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.
260 EZL ( 301-) A -
Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.
49 ASP ( 52-) A -
In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.
49 ASP ( 52-) 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: B-factors outside the range 0.0 - 100.0
In principle, B-factors can have a very wide range of values, but in
practice, B-factors should not be zero while B-factors above 100.0
are a good indicator that the location of that atom is meaningless. Be
aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms
with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with
a B-factor of zero were observed.
6 LYS ( 9-) A High 249 ASN ( 253-) A High
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: Aspartic acid convention problem
The aspartic acid residues listed in the table below have their chi-2 not
between -90.0 and 90.0, or their proton on OD1 instead of OD2.
16 ASP ( 19-) A 72 ASP ( 75-) A 82 ASP ( 85-) A 161 ASP ( 165-) A 171 ASP ( 175-) A
11 GLU ( 14-) A 23 GLU ( 26-) A 183 GLU ( 187-) A 210 GLU ( 214-) A
RMS Z-score for bond lengths: 0.495
RMS-deviation in bond distances: 0.010
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
| 1.000825 -0.000010 -0.001490| | -0.000010 0.999682 -0.001068| | -0.001490 -0.001068 0.995525|Proposed new scale matrix
| 0.023333 0.000007 0.006086| | 0.000000 0.024001 0.000026| | 0.000021 0.000015 0.014258|With corresponding cell
A = 42.875 B = 41.666 C = 72.512 Alpha= 90.118 Beta= 104.704 Gamma= 90.001
The CRYST1 cell dimensions
A = 42.840 B = 41.680 C = 72.760 Alpha= 90.000 Beta= 104.500 Gamma= 90.000
(Under-)estimated Z-score: 4.765
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.
7 HIS ( 10-) A -C N CA 114.44 -4.0 12 HIS ( 15-) A CG ND1 CE1 109.67 4.1 14 HIS ( 17-) A CG ND1 CE1 110.29 4.7 24 ARG ( 27-) A CA CB CG 124.19 5.0 82 ASP ( 85-) A CA CB CG 108.47 -4.1 90 PHE ( 93-) A CA CB CG 119.07 5.3 92 PHE ( 95-) A CA CB CG 118.84 5.0 116 HIS ( 119-) A CG ND1 CE1 111.19 5.6 123 LYS ( 127-) A -O -C N 130.28 4.5 123 LYS ( 127-) A -C N CA 109.51 -6.8 176 ASP ( 180-) A CA CB CG 116.70 4.1 205 TRP ( 209-) A CZ3 CE3 CD2 113.27 -4.1 227 PHE ( 231-) A CA CB CG 119.80 6.0 243 PRO ( 247-) A CD N CA 103.40 -6.1
11 GLU ( 14-) A 16 ASP ( 19-) A 23 GLU ( 26-) A 72 ASP ( 75-) A 82 ASP ( 85-) A 161 ASP ( 165-) A 171 ASP ( 175-) A 183 GLU ( 187-) A 210 GLU ( 214-) 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.
243 PRO ( 247-) A N -8.9 -31.52 -2.48 The average deviation= 0.995
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.
80 PRO ( 83-) A -2.6 198 PRO ( 202-) A -2.3 42 LYS ( 45-) A -2.3 21 LYS ( 24-) A -2.1 159 VAL ( 163-) A -2.1 172 PHE ( 176-) A -2.1 163 ILE ( 167-) A -2.1 147 GLY ( 151-) A -2.1
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.
26 SER ( 29-) A PRO omega poor 54 LEU ( 57-) A omega poor 62 SER ( 65-) A Poor phi/psi 89 GLN ( 92-) A omega poor 108 LYS ( 111-) A Poor phi/psi 163 ILE ( 167-) A omega poor 174 ASN ( 178-) A Poor phi/psi 193 SER ( 197-) A omega poor 197 PRO ( 201-) A PRO omega poor 199 LEU ( 203-) A Poor phi/psi 203 VAL ( 207-) A omega poor 239 ASP ( 243-) A Poor phi/psi 248 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.459
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!
4 TYR ( 7-) A 0 7 HIS ( 10-) A 0 16 ASP ( 19-) A 0 17 PHE ( 20-) A 0 21 LYS ( 24-) A 0 24 ARG ( 27-) A 0 25 GLN ( 28-) A 0 26 SER ( 29-) A 0 47 SER ( 50-) A 0 51 ALA ( 54-) A 0 59 ASN ( 62-) A 0 61 HIS ( 64-) A 0 69 ASP ( 72-) A 0 70 SER ( 73-) A 0 72 ASP ( 75-) A 0 73 LYS ( 76-) A 0 74 ALA ( 77-) A 0 77 LYS ( 80-) A 0 80 PRO ( 83-) A 0 82 ASP ( 85-) A 0 89 GLN ( 92-) A 0 96 SER ( 99-) A 0 100 GLN ( 103-) A 0 104 HIS ( 107-) A 0 108 LYS ( 111-) A 0And so on for a total of 114 lines.
246 PRO ( 250-) A 0.20 LOW
80 PRO ( 83-) A -64.7 envelop C-beta (-72 degrees) 198 PRO ( 202-) A -63.8 envelop C-beta (-72 degrees) 243 PRO ( 247-) A 145.8 envelop C-alpha (144 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.
12 HIS ( 15-) A ND1 <-> 15 LYS ( 18-) A NZ 0.25 2.75 INTRA 249 ASN ( 253-) A ND2 <-> 261 HOH ( 412 ) A O 0.20 2.50 INTRA BF 164 LYS ( 168-) A NZ <-> 261 HOH ( 454 ) A O 0.20 2.50 INTRA BF 168 LYS ( 172-) A NZ <-> 230 GLU ( 234-) A OE1 0.20 2.50 INTRA BF 168 LYS ( 172-) A NZ <-> 261 HOH ( 331 ) A O 0.17 2.53 INTRA 248 LYS ( 252-) A NZ <-> 261 HOH ( 377 ) A O 0.11 2.59 INTRA 38 ASP ( 41-) A OD1 <-> 40 SER ( 43-) A N 0.10 2.60 INTRA 171 ASP ( 175-) A OD2 <-> 261 HOH ( 368 ) A O 0.10 2.30 INTRA BF 38 ASP ( 41-) A OD1 <-> 40 SER ( 43-) A OG 0.10 2.30 INTRA BF 104 HIS ( 107-) A NE2 <-> 190 TYR ( 194-) A OH 0.06 2.64 INTRA BL 122 THR ( 125-) A C <-> 123 LYS ( 127-) A CA 0.04 2.26 INTRA BL 100 GLN ( 103-) A NE2 <-> 239 ASP ( 243-) A OD1 0.04 2.66 INTRA 72 ASP ( 75-) A OD1 <-> 86 ARG ( 89-) A NE 0.02 2.68 INTRA 9 GLY ( 12-) A CA <-> 10 PRO ( 13-) A CD 0.02 2.78 INTRA BL 216 SER ( 220-) A O <-> 220 LEU ( 224-) A CG 0.01 2.79 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.
7 HIS ( 10-) A -6.41 97 LEU ( 100-) A -5.10 132 GLN ( 136-) A -5.05
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.
261 HOH ( 328 ) A O -25.39 -8.98 2.12 261 HOH ( 341 ) A O -13.58 -18.52 14.89
261 HOH ( 364 ) A O Metal-coordinating Histidine residue 91 fixed to 1 Metal-coordinating Histidine residue 93 fixed to 1 Metal-coordinating Histidine residue 116 fixed to 1
1 HIS ( 4-) A 14 HIS ( 17-) A 174 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.
28 VAL ( 31-) A N 97 LEU ( 100-) A N 155 LYS ( 159-) A N 196 THR ( 200-) A N 200 LEU ( 204-) A N 226 ASN ( 230-) A ND2 228 ASN ( 232-) A N 240 ASN ( 244-) A ND2 241 TRP ( 245-) A N 256 PHE ( 260-) A N Only metal coordination for 93 HIS ( 96-) A NE2 Only metal coordination for 116 HIS ( 119-) A ND1
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 : -0.195 2nd generation packing quality : 0.566 Ramachandran plot appearance : -1.062 chi-1/chi-2 rotamer normality : -1.459 Backbone conformation : -0.969
Bond lengths : 0.495 (tight) Bond angles : 1.223 Omega angle restraints : 1.120 Side chain planarity : 0.536 (tight) Improper dihedral distribution : 0.881 B-factor distribution : 1.418 Inside/Outside distribution : 0.948
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 : 1.50
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.2 2nd generation packing quality : -0.3 Ramachandran plot appearance : -1.4 chi-1/chi-2 rotamer normality : -2.0 Backbone conformation : -1.5
Bond lengths : 0.495 (tight) Bond angles : 1.223 Omega angle restraints : 1.120 Side chain planarity : 0.536 (tight) Improper dihedral distribution : 0.881 B-factor distribution : 1.418 Inside/Outside distribution : 0.948 ==============
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.