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.
258 AZM ( 264-) A -
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.
255 PHE ( 260-) 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'.
255 PHE ( 260-) A O
Obviously, the temperature at which the X-ray data was collected has some importance too:
Temperature cannot be read from the PDB file. This most likely means that
the temperature is listed as NULL (meaning unknown) in the PDB file.
Warning: More than 5 percent of buried atoms has low B-factor
For normal protein structures, no more than about 1 percent of the B factors
of buried atoms is below 5.0. The fact that this value is much higher in the
current structure could be a signal that the B-factors were restraints or
constraints to too-low values, misuse of B-factor field in the PDB file, or
a TLS/scaling problem. If the average B factor is low too, it is probably a
low temperature structure determination.
Percentage of buried atoms with B less than 5 : 27.72
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
Warning: Unusual bond lengths
The bond lengths listed in the table below were found to deviate more than 4
sigma from standard bond lengths (both standard values and sigmas for amino
acid residues have been taken from Engh and Huber [REF], for DNA they were
taken from Parkinson et al [REF]). In the table below for each unusual bond
the bond length and the number of standard deviations it differs from the
normal value is given.
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.
248 ASN ( 253-) A CA CB 1.62 4.4
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
| 1.002958 -0.000151 0.000524| | -0.000151 1.005795 0.000427| | 0.000524 0.000427 0.996526|Proposed new scale matrix
| 0.023347 0.000000 0.006109| | 0.000004 0.023843 -0.000010| | -0.000007 -0.000006 0.014205|With corresponding cell
A = 42.827 B = 41.941 C = 72.756 Alpha= 89.949 Beta= 104.634 Gamma= 90.015
The CRYST1 cell dimensions
A = 42.700 B = 41.700 C = 73.000 Alpha= 90.000 Beta= 104.600 Gamma= 90.000
(Under-)estimated Z-score: 6.804
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.
1 TRP ( 5-) A CG CD1 NE1 104.61 -4.3 1 TRP ( 5-) A CG CD2 CE2 101.84 -4.5 6 HIS ( 10-) A CA CB CG 109.73 -4.1 6 HIS ( 10-) A CB CG ND1 127.70 4.1 7 ASN ( 11-) A CA CB CG 117.83 5.2 7 ASN ( 11-) A ND2 CG OD1 118.52 -4.1 10 GLU ( 14-) A CA CB CG 126.10 6.0 10 GLU ( 14-) A CB CG CD 120.52 4.7 11 HIS ( 15-) A CA CB CG 118.21 4.4 11 HIS ( 15-) A CB CG ND1 129.12 5.0 11 HIS ( 15-) A CB CG CD2 122.61 -5.0 12 TRP ( 16-) A CG CD1 NE1 104.61 -4.3 12 TRP ( 16-) A CE3 CD2 CG 138.43 4.5 12 TRP ( 16-) A CG CD2 CE2 101.80 -4.5 13 HIS ( 17-) A CA CB CG 118.13 4.3 13 HIS ( 17-) A CB CG ND1 127.95 4.2 20 LYS ( 24-) A CA CB CG 123.38 4.6 20 LYS ( 24-) A CB CG CD 94.84 -7.2 22 GLU ( 26-) A -CA -C N 103.65 -6.1 24 GLN ( 28-) A NE2 CD OE1 117.96 -4.6 32 HIS ( 36-) A CA CB CG 108.11 -5.7 32 HIS ( 36-) A CB CG ND1 128.83 4.8 32 HIS ( 36-) A CB CG CD2 123.64 -4.2 39 SER ( 43-) A -CA -C N 125.39 4.6 41 LYS ( 45-) A CA CB CG 104.89 -4.6And so on for a total of 99 lines.
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.
21 GLY ( 25-) A C 7.8 10.35 0.06 The average deviation= 1.625
85 ARG ( 89-) A 4.59 203 THR ( 208-) A 4.43
Tau angle RMS Z-score : 1.569
Error: Side chain planarity problems
The side chains of the residues listed in the table below contain a planar
group that was found to deviate from planarity by more than 4.0 times the
expected value. For an amino acid residue that has a side chain with a
planar group, the RMS deviation of the atoms to a least squares plane was
determined. The number in the table is the number of standard deviations
this RMS value deviates from the expected value. Not knowing better yet, we
assume that planarity of the groups analyzed should be perfect.
248 ASN ( 253-) A 4.32
Ramachandran Z-score : -3.341
Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
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.
54 ARG ( 58-) A -2.8 234 GLU ( 239-) A -2.4 162 ILE ( 167-) A -2.4 56 LEU ( 60-) A -2.3 188 THR ( 193-) A -2.3 49 GLN ( 53-) A -2.3 26 PRO ( 30-) A -2.2 248 ASN ( 253-) A -2.1 46 SER ( 50-) A -2.1 88 GLN ( 92-) A -2.0 146 GLY ( 151-) A -2.0 75 LEU ( 79-) 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.
25 SER ( 29-) A PRO omega poor 106 ASP ( 110-) A Poor phi/psi 107 LYS ( 111-) A Poor phi/psi 173 ASN ( 178-) A Poor phi/psi 196 PRO ( 201-) A PRO omega poor 247 LYS ( 252-) A Poor phi/psi 248 ASN ( 253-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -3.285
chi-1/chi-2 correlation Z-score : -3.285
Warning: Unusual backbone conformations
For the residues listed in the table below, the backbone formed by itself and
two neighbouring residues on either side is in a conformation that is not
seen very often in the database of solved protein structures. The number
given in the table is the number of similar backbone conformations in the
database with the same amino acid in the centre.
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 TYR ( 7-) A 0 6 HIS ( 10-) A 0 11 HIS ( 15-) A 0 12 TRP ( 16-) A 0 15 ASP ( 19-) A 0 16 PHE ( 20-) A 0 20 LYS ( 24-) A 0 22 GLU ( 26-) A 0 23 ARG ( 27-) A 0 24 GLN ( 28-) A 0 25 SER ( 29-) A 0 46 SER ( 50-) A 0 48 ASP ( 52-) A 0 49 GLN ( 53-) A 0 50 ALA ( 54-) A 0 54 ARG ( 58-) A 0 58 ASN ( 62-) A 0 60 HIS ( 64-) A 0 61 ALA ( 65-) A 0 68 ASP ( 72-) A 0 69 SER ( 73-) A 0 72 LYS ( 76-) A 0 73 ALA ( 77-) A 0 76 LYS ( 80-) A 0 79 PRO ( 83-) A 0And so on for a total of 116 lines.
26 PRO ( 30-) A 0.46 HIGH 79 PRO ( 83-) A 0.46 HIGH 150 PRO ( 155-) A 0.49 HIGH 242 PRO ( 247-) A 0.47 HIGH 245 PRO ( 250-) A 0.48 HIGH
197 PRO ( 202-) A 34.7 envelop C-delta (36 degrees) 210 PRO ( 215-) A 47.7 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.
200 GLU ( 205-) A C <-> 201 CYS ( 206-) A SG 0.29 3.01 INTRA BL 194 THR ( 199-) A OG1 <-> 258 AZM ( 264-) A N1 0.28 2.42 INTRA 88 GLN ( 92-) A OE1 <-> 90 HIS ( 94-) A ND1 0.17 2.53 INTRA BL 4 GLY ( 8-) A O <-> 8 GLY ( 12-) A N 0.16 2.54 INTRA BL 248 ASN ( 253-) A ND2 <-> 259 HOH ( 312 ) A O 0.12 2.58 INTRA 11 HIS ( 15-) A ND1 <-> 14 LYS ( 18-) A NZ 0.10 2.90 INTRA BL 92 HIS ( 96-) A NE2 <-> 115 HIS ( 119-) A ND1 0.10 2.90 INTRA BL 246 LEU ( 251-) A O <-> 249 ARG ( 254-) A NE 0.07 2.63 INTRA BL 242 PRO ( 247-) A O <-> 244 GLN ( 249-) A NE2 0.07 2.63 INTRA BL 222 ARG ( 227-) A NH1 <-> 259 HOH ( 290 ) A O 0.06 2.64 INTRA 47 TYR ( 51-) A OH <-> 118 HIS ( 122-) A NE2 0.06 2.64 INTRA BL 26 PRO ( 30-) A O <-> 244 GLN ( 249-) A N 0.05 2.65 INTRA BL 173 ASN ( 178-) A N <-> 259 HOH ( 302 ) A O 0.04 2.66 INTRA 248 ASN ( 253-) A CG <-> 249 ARG ( 254-) A N 0.03 2.97 INTRA 103 HIS ( 107-) A NE2 <-> 189 TYR ( 194-) A OH 0.02 2.68 INTRA BL 13 HIS ( 17-) A ND1 <-> 259 HOH ( 267 ) A O 0.02 2.68 INTRA BL 49 GLN ( 53-) A N <-> 50 ALA ( 54-) A N 0.02 2.58 INTRA BL 39 SER ( 43-) A N <-> 40 LEU ( 44-) A N 0.02 2.58 INTRA B3 93 TRP ( 97-) A CH2 <-> 236 MET ( 241-) A SD 0.01 3.39 INTRA BL 2 GLY ( 6-) A N <-> 7 ASN ( 11-) A O 0.01 2.69 INTRA BL
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.
6 HIS ( 10-) A -6.09 96 LEU ( 100-) A -5.62
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
247 LYS ( 252-) A 249 - ARG 254- ( A) -4.45
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
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.
259 HOH ( 309 ) A O -20.97 -5.38 -2.95 259 HOH ( 324 ) A O -18.72 -20.91 18.35
6 HIS ( 10-) A 173 ASN ( 178-) 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.
22 GLU ( 26-) A N 27 VAL ( 31-) A N 47 TYR ( 51-) A N 70 GLN ( 74-) A N 96 LEU ( 100-) A N 97 ASP ( 101-) A N 101 SER ( 105-) A OG 120 ASN ( 124-) A ND2 125 ASP ( 130-) A N 164 THR ( 169-) A N 227 ASN ( 232-) A N 239 ASN ( 244-) A ND2 240 TRP ( 245-) A N 255 PHE ( 260-) A N Only metal coordination for 92 HIS ( 96-) A NE2 Only metal coordination for 115 HIS ( 119-) A ND1
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.
65 GLU ( 69-) A OE1
10 GLU ( 14-) A H-bonding suggests Gln 106 ASP ( 110-) 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 : -0.643 2nd generation packing quality : -0.192 Ramachandran plot appearance : -3.341 (poor) chi-1/chi-2 rotamer normality : -3.285 (poor) Backbone conformation : -1.283
Bond lengths : 0.858 Bond angles : 1.705 Omega angle restraints : 0.887 Side chain planarity : 0.885 Improper dihedral distribution : 1.362 Inside/Outside distribution : 0.957
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 : -0.2 2nd generation packing quality : -0.0 Ramachandran plot appearance : -2.2 chi-1/chi-2 rotamer normality : -1.9 Backbone conformation : -1.2
Bond lengths : 0.858 Bond angles : 1.705 Omega angle restraints : 0.887 Side chain planarity : 0.885 Improper dihedral distribution : 1.362 Inside/Outside distribution : 0.957 ==============
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.