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.
The CRYST1 cell dimensions
A = 54.523 B = 79.215 C = 54.685 Alpha= 90.000 Beta= 106.240 Gamma= 90.000
Dimensions of a reduced cell
A = 54.523 B = 54.685 C = 79.215 Alpha= 90.000 Beta= 90.000 Gamma= 73.760
Dimensions of the conventional cell
A = 65.540 B = 87.355 C = 79.215 Alpha= 90.000 Beta= 90.000 Gamma= 90.177
Transformation to conventional cell
| -1.000000 0.000000 -1.000000| | -1.000000 0.000000 1.000000| | 0.000000 1.000000 0.000000|
Crystal class of the cell: MONOCLINIC
Crystal class of the conventional CELL: ORTHORHOMBIC
Space group name: P 1 21 1
Bravais type of conventional cell is: C
Warning: Conventional cell is pseudo-cell
The extra symmetry that would be implied by the transition to the previously
mentioned conventional cell has not been observed. It must be concluded that
the crystal lattice has pseudo-symmetry.
Warning: Ligands for which topology could not be determined
The ligands in the table below are too complicated for the automatic
topology determination. WHAT IF uses a local copy of Daan van Aalten's
Dundee PRODRG server to automatically generate topology information
for ligands. Some molecules are too complicated for this software. If that
happens, WHAT IF / WHAT-CHECK continue with a simplified topology that
lacks certain information. Ligands with a simplified topology can, for
example, not form hydrogen bonds, and that reduces the accuracy of all
hydrogen bond related checking facilities.
The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.
335 DTP ( 404-) A - Fragmented
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'.
39 LYS ( 48-) A CD 39 LYS ( 48-) A CE 39 LYS ( 48-) A NZ 72 LYS ( 81-) A CE 72 LYS ( 81-) A NZ 75 LYS ( 84-) A CD 75 LYS ( 84-) A CE 75 LYS ( 84-) A NZ 81 GLN ( 90-) A CD 81 GLN ( 90-) A OE1 81 GLN ( 90-) A NE2 114 GLU ( 123-) A CG 114 GLU ( 123-) A CD 114 GLU ( 123-) A OE1 114 GLU ( 123-) A OE2 194 GLU ( 203-) A CG 194 GLU ( 203-) A CD 194 GLU ( 203-) A OE1 194 GLU ( 203-) A OE2 196 LYS ( 209-) A CG 196 LYS ( 209-) A CD 196 LYS ( 209-) A CE 196 LYS ( 209-) A NZ 207 LYS ( 220-) A CD 207 LYS ( 220-) A CEAnd so on for a total of 90 lines.
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.
16 PHE ( 25-) A 0.60 75 LYS ( 84-) A 0.50 120 GLU ( 129-) A 0.50 272 TYR ( 296-) A 0.40
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 8
Crystal temperature (K) :104.000
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.
290 PHE ( 320-) A
121 ASP ( 130-) A 258 ASP ( 276-) A
62 GLU ( 71-) A
303 DGUA ( 3-) T N9 C8 N7 113.61 5.0 307 DGUA ( 7-) T N9 C8 N7 113.55 4.9 309 DGUA ( 9-) T N9 C8 N7 113.61 5.0 315 DGUA ( 15-) T N9 C8 N7 113.43 4.7 317 DGUA ( 1-) P N9 C8 N7 113.39 4.6 319 DTHY ( 3-) P C5 C4 O4 122.08 -4.0 319 DTHY ( 3-) P O4 C4 N3 122.43 4.2 320 DGUA ( 4-) P N9 C8 N7 113.46 4.7 322 DTHY ( 6-) P O4 C4 N3 122.32 4.0 323 DGUA ( 7-) P N9 C8 N7 113.57 4.9 325 DGUA ( 9-) P N9 C8 N7 113.56 4.9 327 DGUA ( 1-) D N9 C8 N7 113.66 5.1 328 DTHY ( 2-) D O4 C4 N3 122.35 4.1 330 DGUA ( 4-) D N9 C8 N7 113.31 4.4 331 DGUA ( 5-) D N9 C8 N7 113.47 4.7
62 GLU ( 71-) A 121 ASP ( 130-) A 258 ASP ( 276-) 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.
41 PRO ( 50-) A -2.5 187 THR ( 196-) A -2.3
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.
22 GLN ( 31-) A Poor phi/psi 169 CYS ( 178-) A Poor phi/psi 194 GLU ( 203-) A Poor phi/psi 209 HIS ( 222-) A Poor phi/psi 220 THR ( 233-) A Poor phi/psi 256 GLY ( 274-) A omega poor chi-1/chi-2 correlation Z-score : 0.369
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.
87 SER ( 96-) A 0.39
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 ASN ( 12-) A 0 24 ILE ( 33-) A 0 40 TYR ( 49-) A 0 41 PRO ( 50-) A 0 42 HIS ( 51-) A 0 54 PRO ( 63-) A 0 72 LYS ( 81-) A 0 83 ASP ( 92-) A 0 94 VAL ( 103-) A 0 95 SER ( 104-) A 0 108 GLU ( 117-) A 0 111 LYS ( 120-) A 0 119 ASN ( 128-) A 0 120 GLU ( 129-) A 0 125 HIS ( 134-) A 0 133 TYR ( 142-) A 0 160 VAL ( 169-) A 0 164 TYR ( 173-) A 0 169 CYS ( 178-) A 0 176 ALA ( 185-) A 0 177 GLU ( 186-) A 0 181 ASP ( 190-) A 0 188 HIS ( 197-) A 0 191 PHE ( 200-) A 0 192 THR ( 201-) A 0And so on for a total of 125 lines.
Standard deviation of omega values : 3.242
Warning: Unusual PRO puckering phases
The proline residues listed in the table below have a puckering phase that is
not expected to occur in protein structures. Puckering parameters were
calculated by the method of Cremer and Pople [REF]. Normal PRO rings
approximately show a so-called envelope conformation with the C-gamma atom
above the plane of the ring (phi=+72 degrees), or a half-chair conformation
with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees).
If phi deviates strongly from these values, this is indicative of a very
strange conformation for a PRO residue, and definitely requires a manual
check of the data. 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].
41 PRO ( 50-) A 11.1 half-chair N/C-delta (18 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.
115 ASP ( 124-) A O <-> 119 ASN ( 128-) A ND2 0.42 2.28 INTRA 78 LYS ( 87-) A NZ <-> 336 HOH ( 626 ) A O 0.35 2.35 INTRA BF 313 DCYT ( 13-) T N3 <-> 320 DGUA ( 4-) P N1 0.29 2.71 INTRA BL 301 DCYT ( 1-) T N3 <-> 331 DGUA ( 5-) D N1 0.27 2.73 INTRA 217 LYS ( 230-) A NZ <-> 336 HOH ( 532 ) A O 0.26 2.44 INTRA BL 117 ARG ( 126-) A NH2 <-> 336 HOH ( 518 ) A O 0.24 2.46 INTRA BF 330 DGUA ( 4-) D N3 <-> 339 HOH ( 108 ) D O 0.24 2.46 INTRA 315 DGUA ( 15-) T N1 <-> 318 DCYT ( 2-) P N3 0.23 2.77 INTRA 307 DGUA ( 7-) T N2 <-> 326 DCYT ( 10-) P O2 0.23 2.47 INTRA 302 DCYT ( 2-) T N3 <-> 330 DGUA ( 4-) D N1 0.22 2.78 INTRA 25 HIS ( 34-) A ND1 <-> 336 HOH ( 508 ) A O 0.22 2.48 INTRA 314 DADE ( 14-) T N1 <-> 319 DTHY ( 3-) P N3 0.20 2.80 INTRA BL 321 DADE ( 5-) P N7 <-> 338 HOH ( 103 ) P O 0.20 2.50 INTRA BL 315 DGUA ( 15-) T N2 <-> 318 DCYT ( 2-) P O2 0.19 2.51 INTRA 312 DTHY ( 12-) T N3 <-> 321 DADE ( 5-) P N1 0.18 2.82 INTRA BL 302 DCYT ( 2-) T O2 <-> 330 DGUA ( 4-) D N2 0.18 2.52 INTRA 311 DADE ( 11-) T N1 <-> 322 DTHY ( 6-) P N3 0.17 2.83 INTRA BL 304 DADE ( 4-) T N1 <-> 328 DTHY ( 2-) D N3 0.15 2.85 INTRA BL 303 DGUA ( 3-) T N1 <-> 329 DCYT ( 3-) D N3 0.15 2.85 INTRA BL 337 HOH ( 110 ) T O <-> 338 HOH ( 129 ) P O 0.14 2.26 INTRA 336 HOH ( 504 ) A O <-> 338 HOH ( 119 ) P O 0.14 2.26 INTRA 168 VAL ( 177-) A N <-> 336 HOH ( 548 ) A O 0.11 2.59 INTRA BL 310 DCYT ( 10-) T N3 <-> 323 DGUA ( 7-) P N1 0.11 2.89 INTRA BL 309 DGUA ( 9-) T N1 <-> 324 DCYT ( 8-) P N3 0.11 2.89 INTRA BL 200 GLN ( 213-) A OE1 <-> 336 HOH ( 549 ) A O 0.11 2.29 INTRA BFAnd so on for a total of 62 lines.
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.
272 TYR ( 296-) A -7.72 2 LEU ( 11-) A -5.64 173 ARG ( 182-) A -5.29 45 LYS ( 54-) A -5.15 140 ARG ( 149-) A -5.08
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.
271 LYS ( 295-) A -3.48 296 LYS ( 331-) A -2.58 72 LYS ( 81-) A -2.55
Chain identifier: A
Water, ion, and hydrogenbond related checks
Warning: Buried unsatisfied hydrogen bond donors
The buried hydrogen bond donors listed in the table below have a hydrogen
atom that is not involved in a hydrogen bond in the optimized hydrogen bond
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.
21 SER ( 30-) A OG 42 HIS ( 51-) A N 46 SER ( 55-) A N 180 GLY ( 189-) A N 209 HIS ( 222-) A N 240 ARG ( 258-) A NH2 261 ASN ( 279-) A ND2 269 ILE ( 293-) A N 285 SER ( 315-) A N 299 SER ( 334-) A N Only metal coordination for 181 ASP ( 190-) A OD1 Only metal coordination for 183 ASP ( 192-) A A OD2
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.
120 GLU ( 129-) A OE1 183 ASP ( 192-) A A OD1
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+.
334 MG ( 403-) A -.- -.- Low probability ion. Occ=0.70
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.
336 HOH ( 546 ) A O 0.93 K 6
8 ASP ( 17-) A H-bonding suggests Asn 65 ASP ( 74-) A H-bonding suggests Asn 107 ASP ( 116-) A H-bonding suggests Asn; but Alt-Rotamer 151 ASP ( 160-) A H-bonding suggests Asn 213 ASP ( 226-) A H-bonding suggests Asn 291 ASP ( 321-) 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 : -0.123 2nd generation packing quality : -0.911 Ramachandran plot appearance : 0.285 chi-1/chi-2 rotamer normality : 0.369 Backbone conformation : -0.375
Bond lengths : 0.313 (tight) Bond angles : 0.560 (tight) Omega angle restraints : 0.590 (tight) Side chain planarity : 0.140 (tight) Improper dihedral distribution : 0.336 B-factor distribution : 0.803 Inside/Outside distribution : 0.949
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 : 2.27
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.6 2nd generation packing quality : -0.2 Ramachandran plot appearance : 1.5 chi-1/chi-2 rotamer normality : 1.5 Backbone conformation : -0.3
Bond lengths : 0.313 (tight) Bond angles : 0.560 (tight) Omega angle restraints : 0.590 (tight) Side chain planarity : 0.140 (tight) Improper dihedral distribution : 0.336 B-factor distribution : 0.803 Inside/Outside distribution : 0.949 ==============
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.