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.
398 BMA ( 471-) A - 399 MAN ( 472-) A - 400 MAN ( 473-) A - 401 MAN ( 474-) A - 402 MAN ( 475-) A - 403 MAN ( 476-) A - 404 BGC ( 484-) A - 405 BGC ( 486-) A - 411 3LV ( 488-) A - 412 BGC ( 487-) A - 413 BMA ( 483-) A - 414 MAN ( 477-) 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.
60 ILE ( 140-) A - 85 SER ( 165-) A - 290 SER ( 370-) A - 340 ARG ( 419-) 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.
60 ILE ( 140-) A - 85 SER ( 165-) A - 290 SER ( 370-) A - 340 ARG ( 419-) 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.
390 NAG ( 469-) A - O4 bound to 391 NAG ( 470-) A - C1 391 NAG ( 470-) A - O4 bound to 398 BMA ( 471-) A - C1 392 NAG ( 478-) A - O4 bound to 393 NAG ( 479-) A - C1 394 NAG ( 481-) A - O4 bound to 395 NAG ( 482-) A - C1 395 NAG ( 482-) A - O4 bound to 413 BMA ( 483-) A - C1
Plausible side chain atoms were detected with (near) zero occupancy
When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.
182 LYS ( 261-) A - CE 182 LYS ( 261-) A - NZ 307 LYS ( 387-) A - NZ
1 ILE ( 81-) A CG1 1 ILE ( 81-) A CG2 1 ILE ( 81-) A CD1
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.
2 ARG ( 82-) A 0.67 335 GLU ( 414-) A 0.57 353 LYS ( 432-) A 0.46 356 LYS ( 435-) A 0.69 396 GLC ( 485-) A 0.78
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
Nomenclature related problems
Warning: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
340 ARG ( 419-) A
187 GLU ( 266-) A 204 GLU ( 283-) A 207 GLU ( 286-) A 386 GLU ( 465-) A
RMS Z-score for bond lengths: 0.392
RMS-deviation in bond distances: 0.010
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: 0.644
RMS-deviation in bond angles: 1.384
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.
187 GLU ( 266-) A 204 GLU ( 283-) A 207 GLU ( 286-) A 340 ARG ( 419-) A 386 GLU ( 465-) 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.
109 THR ( 188-) A -2.9 146 THR ( 225-) A -2.5 38 ARG ( 118-) A -2.4 58 THR ( 138-) A -2.4 252 PRO ( 331-) A -2.3 102 THR ( 181-) A -2.2 352 PRO ( 431-) A -2.1 138 THR ( 217-) A -2.1 269 VAL ( 349-) A -2.1 41 TYR ( 121-) A -2.1 148 GLU ( 227-) 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.
37 THR ( 117-) A omega poor 44 CYS ( 124-) A omega poor 68 THR ( 148-) A omega poor 84 SER ( 164-) A Poor phi/psi 101 SER ( 180-) A omega poor 129 ASN ( 208-) A Poor phi/psi 130 ARG ( 209-) A Poor phi/psi 141 ARG ( 220-) A Poor phi/psi 143 ILE ( 222-) A Poor phi/psi 146 THR ( 225-) A Poor phi/psi, omega poor 148 GLU ( 227-) A Poor phi/psi, omega poor 185 LYS ( 264-) A omega poor 197 GLU ( 276-) A omega poor 206 ALA ( 285-) A Poor phi/psi 217 GLN ( 296-) A omega poor 219 SER ( 298-) A omega poor 231 MET ( 310-) A Poor phi/psi 236 GLN ( 315-) A Poor phi/psi 246 ASN ( 325-) A PRO omega poor 266 ASN ( 346-) A Poor phi/psi 279 ASN ( 359-) A Poor phi/psi 301 ASN ( 381-) A Poor phi/psi 323 SER ( 404-) A Poor phi/psi 351 ARG ( 430-) A PRO omega poor 361 SER ( 440-) A Poor phi/psi 362 ASN ( 441-) A omega poor 364 ILE ( 443-) A omega poor chi-1/chi-2 correlation Z-score : -0.463
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 THR ( 88-) A 0 13 THR ( 93-) A 0 15 ASN ( 95-) A 0 23 ASP ( 103-) A 0 31 ASP ( 111-) A 0 32 SER ( 112-) A 0 33 ASP ( 113-) A 0 38 ARG ( 118-) A 0 39 GLU ( 119-) A 0 40 PRO ( 120-) A 0 47 ASP ( 127-) A 0 56 GLN ( 136-) A 0 64 HIS ( 144-) A 0 66 ASN ( 146-) A 0 68 THR ( 148-) A 0 69 ILE ( 149-) A 0 72 ARG ( 152-) A 0 73 SER ( 153-) A 0 81 TRP ( 161-) A 0 83 LEU ( 163-) A 0 84 SER ( 164-) A 0 95 GLU ( 174-) A 0 96 CYS ( 175-) A 0 97 ILE ( 176-) A 0 99 TRP ( 178-) A 0And so on for a total of 227 lines.
Standard deviation of omega values : 7.051
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!
21 GLY ( 101-) A 1.55 11
222 PRO ( 301-) A 0.20 LOW
86 PRO ( 166-) A -13.3 half-chair C-alpha/N (-18 degrees) 380 PRO ( 459-) A 18.0 half-chair N/C-delta (18 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.
395 NAG ( 482-) A O4 <-> 413 BMA ( 483-) A C1 0.97 1.43 INTRA BF 402 MAN ( 475-) A O6 <-> 414 MAN ( 477-) A C1 0.96 1.44 INTRA B3 395 NAG ( 482-) A C4 <-> 413 BMA ( 483-) A C1 0.89 2.31 INTRA 402 MAN ( 475-) A C6 <-> 414 MAN ( 477-) A C1 0.72 2.48 INTRA 95 GLU ( 174-) A OE1 <-> 130 ARG ( 209-) A NH1 0.20 2.50 INTRA 72 ARG ( 152-) A NH1 <-> 411 3LV ( 488-) A O15 0.16 2.54 INTRA 309 LYS ( 389-) A NZ <-> 415 HOH ( 785 ) A O 0.16 2.54 INTRA 340 ARG ( 419-) A A CD <-> 415 HOH ( 875 ) A O 0.11 2.69 INTRA 180 GLU ( 259-) A OE2 <-> 415 HOH ( 711 ) A O 0.09 2.31 INTRA 207 GLU ( 286-) A OE1 <-> 415 HOH ( 850 ) A O 0.09 2.31 INTRA 96 CYS ( 175-) A C <-> 114 CYS ( 193-) A SG 0.08 3.32 INTRA BL 172 GLU ( 251-) A OE1 <-> 415 HOH ( 861 ) A O 0.07 2.33 INTRA 190 ALA ( 269-) A N <-> 233 HIS ( 312-) A NE2 0.06 2.94 INTRA BL 105 HIS ( 184-) A ND1 <-> 107 GLY ( 186-) A N 0.06 2.94 INTRA BL 7 LEU ( 87-) A N <-> 154 HIS ( 233-) A ND1 0.05 2.95 INTRA BL 410 PO4 ( 489-) A O1 <-> 415 HOH ( 949 ) A O 0.05 2.35 INTRA BF 103 SER ( 182-) A C <-> 151 CYS ( 230-) A SG 0.03 3.37 INTRA BL 39 GLU ( 119-) A N <-> 40 PRO ( 120-) A CD 0.03 2.97 INTRA BL 12 CYS ( 92-) A SG <-> 338 CYS ( 417-) A C 0.02 3.38 INTRA BL 45 ASP ( 125-) A N <-> 48 GLU ( 128-) A O 0.02 2.68 INTRA BL 109 THR ( 188-) A CG2 <-> 128 TYR ( 207-) A CZ 0.02 3.18 INTRA BL 204 GLU ( 283-) A OE2 <-> 415 HOH ( 943 ) A O 0.01 2.39 INTRA
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.
2 ARG ( 82-) A -6.99 335 GLU ( 414-) A -6.15 376 GLN ( 455-) A -5.80 75 TYR ( 155-) A -5.49 72 ARG ( 152-) A -5.48 261 TYR ( 341-) A -5.45 373 PHE ( 452-) A -5.44 90 TYR ( 169-) A -5.36 250 ASN ( 329-) A -5.08
66 ASN ( 146-) A -2.74 6 ASN ( 86-) A -2.54
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
373 PHE ( 452-) A - 376 GLN ( 455-) A -1.85
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.
415 HOH ( 823 ) A O -0.32 8.21 76.46 415 HOH ( 826 ) A O 23.21 47.42 62.95 415 HOH ( 829 ) A O 37.39 -4.25 65.08
415 HOH ( 853 ) A O 415 HOH ( 860 ) A O 415 HOH ( 865 ) A O Bound group on Asn; dont flip 6 ASN ( 86-) A Bound to: 392 NAG ( 478-) A Bound group on Asn; dont flip 66 ASN ( 146-) A Bound to: 394 NAG ( 481-) A Bound group on Asn; dont flip 121 ASN ( 200-) A Bound to: 390 NAG ( 469-) A
142 ASN ( 221-) A 301 ASN ( 381-) 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.
17 TRP ( 97-) A NE1 38 ARG ( 118-) A NH2 41 TYR ( 121-) A OH 42 VAL ( 122-) A N 58 THR ( 138-) A N 73 SER ( 153-) A N 84 SER ( 164-) A N 88 THR ( 168-) A OG1 117 GLY ( 196-) A N 130 ARG ( 209-) A NH1 149 SER ( 228-) A N 169 GLY ( 248-) A N 195 HIS ( 274-) A N 213 ARG ( 292-) A NH2 218 GLY ( 297-) A N 248 ARG ( 327-) A NH2 251 ASP ( 330-) A N 270 LYS ( 350-) A N 284 ARG ( 364-) A NH1 284 ARG ( 364-) A NH2 359 TRP ( 438-) A N 359 TRP ( 438-) A NE1
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+.
407 CA ( 490-) A 0.58 0.80 Scores about as good as NA 408 CA ( 491-) A -.- -.- Low probability ion. Occ=0.19 409 K ( 492-) A -.- -.- Low probability ion. Occ=0.65
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.
415 HOH ( 495 ) A O 1.11 K 4 *1 415 HOH ( 542 ) A O 1.10 K 5 *1 415 HOH ( 545 ) A O 0.90 K 4 *1 415 HOH ( 566 ) A O 0.93 K 5 *1 415 HOH ( 612 ) A O 0.96 K 4 *1 415 HOH ( 674 ) A O 0.93 K 5 *1 415 HOH ( 723 ) A O 0.89 K 4 *1 Ion-B 415 HOH ( 906 ) A O 0.94 K 4 *1
106 ASP ( 185-) A H-bonding suggests Asn; but Alt-Rotamer 164 ASP ( 243-) 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 : -0.644 2nd generation packing quality : -2.267 Ramachandran plot appearance : -1.593 chi-1/chi-2 rotamer normality : -0.463 Backbone conformation : -1.522
Bond lengths : 0.392 (tight) Bond angles : 0.644 (tight) Omega angle restraints : 1.282 (loose) Side chain planarity : 0.555 (tight) Improper dihedral distribution : 0.706 B-factor distribution : 0.505 Inside/Outside distribution : 1.079
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 : 1.55
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.3 2nd generation packing quality : -1.8 Ramachandran plot appearance : -2.1 chi-1/chi-2 rotamer normality : -0.9 Backbone conformation : -2.0
Bond lengths : 0.392 (tight) Bond angles : 0.644 (tight) Omega angle restraints : 1.282 (loose) Side chain planarity : 0.555 (tight) Improper dihedral distribution : 0.706 B-factor distribution : 0.505 Inside/Outside distribution : 1.079 ==============
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.