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.
334 JBI ( 465-) 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: 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) :298.000
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
245 ARG ( 301-) A
307 TYR ( 363-) A
214 ASP ( 270-) A 295 ASP ( 351-) A
90 GLU ( 137-) A 243 GLU ( 299-) A 267 GLU ( 323-) 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.
57 HIS ( 104-) A CG CD2 1.41 4.9 73 HIS ( 120-) A CG CD2 1.40 4.1 116 HIS ( 163-) A CG CD2 1.41 5.1 134 HIS ( 181-) A CG CD2 1.40 4.0 140 HIS ( 187-) A CG CD2 1.41 4.9 203 HIS ( 259-) A CG CD2 1.40 4.3 318 HIS ( 385-) A CG CD2 1.40 4.1
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
| 0.996142 0.000868 0.000088| | 0.000868 0.998902 -0.000074| | 0.000088 -0.000074 0.997810|Proposed new scale matrix
| 0.019241 -0.000017 -0.000002| | -0.000012 0.014154 0.000001| | 0.000000 0.000000 0.009420|With corresponding cell
A = 51.972 B = 70.654 C = 106.161 Alpha= 90.005 Beta= 89.996 Gamma= 89.900
The CRYST1 cell dimensions
A = 52.173 B = 70.733 C = 106.396 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 6.221
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.
140 HIS ( 187-) A CG ND1 CE1 110.06 4.5 203 HIS ( 259-) A CG ND1 CE1 109.63 4.0 316 PRO ( 372-) A -C N CD 106.29 -4.6
90 GLU ( 137-) A 214 ASP ( 270-) A 243 GLU ( 299-) A 245 ARG ( 301-) A 267 GLU ( 323-) A 295 ASP ( 351-) A
Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.
Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.
Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.
316 PRO ( 372-) A N 11.5 35.16 -2.48 The average deviation= 1.398
75 ASN ( 122-) A 4.20
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.
315 PRO ( 371-) A -3.1 228 PRO ( 284-) A -3.0 154 CYS ( 201-) A -2.5 41 ARG ( 88-) A -2.4 133 LEU ( 180-) A -2.3 313 GLU ( 369-) A -2.3 185 LYS ( 241-) A -2.2 48 LEU ( 95-) A -2.2 77 ILE ( 124-) A -2.2 6 VAL ( 51-) A -2.1 290 LYS ( 346-) A -2.1 232 LYS ( 288-) A -2.1 171 ARG ( 227-) A -2.1 25 SER ( 72-) A -2.1 141 ARG ( 188-) A -2.1 39 LEU ( 86-) A -2.1 263 PRO ( 319-) 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.
14 LEU ( 61-) A omega poor 19 ASN ( 66-) A Poor phi/psi 29 GLY ( 76-) A omega poor 32 CYS ( 79-) A omega poor 40 ASP ( 87-) A Poor phi/psi 83 PHE ( 130-) A omega poor 112 MET ( 159-) A omega poor 139 ILE ( 186-) A omega poor 141 ARG ( 188-) A Poor phi/psi 154 CYS ( 201-) A Poor phi/psi 155 THR ( 202-) A omega poor 203 HIS ( 259-) A Poor phi/psi 234 LEU ( 290-) A omega poor 240 ASN ( 296-) A omega poor 306 TRP ( 362-) A omega poor 313 GLU ( 369-) A omega poor 315 PRO ( 371-) A Poor phi/psi, PRO omega poor chi-1/chi-2 correlation Z-score : -3.475
chi-1/chi-2 correlation Z-score : -3.475
Warning: Unusual rotamers
The residues listed in the table below have a rotamer that is not seen very
often in the database of solved protein structures. This option determines
for every residue the position specific chi-1 rotamer distribution.
Thereafter it verified whether the actual residue in the molecule has the
most preferred rotamer or not. If the actual rotamer is the preferred one,
the score is 1.0. If the actual rotamer is unique, the score is 0.0. If
there are two preferred rotamers, with a population distribution of 3:2 and
your rotamer sits in the lesser populated rotamer, the score will be 0.667.
No value will be given if insufficient hits are found in the database.
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.
274 SER ( 330-) 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!
7 GLU ( 52-) A 0 8 VAL ( 53-) A 0 9 SER ( 56-) A 0 10 THR ( 57-) A 0 17 TYR ( 64-) A 0 18 GLN ( 65-) A 0 19 ASN ( 66-) A 0 22 PRO ( 69-) A 0 28 GLN ( 75-) A 0 30 ILE ( 77-) A 0 33 ALA ( 80-) A 0 42 ASN ( 89-) A 0 49 SER ( 96-) A 0 50 ARG ( 97-) A 0 52 PHE ( 99-) A 0 53 GLN ( 100-) A 0 70 CYS ( 117-) A 0 71 VAL ( 118-) A 0 72 ASN ( 119-) A 0 81 ASN ( 128-) A 0 85 PRO ( 132-) A 0 86 GLN ( 133-) A 0 87 LYS ( 134-) A 0 92 PHE ( 139-) A 0 93 GLN ( 140-) A 0And so on for a total of 119 lines.
Standard deviation of omega values : 7.960
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]
288 PRO ( 344-) A 0.15 LOW
176 PRO ( 232-) A 109.0 envelop C-beta (108 degrees) 208 PRO ( 264-) A -58.8 half-chair C-beta/C-alpha (-54 degrees) 228 PRO ( 284-) A 137.1 envelop C-alpha (144 degrees) 246 PRO ( 302-) A 124.7 half-chair C-beta/C-alpha (126 degrees) 254 PRO ( 310-) A -118.2 half-chair C-delta/C-gamma (-126 degrees) 301 PRO ( 357-) A -120.5 half-chair C-delta/C-gamma (-126 degrees) 315 PRO ( 371-) A 160.0 half-chair C-alpha/N (162 degrees) 316 PRO ( 372-) A 168.2 half-chair C-alpha/N (162 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.
314 ALA ( 370-) A CB <-> 315 PRO ( 371-) A CD 0.46 2.64 INTRA BF 242 VAL ( 298-) A O <-> 335 HOH ( 517 ) A O 0.46 1.94 INTRA 245 ARG ( 301-) A N <-> 335 HOH ( 517 ) A O 0.42 2.28 INTRA BF 1 ASN ( 46-) A ND2 <-> 335 HOH ( 583 ) A O 0.36 2.34 INTRA BF 60 ARG ( 107-) A NH2 <-> 160 ASP ( 207-) A OD2 0.35 2.35 INTRA 131 LYS ( 178-) A NZ <-> 295 ASP ( 351-) A OD1 0.31 2.39 INTRA BF 177 GLU ( 233-) A CB <-> 182 MET ( 238-) A CG 0.27 2.93 INTRA 50 ARG ( 97-) A NH1 <-> 93 GLN ( 140-) A NE2 0.27 2.58 INTRA BF 28 GLN ( 75-) A NE2 <-> 335 HOH ( 476 ) A O 0.25 2.45 INTRA 27 ALA ( 74-) A N <-> 335 HOH ( 620 ) A O 0.23 2.47 INTRA BF 1 ASN ( 46-) A O <-> 15 LYS ( 62-) A NZ 0.22 2.48 INTRA BL 63 ARG ( 110-) A NH1 <-> 335 HOH ( 550 ) A O 0.19 2.51 INTRA 202 ARG ( 258-) A NH1 <-> 222 GLN ( 278-) A OE1 0.18 2.52 INTRA 242 VAL ( 298-) A C <-> 335 HOH ( 517 ) A O 0.18 2.62 INTRA 241 TYR ( 297-) A O <-> 245 ARG ( 301-) A A NH1 0.17 2.53 INTRA BL 260 SER ( 316-) A N <-> 335 HOH ( 601 ) A O 0.17 2.53 INTRA BF 6 VAL ( 51-) A O <-> 11 PHE ( 58-) A N 0.17 2.53 INTRA 239 ARG ( 295-) A CG <-> 243 GLU ( 299-) A OE2 0.17 2.63 INTRA BF 141 ARG ( 188-) A NH1 <-> 335 HOH ( 538 ) A O 0.15 2.55 INTRA BF 73 HIS ( 120-) A CD2 <-> 75 ASN ( 122-) A N 0.15 2.95 INTRA BL 74 LYS ( 121-) A NZ <-> 311 GLU ( 367-) A OE2 0.15 2.55 INTRA 99 MET ( 146-) A SD <-> 334 JBI ( 465-) A N4 0.13 3.17 INTRA BL 68 MET ( 115-) A CE <-> 335 HOH ( 557 ) A O 0.13 2.67 INTRA 19 ASN ( 66-) A ND2 <-> 335 HOH ( 554 ) A O 0.12 2.58 INTRA 300 HIS ( 356-) A CD2 <-> 302 TYR ( 358-) A N 0.12 2.98 INTRA BLAnd so on for a total of 65 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.
210 ARG ( 266-) A -7.14 87 LYS ( 134-) A -6.04 167 MET ( 219-) A -5.89 166 PHE ( 218-) A -5.82 184 TYR ( 240-) A -5.76 53 GLN ( 100-) A -5.37 202 ARG ( 258-) A -5.35 313 GLU ( 369-) A -5.18 306 TRP ( 362-) A -5.09 72 ASN ( 119-) A -5.03
Chain identifier: A
Note: Second generation quality Z-score plot
The second generation quality Z-score smoothed over a 10 residue window
is plotted as function of the residue number. Low areas in the plot (below
-1.3) indicate unusual packing.
Chain identifier: A
Water, ion, and hydrogenbond related checks
Error: Water molecules without hydrogen bonds
The water molecules listed in the table below do not form any hydrogen bonds,
neither with the protein or DNA/RNA, nor with other water molecules. This is
a strong indication of a refinement problem. The last number on each line is
the identifier of the water molecule in the input file.
335 HOH ( 502 ) A O 335 HOH ( 505 ) A O 335 HOH ( 529 ) A O 335 HOH ( 548 ) A O 335 HOH ( 562 ) A O 335 HOH ( 570 ) A O Marked this atom as acceptor 334 JBI ( 465-) A F1
57 HIS ( 104-) A 73 HIS ( 120-) A 86 GLN ( 133-) A 93 GLN ( 140-) A 300 HIS ( 356-) A 304 ASN ( 360-) 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.
14 LEU ( 61-) A N 29 GLY ( 76-) A N 52 PHE ( 99-) A N 54 ASN ( 101-) A N 88 THR ( 135-) A N 90 GLU ( 137-) A N 102 MET ( 149-) A N 172 TYR ( 228-) A N 186 GLU ( 242-) A N 190 ILE ( 246-) A N 204 LYS ( 260-) A N 245 ARG ( 301-) A A NH1 247 LYS ( 303-) A N 295 ASP ( 351-) A N 305 VAL ( 361-) A N 319 THR ( 386-) A OG1
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.
215 GLN ( 271-) A OE1
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.
335 HOH ( 473 ) A O 1.04 K 4
94 ASP ( 141-) 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 : -0.686 2nd generation packing quality : -0.620 Ramachandran plot appearance : -1.961 chi-1/chi-2 rotamer normality : -3.475 (poor) Backbone conformation : -0.182
Bond lengths : 0.712 Bond angles : 0.857 Omega angle restraints : 1.447 (loose) Side chain planarity : 1.067 Improper dihedral distribution : 1.181 B-factor distribution : 1.213 Inside/Outside distribution : 1.028
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 : 2.10
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.3 2nd generation packing quality : -0.3 Ramachandran plot appearance : -1.0 chi-1/chi-2 rotamer normality : -2.1 Backbone conformation : -0.2
Bond lengths : 0.712 Bond angles : 0.857 Omega angle restraints : 1.447 (loose) Side chain planarity : 1.067 Improper dihedral distribution : 1.181 B-factor distribution : 1.213 Inside/Outside distribution : 1.028 ==============
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.