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.
395 MAL (5044-) 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.
7 LYS ( 7-) A - 184 VAL ( 184-) 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.
7 LYS ( 7-) A - 184 VAL ( 184-) 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: 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'.
1 MET ( 1-) A CG 1 MET ( 1-) A SD 1 MET ( 1-) A CE 27 LYS ( 27-) A CE 27 LYS ( 27-) A NZ 35 LYS ( 35-) A CE 35 LYS ( 35-) A NZ 43 LYS ( 43-) A NZ 46 GLU ( 46-) A CG 46 GLU ( 46-) A CD 46 GLU ( 46-) A OE1 46 GLU ( 46-) A OE2 50 GLN ( 50-) A CG 50 GLN ( 50-) A CD 50 GLN ( 50-) A OE1 50 GLN ( 50-) A NE2 84 LYS ( 84-) A CE 84 LYS ( 84-) A NZ 128 LYS ( 128-) A CE 128 LYS ( 128-) A NZ 138 LYS ( 138-) A CE 138 LYS ( 138-) A NZ 180 LYS ( 180-) A CD 180 LYS ( 180-) A CE 180 LYS ( 180-) A NZ 240 LYS ( 240-) A CE 240 LYS ( 240-) A NZ 296 LYS ( 296-) A CD 296 LYS ( 296-) A CE 296 LYS ( 296-) A NZ 310 GLU ( 310-) A CG 310 GLU ( 310-) A CD 310 GLU ( 310-) A OE1 310 GLU ( 310-) A OE2 314 LYS ( 314-) A CG 314 LYS ( 314-) A CD 314 LYS ( 314-) A CE 314 LYS ( 314-) A NZ 363 LYS ( 363-) A NZ 376 SER ( 383-) A OG 379 LYS ( 386-) A CE 379 LYS ( 386-) 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.
1 MET ( 1-) A 0.60 4 GLU ( 4-) A 0.80 15 ASP ( 15-) A 0.80 23 GLU ( 23-) A 0.80 30 LYS ( 30-) A 0.80 39 GLU ( 39-) A 0.80 50 GLN ( 50-) A 0.80 56 ASP ( 56-) A 0.80 79 GLU ( 79-) A 0.80 88 ASP ( 88-) A 0.80 99 ARG ( 99-) A 0.80 125 ASN ( 125-) A 0.80 138 LYS ( 138-) A 0.80 139 GLU ( 139-) A 0.80 198 ASP ( 198-) A 0.80 201 LYS ( 201-) A 0.80 206 ASN ( 206-) A 0.80 222 GLU ( 222-) A 0.80 234 SER ( 234-) A 0.90 275 GLU ( 275-) A 0.80 279 GLU ( 279-) A 0.80 292 GLU ( 292-) A 0.80 309 GLU ( 309-) A 0.50 310 GLU ( 310-) A 0.50 311 GLU ( 311-) A 0.80 326 GLN ( 326-) A 0.80 359 ASP ( 359-) A 0.80 360 GLU ( 360-) A 0.80 376 SER ( 383-) A 0.80
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
355 ARG ( 355-) A
107 TYR ( 107-) A 342 TYR ( 342-) A 373 TYR ( 380-) A
68 PHE ( 68-) A
59 ASP ( 59-) A 185 ASP ( 185-) A 288 ASP ( 288-) A
5 GLU ( 5-) A 79 GLU ( 79-) A 132 GLU ( 132-) A 139 GLU ( 139-) A 275 GLU ( 275-) A
RMS Z-score for bond lengths: 0.318
RMS-deviation in bond distances: 0.008
Warning: Low bond angle variability
Bond angles were found to deviate less than normal from the standard bond
angles (normal values for protein residues were taken from Engh and Huber
[REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below
is expected to be near 1.0 for a normally restrained data set. The fact that
it is lower than 0.667 in this structure might indicate that too-strong
restraints have been used in the refinement. This can only be a problem for
high resolution X-ray structures.
RMS Z-score for bond angles: 0.553
RMS-deviation in bond angles: 1.156
Error: Nomenclature error(s)
Checking for a hand-check. WHAT IF has over the course of this session
already corrected the handedness of atoms in several residues. These were
administrative corrections. These residues are listed here.
5 GLU ( 5-) A 59 ASP ( 59-) A 79 GLU ( 79-) A 132 GLU ( 132-) A 139 GLU ( 139-) A 185 ASP ( 185-) A 275 GLU ( 275-) A 288 ASP ( 288-) A 355 ARG ( 355-) 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.
246 THR ( 246-) A -2.6 203 LYS ( 203-) A -2.6 272 PRO ( 272-) A -2.5 259 PHE ( 259-) A -2.3 226 THR ( 226-) A -2.2 40 HIS ( 40-) 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.
122 LEU ( 122-) A omega poor 147 ALA ( 147-) A omega poor 169 ALA ( 169-) A Poor phi/psi 203 LYS ( 203-) A Poor phi/psi 286 LEU ( 286-) A Poor phi/psi 375 GLY ( 382-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 1.279
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 ILE ( 3-) A 0 5 GLU ( 5-) A 0 18 TYR ( 18-) A 0 31 ASP ( 31-) A 0 43 LYS ( 43-) A 0 54 THR ( 54-) A 0 56 ASP ( 56-) A 0 63 TRP ( 63-) A 0 65 HIS ( 65-) A 0 74 SER ( 74-) A 0 76 LEU ( 76-) A 0 81 THR ( 81-) A 0 82 PRO ( 82-) A 0 99 ARG ( 99-) A 0 100 TYR ( 100-) A 0 109 ILE ( 109-) A 0 123 LEU ( 123-) A 0 130 TRP ( 130-) A 0 143 LYS ( 143-) A 0 147 ALA ( 147-) A 0 148 LEU ( 148-) A 0 150 PHE ( 150-) A 0 151 ASN ( 151-) A 0 165 ASP ( 165-) A 0 170 PHE ( 170-) A 0And so on for a total of 135 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!
376 SER ( 383-) A 1.68 10
92 PRO ( 92-) A 99.2 envelop C-beta (108 degrees) 124 PRO ( 124-) A -116.1 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.
154 GLU ( 154-) A CD <-> 345 ARG ( 345-) A A NH1 0.30 2.80 INTRA 103 LYS ( 103-) A NZ <-> 396 HOH ( 767 ) A O 0.11 2.59 INTRA BF 159 TRP ( 159-) A N <-> 160 PRO ( 160-) A CD 0.09 2.91 INTRA BL 63 TRP ( 63-) A CH2 <-> 396 HOH ( 440 ) A O 0.08 2.72 INTRA 154 GLU ( 154-) A OE1 <-> 345 ARG ( 345-) A A NH1 0.07 2.63 INTRA 89 LYS ( 89-) A NZ <-> 396 HOH ( 735 ) A O 0.07 2.63 INTRA 1 MET ( 1-) A N <-> 396 HOH ( 780 ) A O 0.07 2.63 INTRA 65 HIS ( 65-) A ND1 <-> 262 VAL ( 262-) A N 0.06 2.94 INTRA BL 279 GLU ( 279-) A OE1 <-> 283 ASN ( 283-) A ND2 0.06 2.64 INTRA 81 THR ( 81-) A N <-> 82 PRO ( 82-) A CD 0.06 2.94 INTRA BL 96 ASP ( 96-) A OD1 <-> 99 ARG ( 99-) A A NH1 0.05 2.65 INTRA 338 SER ( 338-) A A OG <-> 396 HOH ( 592 ) A O 0.02 2.38 INTRA 298 LYS ( 298-) A NZ <-> 396 HOH ( 652 ) 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.
312 LEU ( 312-) A -7.31 355 ARG ( 355-) A -6.28 380 GLU ( 387-) A -5.52 326 GLN ( 326-) A -5.51 73 GLN ( 73-) A -5.50 125 ASN ( 125-) A -5.41 383 VAL ( 390-) A -5.35
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
382 VAL ( 389-) A 384 - HIS 391- ( A) -4.96
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.
314 LYS ( 314-) A -3.33 1 MET ( 1-) A -3.00 310 GLU ( 310-) A -2.68
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.
396 HOH ( 446 ) A O -24.75 -12.19 4.91
101 ASN ( 101-) A 219 ASN ( 219-) A 242 ASN ( 242-) A 366 GLN ( 366-) 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.
7 LYS ( 7-) A N 7 LYS ( 7-) A A NZ 16 LYS ( 16-) A NZ 63 TRP ( 63-) A NE1 67 ARG ( 67-) A NE 106 ALA ( 106-) A N 113 ALA ( 113-) A N 154 GLU ( 154-) A N 156 TYR ( 156-) A N 186 ASN ( 186-) A N 210 ASP ( 210-) A N 231 TRP ( 231-) A N 234 SER ( 234-) A N 305 LEU ( 305-) A N 334 ILE ( 334-) A N 357 THR ( 357-) A OG1 374 VAL ( 381-) A N
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.
396 HOH ( 412 ) A O 0.99 K 4 Ion-B 396 HOH ( 453 ) A O 0.98 K 4 Ion-B 396 HOH ( 529 ) A O 0.94 K 4 396 HOH ( 554 ) A O 1.06 K 4 396 HOH ( 581 ) A O 0.90 K 5 396 HOH ( 627 ) A O 1.09 K 4 396 HOH ( 671 ) A O 0.96 K 5 396 HOH ( 694 ) A O 0.98 K 4 Ion-B 396 HOH ( 722 ) A O 1.09 K 4 396 HOH ( 745 ) A O 0.96 K 5 ION-B 396 HOH ( 761 ) A O 0.99 K 6 ION-B 396 HOH ( 790 ) A O 1.08 K 4 ION-B 396 HOH ( 804 ) A O 0.97 K 4 396 HOH ( 829 ) A O 0.87 K 4 ION-B
66 ASP ( 66-) A H-bonding suggests Asn; Ligand-contact 309 GLU ( 309-) A H-bonding suggests Gln
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 : -0.351 2nd generation packing quality : -1.536 Ramachandran plot appearance : 0.712 chi-1/chi-2 rotamer normality : 1.279 Backbone conformation : -0.240
Bond lengths : 0.318 (tight) Bond angles : 0.553 (tight) Omega angle restraints : 0.933 Side chain planarity : 0.482 (tight) Improper dihedral distribution : 0.639 B-factor distribution : 0.576 Inside/Outside distribution : 0.951
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 : 1.30
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.0 2nd generation packing quality : -1.5 Ramachandran plot appearance : 0.2 chi-1/chi-2 rotamer normality : 0.7 Backbone conformation : -0.5
Bond lengths : 0.318 (tight) Bond angles : 0.553 (tight) Omega angle restraints : 0.933 Side chain planarity : 0.482 (tight) Improper dihedral distribution : 0.639 B-factor distribution : 0.576 Inside/Outside distribution : 0.951 ==============
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.