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.
500 MA1 ( 994-) A - 504 MA1 ( 996-) A - 505 MA3 ( 992-) A - 506 MA2 ( 991-) A -
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: 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
| 0.998494 0.000358 0.000034| | 0.000358 0.997925 -0.000122| | 0.000034 -0.000122 0.998223|Proposed new scale matrix
| 0.017789 -0.000006 0.000000| | -0.000004 0.011414 0.000001| | 0.000000 0.000001 0.009688|With corresponding cell
A = 56.215 B = 87.614 C = 103.218 Alpha= 90.014 Beta= 90.001 Gamma= 89.959
The CRYST1 cell dimensions
A = 56.300 B = 87.800 C = 103.400 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 5.419
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.
195 ARG ( 195-) A N CA C 98.73 -4.5
318 ALA ( 318-) A 5.69 162 LEU ( 162-) A 5.13 336 THR ( 336-) A 5.10 195 ARG ( 195-) A 4.95 292 ALA ( 292-) A 4.73 59 TRP ( 59-) A 4.09
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.
376 THR ( 376-) A -2.6 270 SER ( 270-) A -2.2 163 VAL ( 163-) A -2.2 341 SER ( 341-) A -2.2 66 SER ( 66-) 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.
5 GLN ( 5-) A Poor phi/psi 18 GLU ( 18-) A Poor phi/psi 53 ASN ( 53-) A PRO omega poor 102 MET ( 102-) A Poor phi/psi 129 VAL ( 129-) A PRO omega poor 221 TRP ( 221-) A Poor phi/psi 268 LYS ( 268-) A Poor phi/psi 350 ASN ( 350-) A Poor phi/psi 364 ASN ( 364-) A Poor phi/psi 376 THR ( 376-) A Poor phi/psi 380 ASN ( 380-) A Poor phi/psi 381 ASP ( 381-) A Poor phi/psi 414 SER ( 414-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.158
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!
5 GLN ( 5-) A 0 8 SER ( 8-) A 0 12 SER ( 12-) A 0 17 PHE ( 17-) A 0 18 GLU ( 18-) A 0 19 TRP ( 19-) A 0 30 ARG ( 30-) A 0 31 TYR ( 31-) A 0 32 LEU ( 32-) A 0 43 SER ( 43-) A 0 45 PRO ( 45-) A 0 48 ASN ( 48-) A 0 52 THR ( 52-) A 0 53 ASN ( 53-) A 0 54 PRO ( 54-) A 0 55 SER ( 55-) A 0 56 ARG ( 56-) A 0 57 PRO ( 57-) A 0 58 TRP ( 58-) A 0 59 TRP ( 59-) A 0 62 TYR ( 62-) A 0 63 GLN ( 63-) A 0 64 PRO ( 64-) A 0 67 TYR ( 67-) A 0 69 LEU ( 69-) A 0And so on for a total of 215 lines.
Standard deviation of omega values : 1.421
Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually short
interactomic distance; each bump is listed in only one direction.
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.
505 MA3 ( 992-) A S4 <-> 506 MA2 ( 991-) A C1 1.18 1.82 INTRA B3 505 MA3 ( 992-) A C4 <-> 506 MA2 ( 991-) A C1 0.31 2.89 INTRA 504 MA1 ( 996-) A S1 <-> 507 HOH ( 931 ) A O 0.22 2.78 INTRA 70 CYS ( 70-) A SG <-> 75 ASN ( 75-) A ND2 0.17 3.13 INTRA 389 ARG ( 389-) A NH2 <-> 498 GLC ( 995-) A O3 0.06 2.64 INTRA 11 THR ( 11-) A OG1 <-> 399 ASN ( 399-) A ND2 0.06 2.64 INTRA BL 504 MA1 ( 996-) A C3 <-> 507 HOH ( 885 ) A O 0.05 2.75 INTRA BF 14 VAL ( 14-) A CG2 <-> 37 PHE ( 37-) A CD2 0.04 3.16 INTRA BL 435 GLN ( 435-) A CG <-> 436 LEU ( 436-) A N 0.03 2.97 INTRA 201 HIS ( 201-) A NE2 <-> 497 GLC ( 993-) A C2 0.02 3.08 INTRA 392 ARG ( 392-) A NH1 <-> 393 ASN ( 393-) A OD1 0.02 2.68 INTRA
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.
72 ARG ( 72-) A -7.20 2 TYR ( 2-) A -5.78 7 GLN ( 7-) A -5.64 284 TRP ( 284-) A -5.37 279 ASN ( 279-) A -5.33 118 TYR ( 118-) A -5.32 30 ARG ( 30-) A -5.32 302 GLN ( 302-) A -5.29 88 ASN ( 88-) A -5.29 303 ARG ( 303-) A -5.25 267 ARG ( 267-) A -5.19 53 ASN ( 53-) A -5.16 484 GLU ( 484-) A -5.12
17 PHE ( 17-) A -2.51
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
313 LEU ( 313-) A - 316 TRP ( 316-) A -1.45 355 ASN ( 355-) A - 358 ILE ( 358-) A -1.56
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.
507 HOH ( 588 ) A O 4.60 28.25 27.34 507 HOH ( 832 ) A O 23.74 69.32 27.12 507 HOH ( 894 ) A O 8.08 48.94 -6.99 507 HOH ( 897 ) A O 10.79 46.33 -6.97 507 HOH ( 911 ) A O 4.26 27.04 41.13 507 HOH ( 920 ) A O 41.72 41.17 14.60
507 HOH ( 673 ) A O 507 HOH ( 853 ) A O 507 HOH ( 877 ) A O 507 HOH ( 888 ) A O 507 HOH ( 905 ) A O 507 HOH ( 930 ) A O 507 HOH ( 933 ) A O 507 HOH ( 944 ) A O 507 HOH ( 948 ) A O 507 HOH ( 974 ) A O Marked this atom as acceptor 501 CL ( 498-) A CL Strange metal coordination for HIS 201
5 GLN ( 5-) A 161 GLN ( 161-) A 279 ASN ( 279-) A 305 HIS ( 305-) A 350 ASN ( 350-) A 373 ASN ( 373-) A 399 ASN ( 399-) A 408 ASN ( 408-) 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.
59 TRP ( 59-) A N 78 GLU ( 78-) A N 87 ASN ( 87-) A ND2 100 ASN ( 100-) A ND2 101 HIS ( 101-) A N 134 TRP ( 134-) A NE1 273 LYS ( 273-) A N 281 GLY ( 281-) A N 295 PHE ( 295-) A N 300 ASP ( 300-) A N 316 TRP ( 316-) A NE1 337 ARG ( 337-) A NH2 343 ARG ( 343-) A NE 344 TRP ( 344-) A N 357 TRP ( 357-) A N 370 VAL ( 370-) A N 434 TRP ( 434-) A N 463 THR ( 463-) A OG1 487 PHE ( 487-) A N 495 LYS ( 495-) A N Only metal coordination for 100 ASN ( 100-) A OD1
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 HIS ( 215-) A NE2 272 GLU ( 272-) A OE1
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+.
503 CA ( 500-) A 0.70 0.93 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.
507 HOH ( 536 ) A O 0.92 K 4
188 ASP ( 188-) A H-bonding suggests Asn 390 GLU ( 390-) A H-bonding suggests Gln
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 : -1.002 2nd generation packing quality : -1.870 Ramachandran plot appearance : -1.098 chi-1/chi-2 rotamer normality : -1.158 Backbone conformation : -0.897
Bond lengths : 0.284 (tight) Bond angles : 0.598 (tight) Omega angle restraints : 0.258 (tight) Side chain planarity : 0.333 (tight) Improper dihedral distribution : 0.682 B-factor distribution : 0.798 Inside/Outside distribution : 0.996
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 : 2.03
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.7 2nd generation packing quality : -1.3 Ramachandran plot appearance : -0.5 chi-1/chi-2 rotamer normality : -0.3 Backbone conformation : -1.0
Bond lengths : 0.284 (tight) Bond angles : 0.598 (tight) Omega angle restraints : 0.258 (tight) Side chain planarity : 0.333 (tight) Improper dihedral distribution : 0.682 B-factor distribution : 0.798 Inside/Outside distribution : 0.996 ==============
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.