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.
388 LXC (1389-) A - 418 LXC (1390-) 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.
203 GLU ( 204-) A - A OE2 bound to 396 IOD (1398-) A - A I
In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.
1 ASN ( 2-) 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 ASN ( 2-) A N 1 ASN ( 2-) A CA 1 ASN ( 2-) A O 1 ASN ( 2-) A CB 1 ASN ( 2-) A CG 1 ASN ( 2-) A OD1 1 ASN ( 2-) A ND2
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.
31 ARG ( 32-) A 0.10
Obviously, the temperature at which the X-ray data was collected has some importance too:
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: Phenylalanine convention problem
The phenylalanine residues listed in the table below have their chi-2 not
between -90.0 and 90.0.
60 PHE ( 61-) A
131 GLU ( 132-) A 327 GLU ( 328-) 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.
297 GLY ( 298-) A CA C 1.58 4.0
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
| 0.989448 -0.001532 0.001199| | -0.001532 1.001114 -0.001014| | 0.001199 -0.001014 0.988482|Proposed new scale matrix
| 0.010944 0.000017 -0.000013| | 0.000016 0.010137 0.000010| | -0.000012 0.000010 0.009869|With corresponding cell
A = 91.379 B = 98.652 C = 101.331 Alpha= 90.117 Beta= 89.861 Gamma= 90.177
The CRYST1 cell dimensions
A = 92.354 B = 98.540 C = 102.507 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 20.861
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.
70 HIS ( 71-) A CG ND1 CE1 109.73 4.1 229 HIS ( 230-) A CG ND1 CE1 109.70 4.1 265 ARG ( 266-) A CA CB CG 103.73 -5.2 291 ARG ( 292-) A CG CD NE 118.10 4.5
131 GLU ( 132-) A 327 GLU ( 328-) A
55 ASP ( 56-) A 8.54 327 GLU ( 328-) A 8.01 23 ASP ( 24-) A 7.32 20 GLN ( 21-) A 6.59 254 ASP ( 255-) A 6.32 185 GLU ( 186-) A 5.62 255 GLN ( 256-) A 5.48 375 ASP ( 376-) A 5.24 233 GLN ( 234-) A 4.94 174 ASP ( 175-) A 4.76 171 GLN ( 172-) A 4.68 216 GLU ( 217-) A 4.44 351 ASP ( 352-) A 4.38 221 GLN ( 222-) A 4.37 76 GLN ( 77-) A 4.20 68 GLU ( 69-) A 4.10
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.
89 THR ( 90-) A -2.5 356 PHE ( 357-) A -2.4 204 ARG ( 205-) A -2.2 287 PHE ( 288-) A -2.2 185 GLU ( 186-) A -2.2 186 PRO ( 187-) A -2.1
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.
52 PHE ( 53-) A omega poor 93 PHE ( 94-) A Poor phi/psi 185 GLU ( 186-) A Poor phi/psi, PRO omega poor 333 ARG ( 334-) A Poor phi/psi 356 PHE ( 357-) A Poor phi/psi 370 ALA ( 371-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.131
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 GLN ( 4-) A 0 8 ASP ( 9-) A 0 16 THR ( 17-) 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 60 PHE ( 61-) 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 0 100 ASP ( 101-) A 0 103 PHE ( 104-) A 0 104 THR ( 105-) A 0 105 ALA ( 106-) A 0 108 ARG ( 109-) A 0 128 LEU ( 129-) A 0 130 ALA ( 131-) A 0 131 GLU ( 132-) A 0And so on for a total of 117 lines.
Standard deviation of omega values : 3.477
Warning: Unusual PRO puckering amplitudes
The proline residues listed in the table below have a puckering amplitude
that is outside of normal ranges. Puckering parameters were calculated by
the method of Cremer and Pople [REF]. Normal PRO rings have a puckering
amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom
for a PRO residue, this could indicate disorder between the two different
normal ring forms (with C-gamma below and above the ring, respectively). If
Q is higher than 0.45 Angstrom something could have gone wrong during the
refinement. Be aware that this is a warning with a low confidence level. See:
Who checks the checkers? Four validation tools applied to eight atomic
resolution structures [REF]
86 PRO ( 87-) A 0.19 LOW 96 PRO ( 97-) A 0.16 LOW
181 PRO ( 182-) A 52.0 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.
419 HOH (2072 ) A O <-> 419 HOH (2192 ) A O 0.45 1.75 INTRA 419 HOH (2104 ) A O <-> 419 HOH (2161 ) A O 0.37 1.83 INTRA 288 LYS ( 289-) A NZ <-> 419 HOH (2265 ) A O 0.33 2.37 INTRA 239 LYS ( 240-) A NZ <-> 397 IOD (1399-) A A I 0.32 2.98 INTRA 53 HIS ( 54-) A NE2 <-> 418 LXC (1390-) A C5 0.32 2.78 INTRA 41 ARG ( 42-) A NH2 <-> 419 HOH (2058 ) A O 0.31 2.39 INTRA BF 40 GLN ( 41-) A NE2 <-> 409 IOD (1411-) A A I 0.26 3.04 INTRA BF 34 ASP ( 35-) A OD2 <-> 73 ARG ( 74-) A NH2 0.20 2.50 INTRA 254 ASP ( 255-) A OD1 <-> 419 HOH (2243 ) A O 0.19 2.21 INTRA 419 HOH (2036 ) A O <-> 419 HOH (2092 ) A O 0.18 2.02 INTRA 84 LYS ( 85-) A NZ <-> 419 HOH (2102 ) A O 0.16 2.54 INTRA BF 73 ARG ( 74-) A NE <-> 419 HOH (2090 ) A O 0.16 2.54 INTRA 31 ARG ( 32-) A CG <-> 295 PHE ( 296-) A CE2 0.12 3.08 INTRA 23 ASP ( 24-) A CB <-> 24 PRO ( 25-) A CD 0.11 2.99 INTRA 336 GLU ( 337-) A CG <-> 339 ARG ( 340-) A A NH2 0.11 2.99 INTRA 67 ARG ( 68-) A NH1 <-> 419 HOH (2084 ) A O 0.11 2.59 INTRA 216 GLU ( 217-) A OE2 <-> 419 HOH (2243 ) A O 0.08 2.32 INTRA 192 LEU ( 193-) A N <-> 193 PRO ( 194-) A CD 0.08 2.92 INTRA BL 330 ARG ( 331-) A NH1 <-> 419 HOH (2301 ) A O 0.07 2.63 INTRA 95 HIS ( 96-) A ND1 <-> 97 VAL ( 98-) A N 0.06 2.94 INTRA BL 288 LYS ( 289-) A NZ <-> 419 HOH (2264 ) A O 0.04 2.66 INTRA 244 ASP ( 245-) A OD1 <-> 284 HIS ( 285-) A CD2 0.03 2.77 INTRA BL 322 ASP ( 323-) A OD2 <-> 381 HIS ( 382-) A NE2 0.03 2.67 INTRA BL 353 ARG ( 354-) A NE <-> 358 GLU ( 359-) A OE2 0.03 2.67 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.
25 PHE ( 26-) A -7.06 60 PHE ( 61-) A -6.49 22 ARG ( 23-) A -6.46 236 TRP ( 237-) A -6.27 253 TYR ( 254-) A -6.20 139 ARG ( 140-) A -5.42 99 LYS ( 100-) A -5.41 367 ARG ( 368-) A -5.36 143 GLU ( 144-) A -5.34 339 ARG ( 340-) A -5.30
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.
1 ASN ( 2-) A -3.63 223 ALA ( 224-) A -2.57
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.
419 HOH (2023 ) A O 24.63 62.61 75.74 419 HOH (2059 ) A O 33.15 11.73 48.46
419 HOH (2088 ) A O 419 HOH (2283 ) A O 419 HOH (2343 ) A O Metal-coordinating Histidine residue 219 fixed to 1
184 ASN ( 185-) 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.
15 TRP ( 16-) A N 21 GLY ( 22-) A N 51 THR ( 52-) A OG1 52 PHE ( 53-) A N 87 MET ( 88-) A N 103 PHE ( 104-) A N 120 ARG ( 121-) A NH1 121 ASN ( 122-) A ND2 136 TRP ( 137-) A N 136 TRP ( 137-) A NE1 148 LYS ( 149-) A N 182 LYS ( 183-) A N 184 ASN ( 185-) A N 187 ARG ( 188-) A N 192 LEU ( 193-) A N 194 THR ( 195-) A N 204 ARG ( 205-) A NE 214 ASN ( 215-) A ND2 233 GLN ( 234-) A NE2 240 LEU ( 241-) A N 243 ILE ( 244-) A N 246 ASN ( 247-) A N 262 GLY ( 263-) A N 265 ARG ( 266-) A NH2 284 HIS ( 285-) A N 287 PHE ( 288-) A N 339 ARG ( 340-) A A NH2 Only metal coordination for 180 GLU ( 181-) A OE2 Only metal coordination for 219 HIS ( 220-) A NE2
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.
131 GLU ( 132-) A OE1 233 GLN ( 234-) A OE1
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+.
386 CA (1387-) A -.- -.- Low probability ion. Occ=0.73 387 CA (1388-) A -.- -.- Low probability ion. Occ=0.58
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.
419 HOH (2031 ) A O 0.86 K 4 *2 Ion-B 419 HOH (2069 ) A O 1.08 K 4 *2 419 HOH (2070 ) A O 0.86 K 4 *2 Ion-B 419 HOH (2095 ) A O 0.96 K 4 *2 419 HOH (2124 ) A O 0.88 K 6 *2 419 HOH (2136 ) A O 0.96 NA 4 (or CA *1) 419 HOH (2165 ) A O 0.86 K 4 *2 419 HOH (2208 ) A O 1.07 K 4 *2 419 HOH (2209 ) A O 1.11 K 4 *2 419 HOH (2256 ) A O 0.88 K 4 *2 419 HOH (2270 ) A O 0.91 K 5 *2 419 HOH (2300 ) A O 0.89 K 4 *2
80 ASP ( 81-) A H-bonding suggests Asn 131 GLU ( 132-) A H-bonding suggests Gln; but Alt-Rotamer 189 ASP ( 190-) A H-bonding suggests Asn; but Alt-Rotamer 351 ASP ( 352-) A H-bonding suggests Asn
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 : -0.175 2nd generation packing quality : 1.132 Ramachandran plot appearance : 0.591 chi-1/chi-2 rotamer normality : -0.131 Backbone conformation : 0.204
Bond lengths : 0.936 Bond angles : 0.971 Omega angle restraints : 0.632 (tight) Side chain planarity : 2.303 (loose) Improper dihedral distribution : 1.358 B-factor distribution : 1.193 Inside/Outside distribution : 1.052
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 : 1.55
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 : -0.6 Backbone conformation : -0.1
Bond lengths : 0.936 Bond angles : 0.971 Omega angle restraints : 0.632 (tight) Side chain planarity : 2.303 (loose) Improper dihedral distribution : 1.358 B-factor distribution : 1.193 Inside/Outside distribution : 1.052 ==============
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.