 TRP ( 137-) A NE1 148 LYS ( 149-) A N 156 ARG ( 157-) A NH2 184 ASN ( 185-) A N 187 ARG ( 188-) A N 194 THR ( 195-) A N 194 THR ( 195-) A OG1 243 ILE ( 244-) A N 246 ASN ( 247-) A N 284 HIS ( 285-) A N 287 PHE ( 288-) A N 299 TRP ( 300-) A NE1 336 GLU ( 337-) A N Only metal coordination for 180 GLU ( 181-) A OE2 Only metal coordination for 216 GLU ( 217-) A OE1 Only metal coordination for 219 HIS ( 220-) A NE2 Only metal coordination for 244 ASP ( 245-) A OD2 Only metal coordination for 256 ASP ( 257-) A OD1 Only metal coordination for 286 ASP ( 287-) A OD2
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+.
387 MG ( 500-) A 0.73 1.30 Scores about as good as CA 388 MG ( 501-) A -.- -.- Low probability ion. Occ=0.26
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.
392 HOH ( 405 ) A O 0.88 K 4 392 HOH ( 450 ) A O 1.10 K 4 392 HOH ( 456 ) A O 1.11 K 4 Ion-B 392 HOH ( 481 ) A O 1.05 K 4 Ion-B 392 HOH (1037 ) A O 0.95 K 5 392 HOH (1081 ) A O 1.01 K 5 392 HOH (1099 ) A O 0.87 K 5 392 HOH (1118 ) A O 0.93 K 5 392 HOH (1128 ) A O 1.03 K 5 392 HOH (1136 ) A O 1.13 K 4 392 HOH (1185 ) A O 0.95 K 4 392 HOH (1186 ) A O 0.91 K 6 392 HOH (1191 ) A O 0.94 K 5 392 HOH (1243 ) A O 1.02 K 4 Ion-B
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 : -0.252 2nd generation packing quality : 1.272 Ramachandran plot appearance : 0.460 chi-1/chi-2 rotamer normality : 0.829 Backbone conformation : 0.456
Bond lengths : 0.337 (tight) Bond angles : 0.711 Omega angle restraints : 0.954 Side chain planarity : 0.715 Improper dihedral distribution : 0.672 B-factor distribution : 0.437 Inside/Outside distribution : 1.053
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 : 0.97
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.1 2nd generation packing quality : 0.1 Ramachandran plot appearance : -0.1 chi-1/chi-2 rotamer normality : 0.3 Backbone conformation : 0.1
Bond lengths : 0.337 (tight) Bond angles : 0.711 Omega angle restraints : 0.954 Side chain planarity : 0.715 Improper dihedral distribution : 0.672 B-factor distribution : 0.437 Inside/Outside distribution : 1.053 ==============
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.