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.
406 MAL (5044-) 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: 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 ILE ( 3-) A CG1 1 ILE ( 3-) A CG2 1 ILE ( 3-) A CD1 24 LYS ( 26-) A CE 24 LYS ( 26-) A NZ 126 LYS ( 128-) A CG 126 LYS ( 128-) A CD 126 LYS ( 128-) A CE 126 LYS ( 128-) A NZ 174 LYS ( 176-) A CE 174 LYS ( 176-) A NZ 238 LYS ( 240-) A CG 238 LYS ( 240-) A CD 238 LYS ( 240-) A CE 238 LYS ( 240-) A NZ 294 LYS ( 296-) A CG 294 LYS ( 296-) A CD 294 LYS ( 296-) A CE 294 LYS ( 296-) A NZ 308 GLU ( 310-) A CG 308 GLU ( 310-) A CD 308 GLU ( 310-) A OE1 308 GLU ( 310-) A OE2
137 GLU ( 139-) A High
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 1
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: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
343 ARG ( 345-) A
170 TYR ( 172-) A 175 TYR ( 177-) A 340 TYR ( 342-) A
66 PHE ( 68-) A 91 PHE ( 93-) A 193 PHE ( 195-) A
13 ASP ( 15-) A 54 ASP ( 56-) A 57 ASP ( 59-) A 206 ASP ( 208-) A 286 ASP ( 288-) A
2 GLU ( 4-) A 3 GLU ( 5-) A 273 GLU ( 275-) A 287 GLU ( 289-) A 290 GLU ( 292-) A 309 GLU ( 311-) A 327 GLU ( 329-) A
RMS Z-score for bond lengths: 0.262
RMS-deviation in bond distances: 0.006
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
| 0.999078 0.000000 0.000246| | 0.000000 0.999368 -0.000302| | 0.000246 -0.000302 0.997298|Proposed new scale matrix
| 0.012920 0.000000 -0.000003| | 0.000000 0.012916 0.000004| | -0.000001 0.000002 0.005808|With corresponding cell
A = 77.400 B = 77.422 C = 172.185 Alpha= 90.035 Beta= 89.972 Gamma= 90.001
The CRYST1 cell dimensions
A = 77.470 B = 77.470 C = 172.640 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 3.896
Warning: Low bond angle variability
Bond angles were found to deviate less than normal from the standard bond
angles (normal values for protein residues were taken from Engh and Huber
[REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below
is expected to be near 1.0 for a normally restrained data set. The fact that
it is lower than 0.667 in this structure might indicate that too-strong
restraints have been used in the refinement. This can only be a problem for
high resolution X-ray structures.
RMS Z-score for bond angles: 0.457
RMS-deviation in bond angles: 0.984
Error: Nomenclature error(s)
Checking for a hand-check. WHAT IF has over the course of this session
already corrected the handedness of atoms in several residues. These were
administrative corrections. These residues are listed here.
2 GLU ( 4-) A 3 GLU ( 5-) A 13 ASP ( 15-) A 54 ASP ( 56-) A 57 ASP ( 59-) A 206 ASP ( 208-) A 273 GLU ( 275-) A 286 ASP ( 288-) A 287 GLU ( 289-) A 290 GLU ( 292-) A 309 GLU ( 311-) A 327 GLU ( 329-) A 343 ARG ( 345-) A
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.
244 THR ( 246-) A -2.5 201 LYS ( 203-) A -2.4 103 ILE ( 105-) A -2.4 38 HIS ( 40-) A -2.1 270 PRO ( 272-) A -2.1 257 PHE ( 259-) A -2.1 121 LEU ( 123-) 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.
167 ALA ( 169-) A Poor phi/psi 201 LYS ( 203-) A Poor phi/psi 238 LYS ( 240-) A Poor phi/psi 382 GLU ( 384-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.632
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!
16 TYR ( 18-) A 0 29 ASP ( 31-) A 0 41 LYS ( 43-) A 0 51 ALA ( 53-) A 0 61 TRP ( 63-) A 0 63 HIS ( 65-) A 0 72 SER ( 74-) A 0 74 LEU ( 76-) A 0 79 THR ( 81-) A 0 80 PRO ( 82-) A 0 107 ILE ( 109-) A 0 108 ALA ( 110-) A 0 126 LYS ( 128-) A 0 127 THR ( 129-) A 0 128 TRP ( 130-) A 0 141 LYS ( 143-) A 0 145 ALA ( 147-) A 0 146 LEU ( 148-) A 0 148 PHE ( 150-) A 0 149 ASN ( 151-) A 0 163 ASP ( 165-) A 0 168 PHE ( 170-) A 0 171 GLU ( 173-) A 0 179 ASP ( 181-) A 0 183 ASP ( 185-) A 0And so on for a total of 127 lines.
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.
82 LYS ( 84-) A N <-> 393 SO4 ( 392-) A O2 0.19 2.51 INTRA 178 LYS ( 180-) A NZ <-> 407 HOH ( 534 ) A O 0.16 2.54 INTRA BF 271 ASN ( 273-) A ND2 <-> 407 HOH ( 558 ) A O 0.11 2.59 INTRA 63 HIS ( 65-) A ND1 <-> 260 VAL ( 262-) A N 0.11 2.89 INTRA BL 131 ILE ( 133-) A N <-> 132 PRO ( 134-) A CD 0.10 2.90 INTRA BF 157 TRP ( 159-) A N <-> 158 PRO ( 160-) A CD 0.08 2.92 INTRA BL 397 SO4 ( 396-) A O2 <-> 407 HOH ( 604 ) A O 0.06 2.34 INTRA BF 65 ARG ( 67-) A NH1 <-> 407 HOH ( 423 ) A O 0.06 2.64 INTRA 296 LYS ( 298-) A NZ <-> 407 HOH ( 633 ) A O 0.05 2.65 INTRA BF 40 ASP ( 42-) A N <-> 391 SO4 ( 2-) A O2 0.05 2.65 INTRA BF 87 LYS ( 89-) A NZ <-> 407 HOH ( 670 ) A O 0.04 2.66 INTRA BF 79 THR ( 81-) A N <-> 80 PRO ( 82-) A CD 0.03 2.97 INTRA BL 324 GLN ( 326-) A A OE1 <-> 407 HOH ( 481 ) A O 0.03 2.37 INTRA 109 VAL ( 111-) A N <-> 300 ALA ( 302-) A O 0.03 2.67 INTRA 125 PRO ( 127-) A CD <-> 223 MET ( 225-) A SD 0.03 3.37 INTRA BF 97 ARG ( 99-) A A NH2 <-> 407 HOH ( 679 ) A O 0.02 2.68 INTRA BF 401 GOL ( 400-) A C3 <-> 407 HOH ( 653 ) A O 0.02 2.78 INTRA BF 135 ASP ( 137-) A OD2 <-> 202 HIS ( 204-) A ND1 0.02 2.68 INTRA BF 379 LYS ( 381-) A NZ <-> 407 HOH ( 678 ) A O 0.01 2.69 INTRA BF
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.
353 ARG ( 355-) A -6.56 172 ASN ( 174-) A -5.73 71 GLN ( 73-) A -5.62 324 GLN ( 326-) A -5.58 123 ASN ( 125-) A -5.41 48 GLN ( 50-) A -5.26 170 TYR ( 172-) A -5.21 312 LYS ( 314-) A -5.13 65 ARG ( 67-) A -5.07 281 ASN ( 283-) A -5.02
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
170 TYR ( 172-) A 172 - ASN 174- ( A) -5.25
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.
311 ALA ( 313-) A -2.56
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
10 ILE ( 12-) A - 13 ASP ( 15-) A -1.95
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.
407 HOH ( 490 ) A O -8.88 6.05 12.66 407 HOH ( 575 ) A O 13.39 9.24 6.87 407 HOH ( 612 ) A O 23.44 33.23 -28.00
71 GLN ( 73-) A 217 ASN ( 219-) 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.
14 LYS ( 16-) A NZ 35 THR ( 37-) A OG1 61 TRP ( 63-) A NE1 67 GLY ( 69-) A N 104 ALA ( 106-) A N 111 ALA ( 113-) A N 152 GLU ( 154-) A N 154 TYR ( 156-) A N 182 VAL ( 184-) A N 208 ASP ( 210-) A N 229 TRP ( 231-) A N 232 SER ( 234-) A N 274 LEU ( 276-) A N 303 LEU ( 305-) A N 332 ILE ( 334-) A N 385 VAL ( 387-) A N 388 ALA ( 390-) A N
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.
13 ASP ( 15-) A OD1 171 GLU ( 173-) A OE1 382 GLU ( 384-) A OE1 382 GLU ( 384-) A OE2
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.
407 HOH ( 416 ) A O 0.98 K 4 407 HOH ( 579 ) A O 0.91 K 4 407 HOH ( 643 ) A O 0.95 K 5 ION-B H2O-B 407 HOH ( 649 ) A O 1.10 K 5 ION-B
2 GLU ( 4-) A H-bonding suggests Gln 86 ASP ( 88-) A H-bonding suggests Asn; but Alt-Rotamer 171 GLU ( 173-) A H-bonding suggests Gln 327 GLU ( 329-) 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 : 0.131 2nd generation packing quality : -1.384 Ramachandran plot appearance : 0.916 chi-1/chi-2 rotamer normality : 0.632 Backbone conformation : 0.033
Bond lengths : 0.262 (tight) Bond angles : 0.457 (tight) Omega angle restraints : 0.851 Side chain planarity : 0.371 (tight) Improper dihedral distribution : 0.505 B-factor distribution : 0.799 Inside/Outside distribution : 0.922
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 : 1.90
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.6 2nd generation packing quality : -1.1 Ramachandran plot appearance : 1.5 chi-1/chi-2 rotamer normality : 1.1 Backbone conformation : -0.3
Bond lengths : 0.262 (tight) Bond angles : 0.457 (tight) Omega angle restraints : 0.851 Side chain planarity : 0.371 (tight) Improper dihedral distribution : 0.505 B-factor distribution : 0.799 Inside/Outside distribution : 0.922 ==============
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.