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.
409 DAF (2000-) A - 410 DAF (3000-) A - 417 DAF (4000-) A -
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.
405 GLC (2001-) A - O4 bound to 409 DAF (2000-) A - C1 406 GLC (3001-) A - O4 bound to 410 DAF (3000-) A - C1 407 GLC (3002-) A - O4 bound to 406 GLC (3001-) A - C1 408 GLC (4001-) A - O4 bound to 417 DAF (4000-) A - C1
404 LYS ( 404-) A CG 404 LYS ( 404-) A CD 404 LYS ( 404-) A CE 404 LYS ( 404-) A NZ
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :100.000
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
| 0.997838 0.000244 -0.000667| | 0.000244 0.997602 0.000248| | -0.000667 0.000248 0.999044|Proposed new scale matrix
| 0.010731 -0.000003 0.000007| | -0.000003 0.013747 -0.000003| | 0.000011 -0.000004 0.016305|With corresponding cell
A = 93.186 B = 72.743 C = 61.332 Alpha= 89.972 Beta= 90.077 Gamma= 89.972
The CRYST1 cell dimensions
A = 93.390 B = 72.920 C = 61.390 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 5.201
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.
144 PHE ( 144-) A N CA C 99.71 -4.1 152 HIS ( 152-) A CG ND1 CE1 109.68 4.1 178 ARG ( 178-) A N CA C 98.50 -4.5
178 ARG ( 178-) A 5.06 265 LEU ( 265-) A 4.81 144 PHE ( 144-) A 4.44 311 ALA ( 311-) A 4.43 272 ALA ( 272-) A 4.22 42 PRO ( 42-) A 4.10 187 PRO ( 187-) A 4.06 257 ALA ( 257-) A 4.05
Tau angle RMS Z-score : 1.573
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.
181 PHE ( 181-) A -3.0 299 TRP ( 299-) A -2.4 198 SER ( 198-) A -2.4 201 LEU ( 201-) A -2.3 279 TRP ( 279-) A -2.3 302 PRO ( 302-) A -2.2 294 SER ( 294-) A -2.2 55 GLY ( 55-) A -2.1 8 PHE ( 8-) A -2.1 359 HIS ( 359-) 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.
114 ASP ( 114-) A Poor phi/psi 117 LEU ( 117-) A Poor phi/psi 118 ASP ( 118-) A Poor phi/psi 259 GLU ( 259-) A Poor phi/psi 294 SER ( 294-) A Poor phi/psi 361 GLY ( 361-) A Poor phi/psi 369 ASP ( 369-) A Poor phi/psi 398 ASP ( 398-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.644
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.
73 SER ( 73-) A 0.35
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!
8 PHE ( 8-) A 0 16 SER ( 16-) A 0 19 TRP ( 19-) A 0 43 PRO ( 43-) A 0 45 HIS ( 45-) A 0 47 VAL ( 47-) A 0 49 ASN ( 49-) A 0 50 GLU ( 50-) A 0 52 TYR ( 52-) A 0 53 MET ( 53-) A 0 54 PRO ( 54-) A 0 56 ARG ( 56-) A 0 59 ASP ( 59-) A 0 60 ILE ( 60-) A 0 63 SER ( 63-) A 0 65 TYR ( 65-) A 0 81 LYS ( 81-) A 0 90 VAL ( 90-) A 0 91 ILE ( 91-) A 0 92 ASN ( 92-) A 0 102 ARG ( 102-) A 0 105 TYR ( 105-) A 0 106 CYS ( 106-) A 0 114 ASP ( 114-) A 0 116 ARG ( 116-) A 0And so on for a total of 166 lines.
Standard deviation of omega values : 1.809
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!
361 GLY ( 361-) A 1.76 13
302 PRO ( 302-) A 0.46 HIGH
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.
408 GLC (4001-) A O4 <-> 417 DAF (4000-) A C1 1.00 1.40 INTRA B3 408 GLC (4001-) A C4 <-> 417 DAF (4000-) A C1 0.77 2.43 INTRA 72 LYS ( 72-) A NZ <-> 418 HOH (1509 ) A O 0.32 2.38 INTRA 360 GLU ( 360-) A OE1 <-> 379 ARG ( 379-) A NH2 0.26 2.44 INTRA 227 GLN ( 227-) A NE2 <-> 418 HOH (1517 ) A O 0.23 2.47 INTRA BL 251 LYS ( 251-) A NZ <-> 288 ASP ( 288-) A OD1 0.20 2.50 INTRA BL 159 ARG ( 159-) A NE <-> 418 HOH (1507 ) A O 0.18 2.52 INTRA 389 GLY ( 389-) A N <-> 418 HOH (1373 ) A O 0.17 2.53 INTRA 92 ASN ( 92-) A ND2 <-> 93 HIS ( 93-) A ND1 0.15 2.85 INTRA BL 310 TYR ( 310-) A OH <-> 326 HIS ( 326-) A ND1 0.15 2.55 INTRA BL 332 PHE ( 332-) A N <-> 418 HOH (1443 ) A O 0.15 2.55 INTRA BL 251 LYS ( 251-) A NZ <-> 287 VAL ( 287-) A O 0.13 2.57 INTRA BL 259 GLU ( 259-) A OE1 <-> 305 LYS ( 305-) A NZ 0.13 2.57 INTRA 155 ASP ( 155-) A CB <-> 418 HOH (1617 ) A O 0.12 2.68 INTRA 79 HIS ( 79-) A NE2 <-> 175 ASP ( 175-) A OD2 0.12 2.58 INTRA BL 95 CYS ( 95-) A SG <-> 418 HOH (1685 ) A O 0.12 2.88 INTRA 331 GLY ( 331-) A N <-> 418 HOH (1443 ) A O 0.12 2.58 INTRA BL 159 ARG ( 159-) A NH1 <-> 418 HOH (1506 ) A O 0.11 2.59 INTRA 29 ASP ( 29-) A OD2 <-> 333 LYS ( 333-) A NZ 0.10 2.60 INTRA 342 ILE ( 342-) A O <-> 346 ASN ( 346-) A ND2 0.09 2.61 INTRA BL 36 THR ( 36-) A OG1 <-> 37 HIS ( 37-) A ND1 0.09 2.61 INTRA BL 11 GLU ( 11-) A OE1 <-> 14 LYS ( 14-) A NZ 0.08 2.62 INTRA BL 162 LYS ( 162-) A NZ <-> 418 HOH ( 918 ) A O 0.07 2.63 INTRA BL 53 MET ( 53-) A N <-> 54 PRO ( 54-) A CD 0.07 2.93 INTRA BL 382 VAL ( 382-) A N <-> 383 GLY ( 383-) A N 0.07 2.53 INTRA BLAnd so on for a total of 63 lines.
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.
380 TYR ( 380-) A -7.41 345 ARG ( 345-) A -5.51 269 GLN ( 269-) A -5.35
102 ARG ( 102-) A -2.58
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.
418 HOH (1619 ) A O -6.05 29.18 -10.21 418 HOH (1627 ) A O -6.48 21.24 22.24
49 ASN ( 49-) A 84 GLN ( 84-) A 227 GLN ( 227-) A 335 GLN ( 335-) 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.
8 PHE ( 8-) A N 12 SER ( 12-) A OG 93 HIS ( 93-) A N 94 ARG ( 94-) A NH1 167 TRP ( 167-) A NE1 193 TYR ( 193-) A OH 249 THR ( 249-) A OG1 263 TRP ( 263-) A N 266 ILE ( 266-) A N 382 VAL ( 382-) A N Only metal coordination for 92 ASN ( 92-) 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.
290 HIS ( 290-) A NE2
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+.
413 CA ( 500-) A 0.78 1.02 Scores about as good as NA 414 CA ( 501-) A 0.73 0.97 Scores about as good as NA 415 CA ( 502-) A 0.80 1.02 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.
418 HOH ( 723 ) A O 1.13 K 4 Ion-B 418 HOH ( 785 ) A O 0.87 K 4 418 HOH ( 825 ) A O 0.91 K 5 418 HOH ( 827 ) A O 1.00 K 4 418 HOH ( 904 ) A O 1.08 K 4 418 HOH (1533 ) A O 0.91 K 4 Ion-B 418 HOH (1540 ) A O 1.02 K 4
398 ASP ( 398-) 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 : -0.409 2nd generation packing quality : -1.769 Ramachandran plot appearance : -1.603 chi-1/chi-2 rotamer normality : -0.644 Backbone conformation : -1.012
Bond lengths : 0.418 (tight) Bond angles : 0.717 Omega angle restraints : 0.329 (tight) Side chain planarity : 0.322 (tight) Improper dihedral distribution : 0.681 B-factor distribution : 0.876 Inside/Outside distribution : 0.959
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 : 2.00
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.1 2nd generation packing quality : -1.2 Ramachandran plot appearance : -1.0 chi-1/chi-2 rotamer normality : 0.1 Backbone conformation : -1.2
Bond lengths : 0.418 (tight) Bond angles : 0.717 Omega angle restraints : 0.329 (tight) Side chain planarity : 0.322 (tight) Improper dihedral distribution : 0.681 B-factor distribution : 0.876 Inside/Outside distribution : 0.959 ==============
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.