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.
343 ACE ( 0-) B -
For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.
340 ALA ( 1-) B - N bound to 343 ACE ( 0-) B - C
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'.
1 ARG ( 42-) A CG 1 ARG ( 42-) A CD 1 ARG ( 42-) A NE 1 ARG ( 42-) A CZ 1 ARG ( 42-) A NH1 1 ARG ( 42-) A NH2 2 ASP ( 43-) A CG 2 ASP ( 43-) A OD1 2 ASP ( 43-) A OD2 332 TYR ( 373-) A CG 332 TYR ( 373-) A CD1 332 TYR ( 373-) A CD2 332 TYR ( 373-) A CE1 332 TYR ( 373-) A CE2 332 TYR ( 373-) A CZ 332 TYR ( 373-) A OH 336 LYS ( 377-) A CG 336 LYS ( 377-) A CD 336 LYS ( 377-) A CE 336 LYS ( 377-) A NZ 338 LYS ( 379-) A CG 338 LYS ( 379-) A CD 338 LYS ( 379-) A CE 338 LYS ( 379-) A NZ
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.
339 GLY ( 380-) A
Obviously, the temperature at which the X-ray data was collected has some importance too:
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: Tyrosine convention problem
The tyrosine residues listed in the table below have their chi-2 not between
-90.0 and 90.0
121 TYR ( 162-) A 129 TYR ( 170-) A 151 TYR ( 192-) A 164 TYR ( 205-) A 167 TYR ( 208-) A 227 TYR ( 268-) A 287 TYR ( 328-) A
33 PHE ( 74-) A 44 PHE ( 85-) A 48 PHE ( 89-) A 80 PHE ( 121-) A 124 PHE ( 165-) A 142 PHE ( 183-) A 153 PHE ( 194-) A 156 PHE ( 197-) A 183 PHE ( 224-) A 186 PHE ( 227-) A 244 PHE ( 285-) A
238 ASP ( 279-) A 241 ASP ( 282-) A 260 ASP ( 301-) A
42 GLU ( 83-) A 168 GLU ( 209-) A 205 GLU ( 246-) A
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
| 0.995141 -0.000612 -0.000448| | -0.000612 0.996497 -0.000255| | -0.000448 -0.000255 0.997085|Proposed new scale matrix
| 0.008759 0.000007 0.004549| | 0.000012 0.018881 0.000005| | 0.000008 0.000005 0.017616|With corresponding cell
A = 114.200 B = 52.963 C = 63.981 Alpha= 89.994 Beta= 117.473 Gamma= 90.070
The CRYST1 cell dimensions
A = 114.760 B = 53.150 C = 64.170 Alpha= 90.000 Beta= 117.480 Gamma= 90.000
(Under-)estimated Z-score: 9.512
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.
103 LEU ( 144-) A N CA C 99.41 -4.2 175 LEU ( 216-) A CA CB CG 133.77 5.0 191 SER ( 232-) A N CA C 99.80 -4.1
42 GLU ( 83-) A 168 GLU ( 209-) A 205 GLU ( 246-) A 238 ASP ( 279-) A 241 ASP ( 282-) A 260 ASP ( 301-) A
103 LEU ( 144-) A 4.80 205 GLU ( 246-) A 4.59 167 TYR ( 208-) A 4.52 191 SER ( 232-) A 4.50 291 HIS ( 332-) A 4.43 102 TYR ( 143-) A 4.33 101 ILE ( 142-) A 4.30 183 PHE ( 224-) A 4.07 322 LYS ( 363-) A 4.06
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.
118 GLU ( 159-) A -2.4 35 ILE ( 76-) A -2.4 125 ARG ( 166-) A -2.3 197 SER ( 238-) A -2.2 103 LEU ( 144-) A -2.2 313 GLY ( 354-) A -2.1 273 SER ( 314-) 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.
45 TYR ( 86-) A Poor phi/psi 49 GLY ( 90-) A PRO omega poor 181 ASP ( 222-) A Poor phi/psi 192 ARG ( 233-) A Poor phi/psi 198 GLY ( 239-) A Poor phi/psi 273 SER ( 314-) A Poor phi/psi 311 VAL ( 352-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.543
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!
12 THR ( 53-) A 0 14 ARG ( 55-) A 0 20 LEU ( 61-) A 0 21 TYR ( 62-) A 0 22 SER ( 63-) A 0 35 ILE ( 76-) A 0 39 LEU ( 80-) A 0 44 PHE ( 85-) A 0 45 TYR ( 86-) A 0 46 ALA ( 87-) A 0 48 PHE ( 89-) A 0 50 PRO ( 91-) A 0 72 MET ( 113-) A 0 73 LEU ( 114-) A 0 74 ARG ( 115-) A 0 83 SER ( 124-) A 0 102 TYR ( 143-) A 0 118 GLU ( 159-) A 0 129 TYR ( 170-) A 0 134 PHE ( 175-) A 0 151 TYR ( 192-) A 0 153 PHE ( 194-) A 0 154 LEU ( 195-) A 0 156 PHE ( 197-) A 0 158 SER ( 199-) A 0And so on for a total of 109 lines.
Standard deviation of omega values : 1.536
Warning: Backbone oxygen evaluation
The residues listed in the table below have an unusual backbone oxygen
For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.
In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!
313 GLY ( 354-) A 1.65 17
3 PRO ( 44-) A -119.1 half-chair C-delta/C-gamma (-126 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.
176 ASN ( 217-) A ND2 <-> 344 HOH (2086 ) A O 0.17 2.53 INTRA BL 304 ARG ( 345-) A NH2 <-> 316 GLN ( 357-) A NE2 0.15 2.70 INTRA BL 14 ARG ( 55-) A NH2 <-> 72 MET ( 113-) A O 0.11 2.59 INTRA 221 ARG ( 262-) A NE <-> 241 ASP ( 282-) A OD1 0.10 2.60 INTRA 88 GLN ( 129-) A NE2 <-> 344 HOH (2049 ) A O 0.08 2.62 INTRA BL 52 ASN ( 93-) A ND2 <-> 344 HOH (2022 ) A O 0.07 2.63 INTRA BL 146 LYS ( 187-) A NZ <-> 344 HOH (2037 ) A O 0.06 2.64 INTRA 31 HIS ( 72-) A O <-> 78 VAL ( 119-) A N 0.06 2.64 INTRA BL 148 ALA ( 189-) A O <-> 153 PHE ( 194-) A N 0.05 2.65 INTRA 304 ARG ( 345-) A NE <-> 310 SER ( 351-) A O 0.05 2.65 INTRA BL 176 ASN ( 217-) A ND2 <-> 307 ARG ( 348-) A NH1 0.04 2.81 INTRA BL 48 PHE ( 89-) A O <-> 90 ASN ( 131-) A ND2 0.04 2.66 INTRA BL 222 LEU ( 263-) A N <-> 223 ASN ( 264-) A N 0.03 2.57 INTRA B3 194 ARG ( 235-) A NH1 <-> 344 HOH (2094 ) A O 0.03 2.67 INTRA BF 302 TRP ( 343-) A CZ2 <-> 306 CYS ( 347-) A SG 0.03 3.37 INTRA BL 104 GLY ( 145-) A N <-> 344 HOH (2040 ) A O 0.02 2.68 INTRA BF 167 TYR ( 208-) A O <-> 175 LEU ( 216-) A N 0.02 2.68 INTRA BL 302 TRP ( 343-) A CE2 <-> 306 CYS ( 347-) A SG 0.02 3.38 INTRA BL 93 PHE ( 134-) A CE1 <-> 97 CYS ( 138-) A SG 0.01 3.39 INTRA BL 238 ASP ( 279-) A OD2 <-> 240 HIS ( 281-) A NE2 0.01 2.69 INTRA 58 ARG ( 99-) A NE <-> 165 GLU ( 206-) A OE2 0.01 2.69 INTRA 279 ARG ( 320-) A N <-> 340 SEP ( 2-) B O3P 0.01 2.69 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.
129 TYR ( 170-) A -8.08 225 ARG ( 266-) A -6.24 23 ARG ( 64-) A -5.93 192 ARG ( 233-) A -5.71 44 PHE ( 85-) A -5.69 266 GLU ( 307-) A -5.66 150 GLN ( 191-) A -5.51 74 ARG ( 115-) A -5.48 25 LYS ( 66-) A -5.40 172 ASN ( 213-) A -5.28 291 HIS ( 332-) A -5.14 274 LYS ( 315-) A -5.13
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
224 LYS ( 265-) A 226 - MET 267- ( A) -5.19
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.
344 HOH (2007 ) A O 344 HOH (2017 ) A O
4 GLN ( 45-) A 37 ASN ( 78-) A 43 ASN ( 84-) A 85 GLN ( 126-) A 88 GLN ( 129-) A 157 ASN ( 198-) A 160 ASN ( 201-) A 176 ASN ( 217-) A 214 HIS ( 255-) A 316 GLN ( 357-) A 317 GLN ( 358-) 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.
2 ASP ( 43-) A N 4 GLN ( 45-) A N 6 ASP ( 47-) A N 22 SER ( 63-) A N 23 ARG ( 64-) A NE 23 ARG ( 64-) A NH2 27 ALA ( 68-) A N 49 GLY ( 90-) A N 119 THR ( 160-) A OG1 125 ARG ( 166-) A NH2 128 ALA ( 169-) A N 133 ASN ( 174-) A ND2 192 ARG ( 233-) A N 215 ASN ( 256-) A N 223 ASN ( 264-) A N 273 SER ( 314-) A N 280 THR ( 321-) A N 294 MET ( 335-) A N 317 GLN ( 358-) A N
5 ASP ( 46-) A H-bonding suggests Asn 40 GLU ( 81-) A H-bonding suggests Gln 42 GLU ( 83-) A H-bonding suggests Gln 234 ASP ( 275-) A H-bonding suggests Asn; but Alt-Rotamer
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 : -0.389 2nd generation packing quality : -1.125 Ramachandran plot appearance : -0.897 chi-1/chi-2 rotamer normality : -0.543 Backbone conformation : -0.471
Bond lengths : 0.554 (tight) Bond angles : 0.751 Omega angle restraints : 0.279 (tight) Side chain planarity : 0.359 (tight) Improper dihedral distribution : 0.945 B-factor distribution : 0.495 Inside/Outside distribution : 1.025
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 : 2.20
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.2 2nd generation packing quality : -0.5 Ramachandran plot appearance : 0.3 chi-1/chi-2 rotamer normality : 0.6 Backbone conformation : -0.4
Bond lengths : 0.554 (tight) Bond angles : 0.751 Omega angle restraints : 0.279 (tight) Side chain planarity : 0.359 (tight) Improper dihedral distribution : 0.945 B-factor distribution : 0.495 Inside/Outside distribution : 1.025 ==============
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.