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.
299 IZB (1300-) 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: C-terminal nitrogen atoms detected.
It is becoming habit to indicate that a residue is not the true C-terminus
by including only the backbone N of the next residue. This has been
observed in this PDB file.
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. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.
297 LEU ( 299-) A
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) : 93.000
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.
278 PHE ( 280-) A
9 ASP ( 11-) A 287 ASP ( 289-) A
24 GLU ( 26-) A 60 GLU ( 62-) A 130 GLU ( 132-) A 134 GLU ( 136-) A 165 GLU ( 167-) A 184 GLU ( 186-) A 295 GLU ( 297-) A
RMS Z-score for bond lengths: 0.369
RMS-deviation in bond distances: 0.009
Warning: Possible cell scaling problem
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA shows a
significant systematic deviation. It could be that the unit cell used in
refinement was not accurate enough. The deformation matrix given below gives
the deviations found: the three numbers on the diagonal represent the
relative corrections needed along the A, B and C cell axis. These values are
1.000 in a normal case, but have significant deviations here (significant at
the 99.99 percent confidence level)
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
| 0.997674 -0.000902 0.000120| | -0.000902 0.998849 -0.000214| | 0.000120 -0.000214 0.997392|Proposed new scale matrix
| 0.014983 0.000014 -0.000002| | 0.000013 0.014020 0.000003| | -0.000001 0.000002 0.011448|With corresponding cell
A = 66.743 B = 71.326 C = 87.353 Alpha= 90.025 Beta= 89.986 Gamma= 90.104
The CRYST1 cell dimensions
A = 66.900 B = 71.410 C = 87.580 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 4.911
Error: Nomenclature error(s)
Checking for a hand-check. WHAT IF has over the course of this session
already corrected the handedness of atoms in several residues. These were
administrative corrections. These residues are listed here.
9 ASP ( 11-) A 24 GLU ( 26-) A 60 GLU ( 62-) A 130 GLU ( 132-) A 134 GLU ( 136-) A 165 GLU ( 167-) A 184 GLU ( 186-) A 287 ASP ( 289-) A 295 GLU ( 297-) A
213 CYS ( 215-) A 4.40
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.
244 ILE ( 246-) A -2.2 176 THR ( 178-) A -2.1 213 CYS ( 215-) A -2.1 164 GLN ( 166-) 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 ASP ( 63-) A Poor phi/psi 76 GLN ( 78-) A Poor phi/psi 101 LYS ( 103-) A Poor phi/psi 137 ASN ( 139-) A Poor phi/psi 164 GLN ( 166-) A Poor phi/psi 180 PHE ( 182-) A Poor phi/psi 213 CYS ( 215-) A Poor phi/psi 259 ILE ( 261-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.421
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.
188 SER ( 190-) A 0.36 220 SER ( 222-) A 0.40
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!
11 SER ( 13-) A 0 13 SER ( 15-) A 0 29 PRO ( 31-) A 0 30 CYS ( 32-) A 0 44 TYR ( 46-) A 0 47 VAL ( 49-) A 0 58 HIS ( 60-) A 0 59 GLN ( 61-) A 0 61 ASP ( 63-) A 0 65 ILE ( 67-) A 0 66 ASN ( 68-) A 0 75 ALA ( 77-) A 0 76 GLN ( 78-) A 0 90 CYS ( 92-) A 0 102 SER ( 104-) A 0 108 LEU ( 110-) A 0 112 MET ( 114-) A 0 113 GLU ( 115-) A 0 114 LYS ( 116-) A 0 119 CYS ( 121-) A 0 121 GLN ( 123-) A 0 122 TYR ( 124-) A 0 123 TRP ( 125-) A 0 125 GLN ( 127-) A 0 126 LYS ( 128-) A 0And so on for a total of 100 lines.
Standard deviation of omega values : 1.765
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].
124 PRO ( 126-) A 47.9 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.
197 ARG ( 199-) A NH2 <-> 231 LEU ( 233-) A CD1 0.28 2.82 INTRA 245 LYS ( 247-) A O <-> 249 LEU ( 251-) A CD2 0.11 2.69 INTRA 244 ILE ( 246-) A CD1 <-> 269 TYR ( 271-) A CE1 0.10 3.10 INTRA 2 GLU ( 4-) A O <-> 6 GLU ( 8-) A CG 0.09 2.71 INTRA 46 ASP ( 48-) A OD1 <-> 298 IZB (1300-) A N45 0.08 2.62 INTRA BL 213 CYS ( 215-) A SG <-> 216 GLY ( 218-) A N 0.05 3.25 INTRA BL 244 ILE ( 246-) A CG1 <-> 269 TYR ( 271-) A CE1 0.05 3.15 INTRA 288 GLN ( 290-) A OE1 <-> 299 HOH (2268 ) A O 0.04 2.36 INTRA BF 184 GLU ( 186-) A CG <-> 299 HOH (2217 ) A O 0.04 2.76 INTRA 122 TYR ( 124-) A OH <-> 212 HIS ( 214-) A NE2 0.04 2.66 INTRA BL 95 GLU ( 97-) A CB <-> 136 THR ( 138-) A CG2 0.03 3.17 INTRA 123 TRP ( 125-) A C <-> 131 MET ( 133-) A SD 0.03 3.37 INTRA 298 IZB (1300-) A O1 <-> 299 HOH (2275 ) A O 0.02 2.38 INTRA 184 GLU ( 186-) A CD <-> 299 HOH (2217 ) A O 0.02 2.78 INTRA 115 GLY ( 117-) A N <-> 299 HOH (2147 ) A O 0.01 2.69 INTRA 184 GLU ( 186-) A OE2 <-> 299 HOH (2217 ) A O 0.01 2.39 INTRA 213 CYS ( 215-) A SG <-> 298 IZB (1300-) A S5 0.01 3.59 INTRA BL 179 ASP ( 181-) A OD1 <-> 298 IZB (1300-) A C1 0.01 2.79 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.
180 PHE ( 182-) A -6.29 237 LYS ( 239-) A -6.20 184 GLU ( 186-) A -5.48 205 GLU ( 207-) A -5.39 45 ARG ( 47-) A -5.18
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.
52 HIS ( 54-) A -2.70
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.
299 HOH (2064 ) A O 28.53 6.90 62.89
38 ASN ( 40-) A 164 GLN ( 166-) A 294 HIS ( 296-) 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.
28 PHE ( 30-) A N 71 LYS ( 73-) A N 109 ASN ( 111-) A ND2 121 GLN ( 123-) A NE2 123 TRP ( 125-) A N 151 TYR ( 153-) A N 163 THR ( 165-) A OG1 176 THR ( 178-) A N 185 SER ( 187-) A N 213 CYS ( 215-) A N 214 SER ( 216-) A N 215 ALA ( 217-) A N 218 GLY ( 220-) A N 219 ARG ( 221-) A N 219 ARG ( 221-) A NE 219 ARG ( 221-) A NH2 258 LEU ( 260-) A N 264 GLN ( 266-) A NE2 287 ASP ( 289-) A N
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+.
297 CA (1299-) A 0.53 0.75 Scores about as good as NA
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.
299 HOH (2257 ) A O 1.03 K 4
20 ASP ( 22-) A H-bonding suggests Asn 287 ASP ( 289-) 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 : 0.449 2nd generation packing quality : -1.377 Ramachandran plot appearance : 1.107 chi-1/chi-2 rotamer normality : -0.421 Backbone conformation : -0.036
Bond lengths : 0.369 (tight) Bond angles : 0.674 Omega angle restraints : 0.321 (tight) Side chain planarity : 0.289 (tight) Improper dihedral distribution : 0.644 B-factor distribution : 0.532 Inside/Outside distribution : 1.000
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 : 1.80
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.8 2nd generation packing quality : -1.2 Ramachandran plot appearance : 1.2 chi-1/chi-2 rotamer normality : -0.2 Backbone conformation : -0.3
Bond lengths : 0.369 (tight) Bond angles : 0.674 Omega angle restraints : 0.321 (tight) Side chain planarity : 0.289 (tight) Improper dihedral distribution : 0.644 B-factor distribution : 0.532 Inside/Outside distribution : 1.000 ==============
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.