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.
580 EAL (3002-) A -
In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.
575 GLN ( 618-) 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 ASP ( 40-) A CG 1 ASP ( 40-) A OD1 1 ASP ( 40-) A OD2 25 GLU ( 64-) A CG 25 GLU ( 64-) A CD 25 GLU ( 64-) A OE1 25 GLU ( 64-) A OE2 78 LYS ( 117-) A CG 78 LYS ( 117-) A CD 78 LYS ( 117-) A CE 78 LYS ( 117-) A NZ 259 SER ( 298-) A OG 264 GLU ( 303-) A CG 264 GLU ( 303-) A CD 264 GLU ( 303-) A OE1 264 GLU ( 303-) A OE2 268 LYS ( 307-) A CG 268 LYS ( 307-) A CD 268 LYS ( 307-) A CE 268 LYS ( 307-) A NZ 397 ASP ( 440-) A CG 397 ASP ( 440-) A OD1 397 ASP ( 440-) A OD2
In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.
575 GLN ( 618-) A
Obviously, the temperature at which the X-ray data was collected has some importance too:
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
134 ARG ( 173-) A 147 ARG ( 186-) A 182 ARG ( 221-) A 214 ARG ( 253-) A 446 ARG ( 489-) A
136 TYR ( 175-) A 174 TYR ( 213-) A 220 TYR ( 259-) A 321 TYR ( 360-) A 351 TYR ( 390-) A 438 TYR ( 481-) A 449 TYR ( 492-) A 480 TYR ( 523-) A 552 TYR ( 595-) A
157 PHE ( 196-) A 254 PHE ( 293-) A 283 PHE ( 322-) A 284 PHE ( 323-) A 326 PHE ( 365-) A 352 PHE ( 391-) A 429 PHE ( 472-) A 553 PHE ( 596-) A
282 ASP ( 321-) A
94 GLU ( 133-) A
RMS Z-score for bond lengths: 0.249
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
| 0.998568 0.000009 -0.000279| | 0.000009 0.998872 0.000170| | -0.000279 0.000170 0.998301|Proposed new scale matrix
| 0.017655 0.000000 0.000005| | 0.000000 0.011729 -0.000002| | 0.000002 -0.000001 0.007491|With corresponding cell
A = 56.640 B = 85.257 C = 133.498 Alpha= 89.980 Beta= 90.032 Gamma= 90.001
The CRYST1 cell dimensions
A = 56.720 B = 85.350 C = 133.730 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 4.684
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.
542 PRO ( 585-) A N CA C 123.35 4.6
RMS Z-score for bond angles: 0.610
RMS-deviation in bond angles: 1.321
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.
94 GLU ( 133-) A 134 ARG ( 173-) A 147 ARG ( 186-) A 182 ARG ( 221-) A 214 ARG ( 253-) A 282 ASP ( 321-) A 446 ARG ( 489-) A
423 GLN ( 466-) A 5.81 373 ALA ( 412-) A 5.21 158 TYR ( 197-) A 4.88 420 LEU ( 463-) A 4.79 428 VAL ( 471-) A 4.49 539 THR ( 582-) A 4.48 421 VAL ( 464-) A 4.27 132 THR ( 171-) A 4.15 542 PRO ( 585-) A 4.11 251 VAL ( 290-) A 4.05 411 LYS ( 454-) A 4.05
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.
542 PRO ( 585-) A -2.8 124 PRO ( 163-) A -2.8 355 TYR ( 394-) A -2.3 134 ARG ( 173-) A -2.2 474 SER ( 517-) A -2.2 438 TYR ( 481-) A -2.1 478 ILE ( 521-) A -2.1 201 LEU ( 240-) 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.
84 GLU ( 123-) A Poor phi/psi 116 ASN ( 155-) A Poor phi/psi 117 GLY ( 156-) A Poor phi/psi 123 GLU ( 162-) A PRO omega poor 392 ASN ( 431-) A Poor phi/psi 511 GLN ( 554-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.600
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.
180 SER ( 219-) A 0.36 418 SER ( 461-) A 0.36
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!
32 THR ( 71-) A 0 63 PHE ( 102-) A 0 84 GLU ( 123-) A 0 85 ARG ( 124-) A 0 116 ASN ( 155-) A 0 118 SER ( 157-) A 0 122 LEU ( 161-) A 0 123 GLU ( 162-) A 0 133 SER ( 172-) A 0 174 TYR ( 213-) A 0 175 VAL ( 214-) A 0 219 HIS ( 258-) A 0 220 TYR ( 259-) A 0 224 HIS ( 263-) A 0 234 HIS ( 273-) A 0 235 LEU ( 274-) A 0 240 TRP ( 279-) A 0 242 GLN ( 281-) A 0 243 THR ( 282-) A 0 244 TRP ( 283-) A 0 245 SER ( 284-) A 0 247 ILE ( 286-) A 0 251 VAL ( 290-) A 0 254 PHE ( 293-) A 0 257 ALA ( 296-) A 0And so on for a total of 153 lines.
Standard deviation of omega values : 1.301
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.
348 HIS ( 387-) A ND1 <-> 371 HIS ( 410-) A ND1 0.24 2.76 INTRA BL 134 ARG ( 173-) A NH2 <-> 249 ASP ( 288-) A OD1 0.23 2.47 INTRA 536 GLN ( 579-) A NE2 <-> 541 GLN ( 584-) A CA 0.23 2.87 INTRA 65 VAL ( 104-) A O <-> 74 LYS ( 113-) A NZ 0.20 2.50 INTRA 261 ASP ( 300-) A CG <-> 264 GLU ( 303-) A CB 0.18 3.02 INTRA BF 464 ASP ( 507-) A N <-> 465 PRO ( 508-) A CD 0.13 2.87 INTRA BL 387 HIS ( 426-) A NE2 <-> 580 HOH (2327 ) A O 0.12 2.58 INTRA 271 TRP ( 310-) A CZ2 <-> 275 ARG ( 314-) A NH2 0.12 2.98 INTRA 116 ASN ( 155-) A OD1 <-> 117 GLY ( 156-) A N 0.11 2.49 INTRA BF 121 GLN ( 160-) A OE1 <-> 304 LYS ( 343-) A NZ 0.11 2.59 INTRA 295 GLU ( 334-) A OE2 <-> 299 LYS ( 338-) A NZ 0.10 2.60 INTRA BF 531 TRP ( 574-) A N <-> 532 PRO ( 575-) A CD 0.10 2.90 INTRA BL 261 ASP ( 300-) A O <-> 265 ALA ( 304-) A N 0.10 2.60 INTRA 354 GLN ( 393-) A OE1 <-> 524 LYS ( 567-) A NZ 0.10 2.60 INTRA 152 ARG ( 191-) A NE <-> 462 ASP ( 505-) A OD1 0.09 2.61 INTRA 367 ASN ( 406-) A OD1 <-> 369 GLY ( 408-) A N 0.09 2.61 INTRA BL 242 GLN ( 281-) A OE1 <-> 468 LYS ( 511-) A NZ 0.09 2.61 INTRA BL 507 CYS ( 550-) A SG <-> 508 ASP ( 551-) A N 0.09 3.11 INTRA BL 271 TRP ( 310-) A CE2 <-> 275 ARG ( 314-) A NH2 0.09 3.01 INTRA 529 ARG ( 572-) A NE <-> 533 GLU ( 576-) A OE2 0.09 2.61 INTRA 32 THR ( 71-) A O <-> 309 ARG ( 348-) A NH1 0.08 2.62 INTRA 396 SER ( 439-) A OG <-> 399 HIS ( 442-) A ND1 0.07 2.63 INTRA BF 529 ARG ( 572-) A NH2 <-> 533 GLU ( 576-) A OE2 0.07 2.63 INTRA 400 ASP ( 443-) A CG <-> 505 HIS ( 548-) A NE2 0.06 3.04 INTRA 307 ASP ( 346-) A OD2 <-> 309 ARG ( 348-) A NE 0.05 2.65 INTRA BFAnd so on for a total of 58 lines.
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.
460 GLN ( 503-) A -5.85 570 LYS ( 613-) A -5.77 223 GLN ( 262-) A -5.69 219 HIS ( 258-) A -5.65 67 GLN ( 106-) A -5.45 450 GLN ( 493-) A -5.12 500 HIS ( 543-) A -5.11 458 ARG ( 501-) A -5.07 218 ARG ( 257-) A -5.06
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
218 ARG ( 257-) A 220 - TYR 259- ( A) -5.00
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.
184 MET ( 223-) A -3.03 83 LEU ( 122-) A -2.97
Chain identifier: A
Water, ion, and hydrogenbond related checks
Error: Water molecules without hydrogen bonds
The water molecules listed in the table below do not form any hydrogen bonds,
neither with the protein or DNA/RNA, nor with other water molecules. This is
a strong indication of a refinement problem. The last number on each line is
the identifier of the water molecule in the input file.
580 HOH (2288 ) A O 580 HOH (2423 ) A O Marked this atom as acceptor 577 CL ( 703-) A CL Marked this atom as acceptor 578 CL ( 704-) A CL Metal-coordinating Histidine residue 344 fixed to 1 Metal-coordinating Histidine residue 348 fixed to 1
52 HIS ( 91-) A 389 HIS ( 428-) A 511 GLN ( 554-) A 567 HIS ( 610-) 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.
125 ASP ( 164-) A N 176 ASP ( 215-) A N 234 HIS ( 273-) A N 234 HIS ( 273-) A ND1 238 ASN ( 277-) A N 243 THR ( 282-) A N 272 THR ( 311-) A N 376 ASP ( 415-) A N 394 LEU ( 433-) A N 398 GLU ( 441-) A N 417 PHE ( 460-) A N 446 ARG ( 489-) A NE 456 VAL ( 499-) A N 470 HIS ( 513-) A N 470 HIS ( 513-) A ND1 477 TYR ( 520-) A OH 479 ARG ( 522-) A N 505 HIS ( 548-) A NE2 514 GLU ( 557-) A N 536 GLN ( 579-) A NE2 575 GLY (2000-) A N Only metal coordination for 344 HIS ( 383-) A NE2 Only metal coordination for 372 GLU ( 411-) A OE1
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.
234 HIS ( 273-) A NE2 314 HIS ( 353-) A NE2 330 GLN ( 369-) A OE1 345 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.
580 HOH (2257 ) A O 1.07 K 4 Ion-B 580 HOH (2383 ) A O 0.91 K 4
13 ASP ( 52-) A H-bonding suggests Asn; but Alt-Rotamer 193 ASP ( 232-) A H-bonding suggests Asn 295 GLU ( 334-) A H-bonding suggests Gln; but Alt-Rotamer 364 GLU ( 403-) A H-bonding suggests Gln 410 ASP ( 453-) A H-bonding suggests Asn 430 ASP ( 473-) A H-bonding suggests Asn; but Alt-Rotamer
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 : 0.046 2nd generation packing quality : -0.975 Ramachandran plot appearance : 0.370 chi-1/chi-2 rotamer normality : -0.600 Backbone conformation : -0.309
Bond lengths : 0.249 (tight) Bond angles : 0.610 (tight) Omega angle restraints : 0.237 (tight) Side chain planarity : 0.254 (tight) Improper dihedral distribution : 0.525 B-factor distribution : 0.509 Inside/Outside distribution : 0.995
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 : 1.82
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.4 2nd generation packing quality : -1.0 Ramachandran plot appearance : 0.5 chi-1/chi-2 rotamer normality : -0.3 Backbone conformation : -0.5
Bond lengths : 0.249 (tight) Bond angles : 0.610 (tight) Omega angle restraints : 0.237 (tight) Side chain planarity : 0.254 (tight) Improper dihedral distribution : 0.525 B-factor distribution : 0.509 Inside/Outside distribution : 0.995 ==============
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.