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 VZ4 ( 263-) A - 261 DMS ( 265-) A - 262 VZ4 ( 264-) 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.
77 LYS ( 80-) A - 84 THR ( 87-) A - 132 GLN ( 136-) A - 213 SER ( 217-) A - 250 ARG ( 254-) 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.
77 LYS ( 80-) A - 84 THR ( 87-) A - 132 GLN ( 136-) A - 250 ARG ( 254-) 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: Occupancies atoms do not add up to 1.0.
In principle, the occupancy of all alternates of one atom should add up till
1.0. A valid exception is the missing atom (i.e. an atom not seen in the
electron density) that is allowed to have a 0.0 occupancy. Sometimes this
even happens when there are no alternate atoms given...
Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.
WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.
213 SER ( 217-) A 0.76
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 5
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
55 ARG ( 58-) A
4 TYR ( 7-) A 111 TYR ( 114-) A
72 ASP ( 75-) A
23 GLU ( 26-) A 66 GLU ( 69-) A 235 GLU ( 239-) A
RMS Z-score for bond lengths: 0.435
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
| 0.999396 -0.000262 0.000829| | -0.000262 1.000302 -0.000290| | 0.000829 -0.000290 0.996232|Proposed new scale matrix
| 0.023670 0.000008 0.006043| | 0.000006 0.024208 0.000007| | -0.000012 0.000004 0.014310|With corresponding cell
A = 42.238 B = 41.309 C = 72.108 Alpha= 90.025 Beta= 104.274 Gamma= 90.030
The CRYST1 cell dimensions
A = 42.263 B = 41.297 C = 72.397 Alpha= 90.000 Beta= 104.320 Gamma= 90.000
(Under-)estimated Z-score: 3.989
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.
23 GLU ( 26-) A 55 ARG ( 58-) A 66 GLU ( 69-) A 72 ASP ( 75-) A 235 GLU ( 239-) 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.
198 PRO ( 202-) A -2.3 89 GLN ( 92-) A -2.2 172 PHE ( 176-) A -2.1 159 VAL ( 163-) A -2.0 147 GLY ( 151-) 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.
26 SER ( 29-) A PRO omega poor 54 LEU ( 57-) A omega poor 73 LYS ( 76-) A Poor phi/psi 89 GLN ( 92-) A omega poor 108 LYS ( 111-) A Poor phi/psi 137 LEU ( 141-) 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 211 PRO ( 215-) A omega poor 239 ASP ( 243-) A Poor phi/psi 248 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.719
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 35 ALA ( 38-) A 0 47 SER ( 50-) A 0 51 ALA ( 54-) A 0 59 ASN ( 62-) A 0 61 HIS ( 64-) A 0 63 PHE ( 66-) 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 88 ILE ( 91-) A 0 89 GLN ( 92-) A 0 96 SER ( 99-) A 0And so on for a total of 121 lines.
18 PRO ( 21-) A -121.6 half-chair C-delta/C-gamma (-126 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.
262 VZ4 ( 264-) A CAO <-> 263 HOH ( 604 ) A B O 1.45 1.35 INTRA 262 VZ4 ( 264-) A CAA <-> 263 HOH ( 602 ) A B O 1.00 1.70 INTRA 262 VZ4 ( 264-) A CAY <-> 263 HOH ( 604 ) A B O 0.97 1.83 INTRA 262 VZ4 ( 264-) A CAB <-> 263 HOH ( 604 ) A B O 0.76 2.04 INTRA 209 LYS ( 213-) A A NZ <-> 263 HOH ( 609 ) A B O 0.69 2.01 INTRA 263 HOH ( 361 ) A A O <-> 263 HOH ( 614 ) A B O 0.60 1.60 INTRA 262 VZ4 ( 264-) A CAN <-> 263 HOH ( 604 ) A B O 0.49 2.31 INTRA 210 GLU ( 214-) A A OE2 <-> 263 HOH ( 427 ) A B O 0.48 1.92 INTRA BL 263 HOH ( 303 ) A B O <-> 263 HOH ( 323 ) A A O 0.38 1.82 INTRA 262 VZ4 ( 264-) A CAI <-> 263 HOH ( 602 ) A B O 0.33 2.37 INTRA 263 HOH ( 337 ) A B O <-> 263 HOH ( 613 ) A A O 0.24 1.96 INTRA BL 263 HOH ( 410 ) A A O <-> 263 HOH ( 498 ) A B O 0.23 1.97 INTRA 12 HIS ( 15-) A ND1 <-> 15 LYS ( 18-) A NZ 0.22 2.78 INTRA BL 61 HIS ( 64-) A A ND1 <-> 263 HOH ( 595 ) A O 0.21 2.49 INTRA 262 VZ4 ( 264-) A CAQ <-> 263 HOH ( 604 ) A B O 0.17 2.63 INTRA 155 LYS ( 159-) A NZ <-> 263 HOH ( 610 ) A O 0.17 2.53 INTRA 261 DMS ( 265-) A O <-> 263 HOH ( 470 ) A O 0.12 2.28 INTRA 84 THR ( 87-) A A CG2 <-> 122 THR ( 125-) A OG1 0.10 2.70 INTRA BL 161 ASP ( 165-) A OD1 <-> 263 HOH ( 517 ) A O 0.09 2.31 INTRA BF 263 HOH ( 485 ) A B O <-> 263 HOH ( 631 ) A A O 0.08 2.12 INTRA 263 HOH ( 299 ) A A O <-> 263 HOH ( 342 ) A B O 0.07 2.13 INTRA BL 33 HIS ( 36-) A A O <-> 263 HOH ( 352 ) A O 0.07 2.33 INTRA 246 PRO ( 250-) A CD <-> 263 HOH ( 546 ) A O 0.06 2.74 INTRA 241 TRP ( 245-) A O <-> 261 DMS ( 265-) A C2 0.04 2.76 INTRA 248 LYS ( 252-) A NZ <-> 263 HOH ( 376 ) A O 0.04 2.66 INTRA 261 DMS ( 265-) A C2 <-> 263 HOH ( 465 ) A O 0.04 2.76 INTRA 158 ASP ( 162-) A OD2 <-> 263 HOH ( 419 ) A O 0.03 2.37 INTRA 45 SER ( 48-) A CB <-> 77 LYS ( 80-) A A CG 0.03 3.17 INTRA 35 ALA ( 38-) A O <-> 263 HOH ( 352 ) A O 0.02 2.38 INTRA 104 HIS ( 107-) A NE2 <-> 190 TYR ( 194-) A OH 0.02 2.68 INTRA BL 262 VZ4 ( 264-) A CAH <-> 263 HOH ( 602 ) A B O 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 -6.27 97 LEU ( 100-) A -5.16
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.
248 LYS ( 252-) A -3.16 15 LYS ( 18-) A -2.63 251 GLN ( 255-) A -2.59
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.
263 HOH ( 490 ) A O -25.00 -9.50 15.48 263 HOH ( 560 ) A O -12.07 -3.05 39.94 263 HOH ( 581 ) A O 10.54 -4.57 -5.19 263 HOH ( 592 ) A O -4.17 -20.21 15.76 263 HOH ( 600 ) A O -12.03 20.96 29.84
263 HOH ( 615 ) 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
50 GLN ( 53-) 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 63 PHE ( 66-) A N 71 GLN ( 74-) A N 89 GLN ( 92-) A A NE2 92 PHE ( 95-) A N 97 LEU ( 100-) A N 154 GLN ( 158-) A NE2 196 THR ( 200-) A N 200 LEU ( 204-) A N 226 ASN ( 230-) A ND2 240 ASN ( 244-) A ND2 241 TRP ( 245-) A N 256 PHE ( 260-) A N Only metal coordination for 91 HIS ( 94-) A NE2 Only metal coordination for 93 HIS ( 96-) A NE2 Only metal coordination for 116 HIS ( 119-) 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.
263 HOH ( 356 ) A O 0.90 K 4 263 HOH ( 362 ) A O 1.06 K 4 263 HOH ( 372 ) A O 0.93 K 5 263 HOH ( 406 ) A A O 1.05 MG 5 263 HOH ( 408 ) A O 1.12 K 4 263 HOH ( 412 ) A A O 1.20 NA 5 *2 (or CA) 263 HOH ( 469 ) A O 0.85 K 4 Ion-B 263 HOH ( 543 ) A O 1.08 K 4 ION-B H2O-B 263 HOH ( 567 ) A O 0.98 NA 5 *2 ION-B
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 : -0.112 2nd generation packing quality : 0.199 Ramachandran plot appearance : -0.981 chi-1/chi-2 rotamer normality : 0.719 Backbone conformation : -1.020
Bond lengths : 0.435 (tight) Bond angles : 0.705 Omega angle restraints : 1.148 Side chain planarity : 0.734 Improper dihedral distribution : 0.764 B-factor distribution : 0.982 Inside/Outside distribution : 0.958
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 : 0.1 2nd generation packing quality : -0.4 Ramachandran plot appearance : -1.4 chi-1/chi-2 rotamer normality : 0.2 Backbone conformation : -1.5
Bond lengths : 0.435 (tight) Bond angles : 0.705 Omega angle restraints : 1.148 Side chain planarity : 0.734 Improper dihedral distribution : 0.764 B-factor distribution : 0.982 Inside/Outside distribution : 0.958 ==============
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.