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.
344 ADP ( 401-) A - 345 HC7 ( 396-) A -
The left-hand residue has been removed, and the right hand residue has been kept for validation. Be aware that WHAT IF calls everything a residue. Two residues are defined as overlapping if the two smallest ellipsoids encompassing the two residues interpenetrate by 33% of the longest axis. Many artefacts can actually cause this problem. The most often observed reason is alternative residue conformations expressed by two residues that accidentally both got 1.0 occupancy for all atoms.
345 SO4 ( 400-) A - 344 ADP ( 401-) A - 1.3
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'.
2 ARG ( 43-) A CD 2 ARG ( 43-) A NE 2 ARG ( 43-) A CZ 2 ARG ( 43-) A NH1 2 ARG ( 43-) A NH2 7 ARG ( 48-) A NE 7 ARG ( 48-) A CZ 7 ARG ( 48-) A NH1 7 ARG ( 48-) A NH2 10 GLN ( 51-) A OE1 10 GLN ( 51-) A NE2 21 ARG ( 62-) A CZ 21 ARG ( 62-) A NH1 21 ARG ( 62-) A NH2 63 ILE ( 109-) A CG1 63 ILE ( 109-) A CG2 63 ILE ( 109-) A CD1 64 LEU ( 110-) A CG 64 LEU ( 110-) A CD1 64 LEU ( 110-) A CD2 108 LYS ( 154-) A NZ 114 GLU ( 160-) A CG 114 GLU ( 160-) A CD 114 GLU ( 160-) A OE1 114 GLU ( 160-) A OE2And so on for a total of 59 lines.
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
38 ARG ( 84-) A 180 ARG ( 226-) A
15 TYR ( 56-) A 31 TYR ( 72-) A 221 TYR ( 270-) A
37 PHE ( 83-) A 77 PHE ( 123-) A 93 PHE ( 139-) A 128 PHE ( 174-) A 226 PHE ( 275-) A 263 PHE ( 312-) A 302 PHE ( 351-) A 303 PHE ( 352-) A 331 PHE ( 380-) A
209 ASP ( 258-) A
26 GLU ( 67-) A 73 GLU ( 119-) A 280 GLU ( 329-) A
26 GLU ( 67-) A 38 ARG ( 84-) A 73 GLU ( 119-) A 180 ARG ( 226-) A 209 ASP ( 258-) A 280 GLU ( 329-) 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.
245 PRO ( 294-) A -2.5 134 PRO ( 180-) A -2.3 216 PHE ( 265-) 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.
61 GLY ( 107-) A Poor phi/psi, omega poor 84 SER ( 130-) A Poor phi/psi 103 PRO ( 149-) A omega poor 104 SER ( 150-) A Poor phi/psi, omega poor 134 PRO ( 180-) A Poor phi/psi 139 PRO ( 185-) A Poor phi/psi 195 ASN ( 241-) A Poor phi/psi 215 ASP ( 264-) A Poor phi/psi 244 TRP ( 293-) A PRO omega poor 246 PHE ( 295-) A Poor phi/psi, omega poor 316 THR ( 365-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.180
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.
69 SER ( 115-) A 0.37 327 SER ( 376-) A 0.37 294 SER ( 343-) 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!
16 LEU ( 57-) A 0 20 TRP ( 61-) A 0 32 PRO ( 73-) A 0 33 VAL ( 74-) A 0 34 ASN ( 80-) A 0 35 LEU ( 81-) A 0 44 HIS ( 90-) A 0 50 GLU ( 96-) A 0 53 ARG ( 99-) A 0 62 ALA ( 108-) A 0 63 ILE ( 109-) A 0 83 ARG ( 129-) A 0 84 SER ( 130-) A 0 85 LEU ( 131-) A 0 90 TYR ( 136-) A 0 95 GLU ( 141-) A 0 100 GLN ( 146-) A 0 103 PRO ( 149-) A 0 104 SER ( 150-) A 0 133 MET ( 179-) A 0 134 PRO ( 180-) A 0 137 LYS ( 183-) A 0 139 PRO ( 185-) A 0 140 HIS ( 186-) A 0 159 THR ( 205-) A 0And so on for a total of 102 lines.
25 PRO ( 66-) A 0.20 LOW 32 PRO ( 73-) A 0.11 LOW
115 PRO ( 161-) A 106.4 envelop C-beta (108 degrees) 251 PRO ( 300-) A -114.4 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.
250 ARG ( 299-) A NE <-> 346 HOH ( 643 ) A O 0.23 2.47 INTRA 265 ARG ( 314-) A NH2 <-> 343 SO4 ( 400-) A O4 0.18 2.52 INTRA 147 GLU ( 193-) A OE2 <-> 180 ARG ( 226-) A NH2 0.17 2.53 INTRA 113 ARG ( 159-) A A NH2 <-> 346 HOH ( 482 ) A O 0.16 2.54 INTRA 102 ILE ( 148-) A N <-> 344 ADP ( 401-) A N1 0.14 2.86 INTRA 27 GLU ( 68-) A OE2 <-> 44 HIS ( 90-) A NE2 0.14 2.56 INTRA 129 HIS ( 175-) A ND1 <-> 267 TYR ( 316-) A OH 0.12 2.58 INTRA BL 244 TRP ( 293-) A NE1 <-> 346 HOH ( 527 ) A O 0.09 2.61 INTRA 331 PHE ( 380-) A A CE1 <-> 335 GLN ( 384-) A CD 0.08 3.12 INTRA 338 GLN ( 387-) A NE2 <-> 346 HOH ( 598 ) A O 0.07 2.63 INTRA 58 ARG ( 104-) A NH2 <-> 344 ADP ( 401-) A O1A 0.06 2.64 INTRA 344 ADP ( 401-) A O3' <-> 346 HOH ( 671 ) A O 0.04 2.36 INTRA 265 ARG ( 314-) A NH2 <-> 346 HOH ( 668 ) A O 0.04 2.66 INTRA 301 HIS ( 350-) A ND1 <-> 328 ARG ( 377-) A NE 0.04 2.96 INTRA BL 58 ARG ( 104-) A NH1 <-> 346 HOH ( 606 ) A O 0.04 2.66 INTRA 258 GLU ( 307-) A OE1 <-> 346 HOH ( 668 ) A O 0.03 2.37 INTRA 97 ARG ( 143-) A NE <-> 99 GLU ( 145-) A OE2 0.03 2.67 INTRA BL 301 HIS ( 350-) A NE2 <-> 335 GLN ( 384-) A OE1 0.03 2.67 INTRA BL 331 PHE ( 380-) A A CE1 <-> 335 GLN ( 384-) A CG 0.02 3.18 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.
132 GLU ( 178-) A -6.01 207 GLU ( 253-) A -5.76 44 HIS ( 90-) A -5.74 50 GLU ( 96-) A -5.60 22 ARG ( 63-) A -5.58 113 ARG ( 159-) A -5.54 60 TYR ( 106-) A -5.52 101 TYR ( 147-) A -5.36 280 GLU ( 329-) A -5.17 338 GLN ( 387-) A -5.05
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
60 TYR ( 106-) A 62 - ALA 108- ( A) -4.81
Chain identifier: A
Warning: Abnormal packing Z-score for sequential residues
A stretch of at least four sequential residues with a 2nd generation packing
Z-score below -1.75 was found. This could indicate that these residues are
part of a strange loop or that the residues in this range are incomplete,
but it might also be an indication of misthreading.
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
111 GLU ( 157-) A - 114 GLU ( 160-) A -1.53
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.
346 HOH ( 591 ) A O 40.75 42.88 21.04 346 HOH ( 619 ) A O 24.79 66.70 -7.08 346 HOH ( 622 ) A O 53.67 60.93 -0.81 346 HOH ( 656 ) A O 19.77 45.08 32.87 346 HOH ( 667 ) A O -2.59 75.12 10.06 346 HOH ( 673 ) A O 14.65 76.80 4.46
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.
36 LEU ( 82-) A N 38 ARG ( 84-) A A NE 58 ARG ( 104-) A NH2 97 ARG ( 143-) A NH1 102 ILE ( 148-) A N 104 SER ( 150-) A N 117 LEU ( 163-) A N 220 SER ( 269-) A OG 222 ASN ( 271-) A ND2 241 HIS ( 290-) A N 247 TYR ( 296-) A N 319 PHE ( 368-) A N Only metal coordination for 201 ASN ( 247-) A OD1
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.
234 GLU ( 283-) 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+.
340 MG ( 397-) A -.- -.- Low probability ion. Occ=0.50
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.
346 HOH ( 430 ) A O 0.91 K 4
196 ASP ( 242-) A H-bonding suggests Asn; Ligand-contact 199 GLU ( 245-) 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 : -0.863 2nd generation packing quality : -1.105 Ramachandran plot appearance : 0.979 chi-1/chi-2 rotamer normality : 0.180 Backbone conformation : 0.106
Bond lengths : 0.755 Bond angles : 0.723 Omega angle restraints : 0.980 Side chain planarity : 0.885 Improper dihedral distribution : 0.798 B-factor distribution : 0.518 Inside/Outside distribution : 1.023
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 : 1.42
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.5 2nd generation packing quality : -1.3 Ramachandran plot appearance : 0.4 chi-1/chi-2 rotamer normality : -0.4 Backbone conformation : -0.4
Bond lengths : 0.755 Bond angles : 0.723 Omega angle restraints : 0.980 Side chain planarity : 0.885 Improper dihedral distribution : 0.798 B-factor distribution : 0.518 Inside/Outside distribution : 1.023 ==============
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.