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.
149 PE4 ( 300-) A - 150 NAL ( 504-) B - 151 YCP ( 503-) B - 152 D11 ( 502-) B -
Crystallographers and NMR spectroscopists have an understandable dislike for organic chemistry and quantum chemistry. And they hate making topology entries for small molecules. So, if they find a funny small molecular ligand in their molecule, they generally try to 'recycle' old topologies. If the ligand contains a group that, for example, looks like an amino acid, it is common practice to split the ligand into several 'ligand-residues' and use the amino acid topology for the amino acid fragment. This is all fine, but please change the name into DRG, XXX, or whatever, before depositing the ligand. If you think that the validation software makes errors that are related to these ligands, I suggest you first change the name of the ligand (and make one ligand out of the fragments) and run the validation again. The table lists the residues, or residue-like things, that are found bound between ligands or unrecognized things, and that thus are suspect of actually being part of one big ligand.
146 PHE ( 501-) B -
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'.
146 PHE ( 501-) B CG 146 PHE ( 501-) B CD1 146 PHE ( 501-) B CD2 146 PHE ( 501-) B CE1 146 PHE ( 501-) B CE2 146 PHE ( 501-) B CZ
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 0
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
Warning: Unusual bond lengths
The bond lengths listed in the table below were found to deviate more than 4
sigma from standard bond lengths (both standard values and sigmas for amino
acid residues have been taken from Engh and Huber [REF], for DNA they were
taken from Parkinson et al [REF]). In the table below for each unusual bond
the bond length and the number of standard deviations it differs from the
normal value is given.
Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.
146 PHE ( 501-) B C O 1.36 6.4 147 GLN ( 505-) B C O 1.37 6.8 147 GLN ( 505-) B CD OE1 1.35 5.9
RMS Z-score for bond lengths: 0.564
RMS-deviation in bond distances: 0.012
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
| 1.000555 -0.000823 0.000695| | -0.000823 0.995587 0.000738| | 0.000695 0.000738 0.996397|Proposed new scale matrix
| 0.014549 0.008450 -0.000016| | 0.000014 0.016875 -0.000013| | -0.000009 -0.000009 0.012552|With corresponding cell
A = 68.767 B = 68.560 C = 79.667 Alpha= 89.967 Beta= 89.920 Gamma= 120.196
The CRYST1 cell dimensions
A = 68.727 B = 68.727 C = 79.957 Alpha= 90.000 Beta= 90.000 Gamma= 120.000
(Under-)estimated Z-score: 4.699
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.
147 GLN ( 505-) B CA CB CG 130.76 8.3
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.
24 ASN ( 30-) A Poor phi/psi 39 CYS ( 57-) A omega poor 52 PRO ( 70-) A Poor phi/psi 91 GLN ( 109-) A omega poor 101 ARG ( 119-) A Poor phi/psi 113 GLN ( 131-) A omega poor 129 SER ( 147-) A omega poor 139 HIS ( 157-) A omega poor chi-1/chi-2 correlation Z-score : -0.610
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.
90 SER ( 108-) A 0.36 37 VAL ( 55-) A 0.38
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!
3 PRO ( 9-) A 0 5 TRP ( 11-) A 0 6 GLU ( 12-) A 0 11 ARG ( 17-) A 0 12 SER ( 18-) A 0 13 SER ( 19-) A 0 21 HIS ( 27-) A 0 24 ASN ( 30-) A 0 26 SER ( 32-) A 0 27 GLN ( 33-) A 0 31 PRO ( 37-) A 0 32 SER ( 38-) A 0 33 GLU ( 51-) A 0 34 PRO ( 52-) A 0 35 ALA ( 53-) A 0 46 HIS ( 64-) A 0 51 ARG ( 69-) A 0 52 PRO ( 70-) A 0 53 SER ( 71-) A 0 56 ARG ( 74-) A 0 61 THR ( 79-) A 0 80 SER ( 98-) A 0 83 GLU ( 101-) A 0 92 PHE ( 110-) A 0 101 ARG ( 119-) A 0And so on for a total of 65 lines.
34 PRO ( 52-) A -116.1 envelop C-gamma (-108 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.
151 YCP ( 503-) B N <-> 152 D11 ( 502-) B C 1.40 1.30 INTRA BL 146 PHE ( 501-) B C <-> 152 D11 ( 502-) B N 1.38 1.32 INTRA B3 147 GLN ( 505-) B N <-> 150 NAL ( 504-) B C 1.36 1.34 INTRA B3 150 NAL ( 504-) B N <-> 151 YCP ( 503-) B C 1.33 1.37 INTRA BL 151 YCP ( 503-) B CA <-> 152 D11 ( 502-) B C 0.79 2.41 INTRA BL 146 PHE ( 501-) B CA <-> 152 D11 ( 502-) B N 0.72 2.38 INTRA 151 YCP ( 503-) B CE <-> 152 D11 ( 502-) B C 0.67 2.53 INTRA BL 147 GLN ( 505-) B CA <-> 150 NAL ( 504-) B C 0.64 2.56 INTRA 150 NAL ( 504-) B CA <-> 151 YCP ( 503-) B C 0.56 2.64 INTRA BL 15 ARG ( 21-) A NH2 <-> 153 HOH ( 351 ) A O 0.43 2.27 INTRA 146 PHE ( 501-) B O <-> 152 D11 ( 502-) B N 0.36 2.34 INTRA 32 SER ( 38-) A O <-> 124 ARG ( 142-) A NH1 0.30 2.40 INTRA BF 41 HIS ( 59-) A CD2 <-> 139 HIS ( 157-) A ND1 0.20 2.90 INTRA BL 57 GLN ( 75-) A NE2 <-> 153 HOH ( 339 ) A O 0.16 2.54 INTRA 113 GLN ( 131-) A N <-> 151 YCP ( 503-) B O 0.14 2.56 INTRA 15 ARG ( 21-) A NH1 <-> 153 HOH ( 385 ) A O 0.11 2.59 INTRA 51 ARG ( 69-) A NH2 <-> 152 D11 ( 502-) B O3P 0.11 2.59 INTRA 24 ASN ( 30-) A ND2 <-> 153 HOH ( 305 ) A O 0.11 2.59 INTRA BL 124 ARG ( 142-) A CZ <-> 153 HOH ( 464 ) A O 0.10 2.70 INTRA 45 LYS ( 63-) A NZ <-> 152 D11 ( 502-) B O2P 0.09 2.61 INTRA BL 36 ARG ( 54-) A NH2 <-> 153 HOH ( 453 ) A O 0.09 2.61 INTRA BF 9 MET ( 15-) A SD <-> 14 GLY ( 20-) A C 0.09 3.31 INTRA 91 GLN ( 109-) A NE2 <-> 153 HOH ( 328 ) A O 0.08 2.62 INTRA 124 ARG ( 142-) A NH2 <-> 127 GLU ( 145-) A OE2 0.08 2.62 INTRA 15 ARG ( 21-) A NH2 <-> 153 HOH ( 385 ) A O 0.08 2.62 INTRA 33 GLU ( 51-) A OE2 <-> 109 ARG ( 127-) A NE 0.06 2.64 INTRA 41 HIS ( 59-) A CE1 <-> 95 CYS ( 113-) A SG 0.04 3.36 INTRA 5 TRP ( 11-) A NE1 <-> 153 HOH ( 464 ) A O 0.04 2.66 INTRA 114 LYS ( 132-) A NZ <-> 153 HOH ( 357 ) A O 0.04 2.66 INTRA 84 ASP ( 102-) A OD1 <-> 153 HOH ( 429 ) A O 0.04 2.36 INTRA 27 GLN ( 33-) A NE2 <-> 153 HOH ( 346 ) A O 0.03 2.67 INTRA 6 GLU ( 12-) A N <-> 19 PHE ( 25-) A O 0.02 2.68 INTRA 111 GLN ( 129-) A O <-> 147 GLN ( 505-) B N 0.01 2.69 INTRA 124 ARG ( 142-) A N <-> 127 GLU ( 145-) A OE1 0.01 2.69 INTRA 151 YCP ( 503-) B CA <-> 152 D11 ( 502-) B O 0.01 2.79 INTRA BL 43 LEU ( 61-) A O <-> 94 ASP ( 112-) A N 0.01 2.69 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.
50 ARG ( 68-) A -6.87 30 ARG ( 36-) A -6.27 51 ARG ( 69-) A -6.25 56 ARG ( 74-) A -6.14 11 ARG ( 17-) A -5.28 91 GLN ( 109-) A -5.19
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.
98 ALA ( 116-) A -2.52
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.
153 HOH ( 404 ) A O 35.67 1.76 42.79 153 HOH ( 432 ) A O 38.58 1.68 44.87 153 HOH ( 444 ) A O 45.75 18.24 36.74 153 HOH ( 449 ) A O 40.70 27.78 33.77 153 HOH ( 455 ) A O 54.49 22.58 28.67 153 HOH ( 465 ) A O 44.88 28.68 32.61
153 HOH ( 906 ) A O Unrecognized bound group for 146 Bound atom= 152 D11 ( 502-) B N
21 HIS ( 27-) A 24 ASN ( 30-) A 27 GLN ( 33-) A 91 GLN ( 109-) 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.
26 SER ( 32-) A N 38 ARG ( 56-) A N 45 LYS ( 63-) A NZ 65 GLU ( 83-) A N 113 GLN ( 131-) A N 113 GLN ( 131-) A NE2 124 ARG ( 142-) A NH2
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.
41 HIS ( 59-) A NE2 139 HIS ( 157-) A ND1
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.
153 HOH ( 383 ) A O 1.13 K 6 Ion-B 153 HOH ( 444 ) A O 0.94 K 4 ION-B 153 HOH ( 445 ) A O 0.93 K 4 Ion-B
69 GLU ( 87-) 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 : -1.115 2nd generation packing quality : -0.060 Ramachandran plot appearance : 0.902 chi-1/chi-2 rotamer normality : -0.610 Backbone conformation : -0.284
Bond lengths : 0.564 (tight) Bond angles : 0.701 Omega angle restraints : 1.062 Side chain planarity : 0.603 (tight) Improper dihedral distribution : 0.668 B-factor distribution : 0.464 Inside/Outside distribution : 1.026
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 : 1.45
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.7 2nd generation packing quality : -0.6 Ramachandran plot appearance : 0.3 chi-1/chi-2 rotamer normality : -1.1 Backbone conformation : -0.8
Bond lengths : 0.564 (tight) Bond angles : 0.701 Omega angle restraints : 1.062 Side chain planarity : 0.603 (tight) Improper dihedral distribution : 0.668 B-factor distribution : 0.464 Inside/Outside distribution : 1.026 ==============
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.