************************************************************************ ********** REPORT OF PROTEIN ANALYSIS by the WHAT IF program ********** ************************************************************************ Date : 2023-10-28 This report was created by WHAT IF version WHATCHECK15.0 This document is a WHAT_CHECK 14.0 report for a PDB-file. Each reported fact has an assigned severity, one of: error : Items marked as errors are considered severe problems requiring immediate attention. warning: Either less severe problems or uncommon structural features. These still need special attention. note : Statistical values, plots, or other verbose results of tests and analyses that have been performed. If alternate conformations are present, only the first is evaluated. Hydrogen atoms are only included if explicitly requested, and even then they are not used in all checks. The software functions less well for non-canonical amino acids and exotic ligands than for the 20 canonical residues and canonical nucleic acids. Some remarks regarding the output: Residues/atoms in tables are normally given in a few parts: A number. This is the internal sequence number of the residue used by WHAT IF. The first residues in the file get number 1, 2, etc. The residue type. Normally this is a three letter amino acid type. The sequence number, between brackets. This is the residue number as it was given in the input file. It can be followed by the insertion code. The chain identifier. A single character. If no chain identifier was given in the input file, this will be a minus sign or a blank. A model number. If no model number exists, like in most X-ray files, this will be a blank or occasionally a minus sign. In case an atom is part of the output, the atom will be listed using the PDB nomenclature for type and identifier. To indicate the normality of a score, the score may be expressed as a Z-value or Z-score. This is just the number of standard deviations that the score deviates from the expected value. A property of Z-values is that the root-mean-square of a group of Z-values (the RMS Z-value) is expected to be 1.0. Z-values above 4.0 and below -4.0 are very uncommon. If a Z-score is used in WHAT IF, the accompanying text will explain how the expected value and standard deviation were obtained. The names of nucleic acids are DGUA, DTHY, OCYT, OADE, etc. The first character is a D or O for DNA or RNA respectively. This circumvents ambiguities in the many old PDB files in which DNA and RNA were both called A, C, G, and T. ========================================= ==== Compound code /zata/tempdir/7n6o/wctemf/7n6o_final.pdb ==== ========================================= # 1 # Note: Introduction WHAT CHECK needs to read a PDB file before it can check it. It does a series of checks upon reading the file. The results of these checks are reported in this section (section 2.1). The rest of the report will be more systematic in that section 2.2 reports on administrative problems. Section 2.3 gives descriptive output that is not directly validating things but more telling you how WHAT CHECK interpreted the input file. Section 2.4 looks at B-factors, occupancies, and the presence/absence of (spurious) atoms. Section 2.5 deals with nomenclature problems. Section 2.6 deals with geometric problems like bond lengths and bond angles. Section 2.7 deals with torsion angle issues. Section 2.8 looks at atomic clashes. Section 2.9 deals with packing, accessibility, etc, issues. Section 2.10 deals with hydrogen bonds, ion packing, and other things that can be summarized under the common name charge-charge interactions. Section 2.11 gives a summary of whole report and tells you (if applicable) which symmetry matrices were used. Section 2.12 tells the crystallographer which are the things most in need of manual correction. And the last section, section 2.13, lists all residues sorted by their need for visual inspection in light of the electron density. # 2 # Warning: Non-triclinic cell with acute angle The crystallographic unit cell does not conform to the convention that all non-orthogonal angles in a non-triclinic cell should be obtuse. The CRYST1 cell dimensions A = 59.130 B = 107.494 C = 66.861 Alpha= 90.000 Beta= 89.880 Gamma= 90.000 # 3 # Warning: Class of conventional cell differs from CRYST1 cell The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment. The CRYST1 cell dimensions A = 59.130 B = 107.494 C = 66.861 Alpha= 90.000 Beta= 89.880 Gamma= 90.000 Dimensions of a reduced cell A = 59.130 B = 66.861 C = 107.494 Alpha= 90.000 Beta= 90.000 Gamma= 90.120 Dimensions of the conventional cell A = 59.130 B = 66.861 C = 107.494 Alpha= 90.000 Beta= 90.000 Gamma= 90.120 Transformation to conventional cell -1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 Crystal class of the cell: MONOCLINIC Crystal class of the conventional cell: ORTHORHOMBIC Space group name: P 1 21 1 Bravais type of conventional cell is: P WARNING. Date error on HEADER card: HEADER 7N6O ATOM 5507 CB ALA C 484 29.047 83.672 13.801 1.00 29.55 C ICNT,ICEXP= 12 16 ATOM 5507 CB ALA C 484 29.047 83.672 13.801 1.00 29.55 C ICNT,ICEXP= 12 16 ATOM 5507 CB ALA C 484 29.047 83.672 13.801 1.00 29.55 C ICNT,ICEXP= 12 16 ATOM 5507 CB ALA C 484 29.047 83.672 13.801 1.00 29.55 C ICNT,ICEXP= 12 16 ATOM 5507 CB ALA C 484 29.047 83.672 13.801 1.00 29.55 C ICNT,ICEXP= 12 16 ATOM 5507 CB ALA C 484 29.047 83.672 13.801 1.00 29.55 C ICNT,ICEXP= 12 16 ATOM 5507 CB ALA C 484 29.047 83.672 13.801 1.00 29.55 C ICNT,ICEXP= 12 16 ATOM 5507 CB ALA C 484 29.047 83.672 13.801 1.00 29.55 C ICNT,ICEXP= 12 16 # 4 # Note: Header records from PDB file Header records from PDB file. HEADER 7N6O # 5 # Error: Missing unit cell information No SCALE matrix is given in the PDB file. # 6 # Note: Proposal for corrected SCALE matrix A corrected SCALE matrix has been derived. Proposed scale matrix 0.016912 0.000000 -0.000035 0.000000 0.009303 0.000000 0.000000 0.000000 0.014956 # 7 # Note: Non crystallographic symmetry RMS plot The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined. In the TeX file, a plot has been inserted here Chain identifiers of the two chains: A and B All-atom RMS fit for the two chains : 0.481 CA-only RMS fit for the two chains : 0.125 # 8 # Note: Non crystallographic symmetry backbone difference plot The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined. In the TeX file, a plot has been inserted here Chain identifiers of the two chains: A and B # 9 # Warning: New symmetry found Independent molecules in the asymmetric unit actually look like symmetry relatives. This fact needs manual checking. # 10 # Warning: Problem detected upon counting molecules and matrices The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file. Space group as read from CRYST card: P 1 21 1 Number of matrices in space group: 2 Highest polymer chain multiplicity in structure: 2 Highest polymer chain multiplicity according to SEQRES: 1 No explicit MTRIX NCS matrices found in the input file Value of Z as found on the CRYST1 card: 0 Polymer chain multiplicity and SEQRES multiplicity disagree 2 1 Z agrees neither with the 3D multiplicity, nor with the SEQRES multiplicity It could be that Z must be one of: 2 4 # 11 # Warning: Matthews Coefficient (Vm) high The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that. Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures). Molecular weight of all polymer chains: 98160.297 Volume of the Unit Cell V= 424975.656 Space group multiplicity: 2 No NCS symmetry matrices (MTRIX records) found in PDB file Matthews coefficient for observed atoms and Z is high: Vm= 4.329 No Matthews coefficient given in REMARK 280 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult. (and the absence of MTRIX records doesn't help) Could it be that Z must be: 2 This number is the multiplication of the spacegroup and NCS symmetry count Matthews coefficient for observed atoms and corrected Z: Vm= 2.165 # 12 # Note: All atoms are sufficiently far away from symmetry axes None of the atoms in the structure is closer than 0.77 Angstrom to a proper symmetry axis. # 13 # Note: Chain identifiers OK WHAT CHECK has not detected any serious chain identifier problems. But be aware that WHAT CHECK doesn't care about the chain identifiers of waters. # 14 # Warning: Ligands or residues without topology The entities (non-canonical residues or ligands) in the table below are too complicated for the automatic topology determination. WHAT IF / WHAT CHECK can use a series of tools to automatically generate topology information for ligands. Some molecules are too complicated for these tools. If that happens, WHAT IF / WHAT CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities. WHAT CHECK first tries to obtain the ligand topology using the Refmac ligand library. It can also use a local copy of that library, and that copy can contain hand-made topology entries. 866 XYP ( 528-) C - Unknown 867 XYP ( 529-) C - Unknown 868 XYP ( 528-) E - Unknown 869 XYP ( 529-) E - Unknown # 15 # Warning: Covalently bound ligands The ligands in this table are covalently bound to something else. It is already difficult to automatically generate topologies for ligands, but when they are covalently bound to something it becomes even more complicated to do everything right. So, if you get weird error messages that seem related to this covalent bond, then please feel free to ignore those, or even better, make a topology entry by hand. The comment `Other ligand` indicates that the covalent bond is to another ligand. In that case you might want to convert the two ligands into one bigger ligand. 866 XYP ( 528-) C - Other ligand 867 XYP ( 529-) C - Other ligand 868 XYP ( 528-) E - Other ligand 869 XYP ( 529-) E - Other ligand # 16 # Warning: Strange inter-chain connections detected The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file. Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible. 599 GLU ( 195-) B - OE2 866 XYP ( 528-) C - O1 # 17 # Note: Strange inter-chain connections corrected Chain identifiers modified to improve future validation options. For the residues listed below, WHAT CHECK thinks that it could 'improve' the chain-name. Often WHAT CHECK is rather smart about this, but if you find strange error messages related to this ligand, or related to the residues listed in the previous section that it is bound to, then you better fix the chain identifiers yourself, and run the validation again. 866 XYP ( 528-) B -C Id: CORCNEU # 18 # Note: No duplicate atom names in ligands All atom names in ligands (if any) seem adequately unique. # 19 # Warning: Alternate atom problems The residues listed in the table below have alternate atoms that do not follow normal logic (like the first of the atoms gets label A and has the highest occupancy). Residues listed here have at least one such problem. The Note Mixed means that the the best solution found by WHAT CHECK has mixed alternate atom labels. If the Note contains Occupancy, then at in at least one case does the not-used alternate atom have a higher occupancy then the one used. Corrected in the Note means that WHAT CHECK found a solution, but that does not mean it is guaranteed solved. If you find weird problems for this residue later-on in the report, especially when those are rotamer or bump related, please look at this residue in the PDB file itself, solve the problem by hand, and run WHAT CHECK again. 402 LEU ( 430-) A - Corrected # 20 # Note: No residues detected inside ligands Either this structure does not contain ligands with amino acid groups inside it, or their naming is proper (enough). # 21 # Warning: Groups attached to potentially hydrogen-bonding atoms Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT CHECK is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogen-bonding related analyses of these residues might be in error. 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. 599 GLU ( 195-) B - OE2 bound to 866 XYP ( 528-) B -C O1 # 22 # Note: No probable side chain atoms with zero occupancy detected. Either there are no side chain atoms with zero occupancy, or the side chain atoms with zero occupancy were not present in the input PDB file (in which case they are listed as missing atoms), or their positions are sufficiently improbable to warrant a zero occupancy. # 23 # Note: No probable backbone atoms with zero occupancy detected. Either there are no backbone atoms with zero occupancy, or the backbone atoms with zero occupancy were left out of the input PDB file (in which case they are listed as missing atoms), or their positions are sufficiently improbable to warrant a zero occupancy. # 24 # Note: All residues have a complete backbone. No residues have missing backbone atoms. # 25 # Note: No C-alpha only residues There are no residues that consist of only an alpha carbon atom. # 26 # Note: Content of the PDB file as interpreted by WHAT CHECK Content of the PDB file as interpreted by WHAT CHECK. WHAT CHECK has read your PDB file, and stored it internally in what is called 'the soup'. The content of this soup is listed here. An extensive explanation of all frequently used WHAT CHECK output formats can be found at swift.cmbi.ru.nl. Look under output formats. A course on reading this 'Molecules' table is part of the WHAT CHECK website. 1 1 ( 29) 433 ( 461) A Protein /zata/tempdir/7n6... 2 434 ( 30) 865 ( 461) B Protein /zata/tempdir/7n6... 3 866 ( 528) 866 ( 528) B XYP <= /zata/tempdir/7n6... 4 867 ( 529) 867 ( 529) C XYP <- /zata/tempdir/7n6... 5 868 ( 528) 868 ( 528) E XYP <- /zata/tempdir/7n6... 6 869 ( 529) 869 ( 529) E XYP <- /zata/tempdir/7n6... 7 870 ( 501) 870 ( 501) A CL /zata/tempdir/7n6... 8 871 ( 502) 871 ( 502) A CL /zata/tempdir/7n6... 9 872 ( 503) 872 ( 503) A CL /zata/tempdir/7n6... 10 873 ( 504) 873 ( 504) A CL /zata/tempdir/7n6... 11 874 ( 505) 874 ( 505) A CL /zata/tempdir/7n6... 12 875 ( 506) 875 ( 506) A CL /zata/tempdir/7n6... 13 876 ( 501) 876 ( 501) B CL /zata/tempdir/7n6... 14 877 ( 502) 877 ( 502) B CL /zata/tempdir/7n6... 15 878 ( 503) 878 ( 503) B CL /zata/tempdir/7n6... 16 879 ( 504) 879 ( 504) B CL /zata/tempdir/7n6... 17 880 ( 505) 880 ( 505) B CL /zata/tempdir/7n6... 18 881 ( HOH ) 881 ( HOH ) A water ( 327) /zata/tempdir/7n6... 19 882 ( HOH ) 882 ( HOH ) B water ( 297) /zata/tempdir/7n6... MODELs skipped upon reading PDB file: 0 X-ray structure. No MODELs found The total number of amino acids found is 865. No nucleic acids observed in input file No sugars recognized in input file Number of water molecules: 624 Residue numbers increase monotonously OK # 27 # Note: Chain identifiers seem OK All ions seem to have a logical chain identifier, or there are no ions present in the input file. ERROR. File not found: TAPEOUT.DAT ERROR. File not found: TAPEOUT.DAT # 28 # Note: Ramachandran plot In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus-signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands. 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 [REF]. In the TeX file, a plot has been inserted here Chain identifier: A # 29 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Chain identifier: B # 30 # Note: Secondary structure This is the secondary structure according to DSSP. Only helix (H), overwound or 3/10-helix (3), strand (S), turn (T) and coil (blank) are shown [REF]. All DSSP related information can be found at swift.cmbi.ru.nl/gv/dssp/ This is not really a structure validation option, but a very scattered secondary structure (i.e. many strands of only a few residues length, many Ts inside helices, etc) tends to indicate a poor structure. A full explanation of the DSSP secondary structure determination program together with a series of examples can be found at the WHAT CHECK website [REF]. Secondary structure assignment 10 20 30 40 50 60 | | | | | | 1 - 60 ASTVTVDWDTTYQTIDGFGVSEAFHQSNNIARLGETKQNEIYDLLFSTTDGAGFSIFRSI ( 29)-( 88) 70 80 90 100 110 120 | | | | | | 61 - 120 LGDGGTWGNADDGPNKTMQPAEDVWDWNESNDDQIPMIRAIQSKYGVDQILYTVWSPPAW ( 89)-( 148) 130 140 150 160 170 180 | | | | | | 121 - 180 MKTNGSVVGGSLRTDKYQAYATYLAEHIKNYKSKFGIEITHIGIQNEPNLETSYSSCRWS ( 149)-( 208) 190 200 210 220 230 240 | | | | | | 181 - 240 PEELRIFMRDYLVPTFDKENITAKVVFAENMSFNEQYAINSLNDPIAVKRVDIVGAHNYG ( 209)-( 268) 250 260 270 280 290 300 | | | | | | 241 - 300 SSYIPFTTTKSKGKGIWMTEVSDMNGNDTTINDGLRWAKEIHDFMTITEGNAWFYWWGAC ( 269)-( 328) 310 320 330 340 350 360 | | | | | | 301 - 360 FKTYNGEGLIQMDLNSKTYKVAKRLYTIGQFSRFIRPGWQRIEATKNPVSNVYVTAYKDP ( 329)-( 388) 370 380 390 400 410 420 | | | | | | 361 - 420 KTGKFAIVAINNGWSKQSITYTLKGFSPASVTPYTTSSTQNLEKGSDITVNNSSFSFELA ( 389)-( 448) 430 | 421 - 433 PNSITTFVGDTES ( 449)-( 461) 440 450 460 470 480 490 | | | | | | 434 - 493 STVTVDWDTTYQTIDGFGVSEAFHQSNNIARLGETKQNEIYDLLFSTTDGAGFSIFRSIL ( 30)-( 89) 500 510 520 530 540 550 | | | | | | 494 - 553 GDGGTWGNADDGPNKTMQPAEDVWDWNESNDDQIPMIRAIQSKYGVDQILYTVWSPPAWM ( 90)-( 149) 560 570 580 590 600 610 | | | | | | 554 - 613 KTNGSVVGGSLRTDKYQAYATYLAEHIKNYKSKFGIEITHIGIQNEPNLETSYSSCRWSP ( 150)-( 209) 620 630 640 650 660 670 | | | | | | 614 - 673 EELRIFMRDYLVPTFDKENITAKVVFAENMSFNEQYAINSLNDPIAVKRVDIVGAHNYGS ( 210)-( 269) 680 690 700 710 720 730 | | | | | | 674 - 733 SYIPFTTTKSKGKGIWMTEVSDMNGNDTTINDGLRWAKEIHDFMTITEGNAWFYWWGACF ( 270)-( 329) 740 750 760 770 780 790 | | | | | | 734 - 793 KTYNGEGLIQMDLNSKTYKVAKRLYTIGQFSRFIRPGWQRIEATKNPVSNVYVTAYKDPK ( 330)-( 389) 800 810 820 830 840 850 | | | | | | 794 - 853 TGKFAIVAINNGWSKQSITYTLKGFSPASVTPYTTSSTQNLEKGSDITVNNSSFSFELAP ( 390)-( 449) 860 | 854 - 865 NSITTFVGDTES ( 450)-( 461) # 31 # Note: No rounded coordinates detected No significant rounding of atom coordinates has been detected. # 32 # Note: No artificial side chains detected No artificial side-chain positions characterized by chi-1=0.0 or chi-1=180.0 have been detected. # 33 # Note: No missing atoms detected in residues All expected atoms are present in residues. This validation option has not looked at 'things' that can or should be attached to the elementary building blocks (amino acids, nucleotides). Even the C-terminal oxygens are treated separately. # 34 # Note: All B-factors fall in the range 0.0 - 100.0 All B-factors are larger than zero, and none are observed above 100.0. # 35 # Note: C-terminus capping The residues listed in the table below are either C-terminal or pseudo C-terminal (i.e. last residue before a missing residue). 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 often see from the residue numbers if there are missing residues; 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. If this happened, the label -N is added to the pseudo C-terminus. Other labels can be +X in case something weird is bound to the backbone C, or +OXT if a spurious OXT atom is found. -OXT indicates that an expected OXT is missing. 'Swap' means that the O' and O'' (O and OXT in PDB files) have been swapped in terms of nomenclature. 'Bad' means that something bad happened that WHAT IF does not understand. In such cases you might get three residue numbers in square brackets; one of those might be what WHAT IF had expected to find, but then it also might not). In case of chain breaks the number of missing residues is listen in round brackets. OK means what it suggests... Be aware that we cannot easily see the difference between these errors and errors in the chain and residue numbering schemes. So do not blindly trust the table below. If you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or a removed single N is the cause. Also, many peptidic ligands get the same chain identifier as the larger protein they are bound to. In such cases there are more than one C-termini and OXTs with the same ID. WHAT IF gives some random warnings about these cases. So, don't take everything at face value, but think for yourself. 433 SER ( 461-) A - OK 865 SER ( 461-) B - OK # 36 # Note: Weights administratively correct All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which makes them administratively correct. # 37 # Note: Normal distribution of occupancy values The distribution of the occupancy values in this file seems 'normal'. Be aware that this evaluation is merely the result of comparing this file with about 500 well-refined high-resolution files in the PDB. If this file has much higher or much lower resolution than the PDB files used in WHAT CHECK's training set, non-normal values might very well be perfectly fine, or normal values might actually be not so normal. So, this check is actually more an indicator and certainly not a check in which I have great confidence. # 38 # Note: All occupancies seem to add up to 0.0 - 1.0. In principle, the occupancy of all alternates of one atom should add up till 0.0 - 1.0. 0.0 is used for the missing atom (i.e. an atom not seen in the electron density). Obviously, there is nothing terribly wrong when a few occupancies add up to a bit more than 1.0, because the mathematics of refinement allow for that. However, if it happens often, it seems worth evaluating this in light of the refinement protocol used. # 39 # Warning: What type of B-factor? WHAT CHECK does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT CHECK complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first. Number of TLS groups mentione in PDB file header: 0 Temperature not mentioned in PDB file. This most likely means that the temperature record is absent. Room temperature assumed # 40 # Note: Number of buried atoms with low B-factor is OK For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0. In liquid nitrogen this percentage is allowed to be higher, of course. Percentage of buried atoms with B less than 5 : 0.00 # 41 # Note: B-factor distribution normal The distribution of B-factors within residues is within expected ranges. A value over 1.5 here would mean that the B-factors show signs of over-refinement. RMS Z-score : 0.584 over 6188 bonds Average difference in B over a bond : 1.30 RMS difference in B over a bond : 1.82 # 42 # Note: B-factor plot The average atomic B-factor per residue is plotted as function of the residue number. In the TeX file, a plot has been inserted here Chain identifier: A # 43 # Note: B-factor plot In the TeX file, a plot has been inserted here Chain identifier: B # 44 # Note: Introduction to the nomenclature section. Nomenclature problems seem, at first, rather unimportant. After all who cares if we call the delta atoms in leucine delta2 and delta1 rather than the other way around. Chemically speaking that is correct. But structures have not been solved and deposited just for chemists to look at them. Most times a structure is used, it is by software in a bioinformatics lab. And if they compare structures in which the one used C delta1 and delta2 and the other uses C delta2 and delta1, then that comparison will fail. Also, we recalculate all structures every so many years to make sure that everybody always can get access to the best coordinates that can be obtained from the (your?) experimental data. These recalculations will be troublesome if there are nomenclature problems. Several nomenclature problems actually are worse than that. At the WHAT CHECK website [REF] you can get an overview of the importance of all nomenclature problems that we list. # 45 # Note: Valine nomenclature OK No errors were detected in valine nomenclature. # 46 # Note: Threonine nomenclature OK No errors were detected in threonine nomenclature. # 47 # Note: Isoleucine nomenclature OK No errors were detected in isoleucine nomenclature. # 48 # Note: Leucine nomenclature OK No errors were detected in leucine nomenclature. # 49 # Note: Arginine nomenclature OK No errors were detected in arginine nomenclature. # 50 # Note: Tyrosine torsion conventions OK No errors were detected in tyrosine torsion angle conventions. # 51 # Note: Phenylalanine torsion conventions OK No errors were detected in phenylalanine torsion angle conventions. # 52 # Note: Aspartic acid torsion conventions OK No errors were detected in aspartic acid torsion angle conventions. # 53 # Note: Glutamic acid torsion conventions OK No errors were detected in glutamic acid torsion angle conventions. # 54 # Note: Phosphate group names OK in DNA/RNA No errors were detected in nucleic acid phosphate group naming conventions (or this structure contains no nucleic acids). # 55 # Note: Heavy atom naming OK No errors were detected in the atom names for non-hydrogen atoms. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids. # 56 # Note: No decreasing residue numbers All residue numbers are strictly increasing within each chain. # 57 # Note: All bond lengths OK All bond lengths are in agreement with standard bond lengths using a tolerance of 4 sigma (both standard values and sigma for amino acids have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). # 58 # Warning: Low bond length variability Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. 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 lengths: 0.502 RMS-deviation in bond distances: 0.013 # 59 # Note: No bond length directionality Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA does not show significant systematic deviations. # 60 # 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. 69 ASN ( 97-) A - CA CB CG 117.31 4.7 71 ASP ( 99-) A - CA CB CG 117.07 4.5 93 ASP ( 121-) A - CA CB CG 117.09 4.5 135 ASP ( 163-) A - CA CB CG 118.22 5.6 246 PHE ( 274-) A - CA CB CG 118.52 4.7 294 PHE ( 322-) A - CA CB CG 119.76 6.0 347 ASN ( 375-) A - CA CB CG 117.06 4.5 386 PHE ( 414-) A - CA CB CG 119.03 5.2 482 ASP ( 78-) B - CA CB CG 116.64 4.0 503 ASP ( 99-) B - CA CB CG 118.02 5.4 567 ASP ( 163-) B - CA CB CG 117.96 5.4 629 ASP ( 225-) B - CA CB CG 116.95 4.4 678 PHE ( 274-) B - CA CB CG 117.97 4.2 726 PHE ( 322-) B - CA CB CG 120.11 6.3 745 ASP ( 341-) B - CA CB CG 117.09 4.5 818 PHE ( 414-) B - CA CB CG 119.73 5.9 # 61 # Note: Normal bond angle variability Bond angles were found to deviate normally from the mean 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, and this is indeed observed for very high resolution X-ray structures. RMS Z-score for bond angles: 0.775 RMS-deviation in bond angles: 1.435 # 62 # Note: Residue hand check OK No atoms are observed that have the wrong handedness. Be aware, though, that WHAT CHECK might have corrected the handedness of some atoms already. The handedness has not been corrected for any case where the problem is worse than just an administrative discomfort. # 63 # Note: Chirality OK All protein atoms have proper chirality, or there is no intact protein present in the PDB file. The average deviation= 0.959 # 64 # Note: Improper dihedral angle distribution OK The RMS Z-score for all improper dihedrals in the structure is within normal ranges. Improper dihedral RMS Z-score : 0.826 # 65 # Note: Tau angles OK All of the tau angles (N-C-alpha-C) of amino acids fall within expected RMS deviations. # 66 # Note: Normal tau angle deviations The RMS Z-score for the tau angles (N-C-alpha-C) in the structure falls within the normal range that we guess to be 0.5 - 1.5. Be aware, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers. Tau angle RMS Z-score : 0.859 # 67 # Note: Side chain planarity OK All of the side chains of residues that have an intact planar group are planar within expected RMS deviations. # 68 # Note: Atoms connected to aromatic rings OK All of the atoms that are connected to planar aromatic rings in side chains of amino-acid residues are in the plane within expected RMS deviations. Since there is no DNA and no protein with hydrogens, no uncalibrated planarity check was performed. # 69 # Warning: Ramachandran Z-score low The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low. Ramachandran Z-score : -3.208 # 70 # Note: Ramachandran check The list contains per-residue Z-scores describing how well each residue fits into the allowed areas of the Ramachandran plot will not be printed because WHAT CHECK found no reason to cry. # 71 # Warning: Torsion angle evaluation shows unusual residues The residues listed in the table below contain bad or abnormal torsion angles. 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 CHECK 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. 402 LEU ( 430-) A - -2.7 733 PHE ( 329-) B - -2.4 301 PHE ( 329-) A - -2.4 693 VAL ( 289-) B - -2.2 261 VAL ( 289-) A - -2.2 349 VAL ( 377-) A - -2.2 345 THR ( 373-) A - -2.2 781 VAL ( 377-) B - -2.2 845 SER ( 441-) B - -2.1 456 PHE ( 52-) B - -2.0 # 72 # Warning: Backbone evaluation reveals unusual conformations The residues listed in the table below have abnormal backbone torsion angles. 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. 12 TYR ( 40-) A - Poor phi/psi 17 GLY ( 45-) A - Poor phi/psi 24 PHE ( 52-) A - Poor phi/psi 25 HIS ( 53-) A - Poor phi/psi 34 GLY ( 62-) A - Poor phi/psi 45 LEU ( 73-) A - omega poor 53 GLY ( 81-) A - Poor phi/psi 61 LEU ( 89-) A - omega poor 64 GLY ( 92-) A - Poor phi/psi 68 GLY ( 96-) A - Poor phi/psi 73 GLY ( 101-) A - Poor phi/psi, omega to (next) 79 GLN ( 107-) A - Omega to (next) Pro poor 84 VAL ( 112-) A - omega poor 95 ILE ( 123-) A - Omega to (next) Pro poor 106 GLY ( 134-) A - Poor phi/psi And so on for a total of 100 lines. # 73 # Error: Chi-1/chi-2 rotamer problems List of residues with a poor chi-1/chi-2 combination. Be aware that for this validation option the individual scores are far less important than the overall score that is given below the table. 61 LEU ( 89-) A - -1.30 325 LEU ( 353-) A - -1.32 402 LEU ( 430-) A - -1.31 493 LEU ( 89-) B - -1.30 757 LEU ( 353-) B - -1.32 43 ASP ( 71-) A - -1.22 111 LEU ( 139-) A - -1.27 170 LEU ( 198-) A - -1.21 186 ILE ( 214-) A - -1.25 192 LEU ( 220-) A - -1.30 273 ASP ( 301-) A - -1.24 424 ILE ( 452-) A - -1.21 465 LEU ( 61-) B - -1.20 475 ASP ( 71-) B - -1.22 543 LEU ( 139-) B - -1.27 And so on for a total of 308 lines. # 74 # Note: chi-1/chi-2 angle correlation Z-score OK The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is within expected ranges for well-refined structures. chi-1/chi-2 correlation Z-score : -1.528 # 75 # Warning: Unusual rotamers The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database. 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. 458 GLN ( 54-) B - 0.35 787 THR ( 383-) B - 0.35 228 VAL ( 256-) A - 0.35 26 GLN ( 54-) A - 0.36 103 SER ( 131-) A - 0.36 535 SER ( 131-) B - 0.37 120 TRP ( 148-) A - 0.37 660 VAL ( 256-) B - 0.38 552 TRP ( 148-) B - 0.38 238 ASN ( 266-) A - 0.38 355 THR ( 383-) A - 0.39 789 TYR ( 385-) B - 0.39 # 76 # Warning: Unusual backbone conformations For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre. 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, especially if a regular DSSP secondary structure (H or S for helix or strand, respectively) is indicated! 25 HIS ( 53-) A - 0 128 VAL ( 156-) A - 0 174 TYR ( 202-) A - 0 207 PHE ( 235-) A - 0 213 PHE ( 241-) A - 0 457 HIS ( 53-) B - 0 560 VAL ( 156-) B - 0 606 TYR ( 202-) B - 0 639 PHE ( 235-) B - 0 645 PHE ( 241-) B - 0 729 TRP ( 325-) B - 0 67 TRP ( 95-) A - 1 72 ASP ( 100-) A - 1 296 TRP ( 324-) A - 1 499 TRP ( 95-) B - 1 504 ASP ( 100-) B - 1 607 SER ( 203-) B - 1 728 TRP ( 324-) B - 1 12 TYR ( 40-) A - 2 23 ALA ( 51-) A - 2 52 ALA ( 80-) A - 2 175 SER ( 203-) A - 2 297 TRP ( 325-) A - 2 444 TYR ( 40-) B - 2 484 ALA ( 80-) B - 2 833 ASN ( 429-) B - 2 # 77 # Note: Backbone conformation Z-score OK The backbone conformation analysis gives a score that is normal for well refined protein structures. Backbone conformation Z-score : -0.634 # 78 # Note: Omega angle restraint OK The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation agrees with this expectation. Omega average and std. deviation= 179.070 6.349 # 79 # Warning: Unusual PRO puckering amplitudes The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF] 118 PRO ( 146-) A - 0.14 LOW 194 PRO ( 222-) A - 0.19 LOW 550 PRO ( 146-) B - 0.11 LOW 626 PRO ( 222-) B - 0.17 LOW # 80 # Warning: Unusual PRO puckering phases The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]. 393 PRO ( 421-) A - -64.4 envelop C-beta (-72 degrees) # 81 # Warning: Backbone oxygen evaluation The residues listed in the table below have an unusual backbone oxygen position. For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT CHECK database with superposable C-alpha coordinates, and some restraints 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! 494 GLY ( 90-) B - 1.97 27 62 GLY ( 90-) A - 1.93 32 # 82 # Note: Peptide bond conformations There was no need to complain about the peptide bond of a single amino acid. # 83 # Error: Abnormally short interatomic distances The pairs of atoms listed in the table below have an unusually short 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. The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome. It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error. Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead. 868 XYP ( 528-) E - C4 <--> 869 XYP ( 529-) E - C1 0.48 2.52 INTRA 167 GLU ( 195-) A - OE2 <--> 868 XYP ( 528-) E - O1 0.36 2.04 INTRA 339 TRP ( 367-) A - NE1 <--> 870 CL ( 501-) A - CL 0.29 2.81 INTRA 167 GLU ( 195-) A - CD <--> 868 XYP ( 528-) E - O1 0.27 2.53 INTRA 866 XYP ( 528-) B - C4 <--> 867 XYP ( 529-) C - C1 0.27 2.73 INTRA 324 ARG ( 352-) A - NH2 <--> 875 CL ( 506-) A - CL 0.23 2.87 INTRA 868 XYP ( 528-) E - O4 <--> 869 XYP ( 529-) E - C2 0.23 2.47 INTRA 756 ARG ( 352-) B - N <--> 878 CL ( 503-) B - CL 0.21 2.89 INTRA 260 GLU ( 288-) A - OE2 <--> 868 XYP ( 528-) E - C1 0.19 2.61 INTRA 614 GLU ( 210-) B - OE2 <--> 617 ARG ( 213-) B - NH2 0.17 2.53 INTRA 182 GLU ( 210-) A - OE2 <--> 185 ARG ( 213-) A - NH2 0.16 2.54 INTRA 43 ASP ( 71-) A - OD2 <--> 50 ASP ( 78-) A - CG 0.16 2.64 INTRA 609 CYS ( 205-) B - N <--> 876 CL ( 501-) B - CL 0.16 2.94 INTRA 692 GLU ( 288-) B - OE2 <--> 866 XYP ( 528-) B - C1 0.14 2.66 INTRA 43 ASP ( 71-) A - OD2 <--> 50 ASP ( 78-) A - OD1 0.14 2.26 INTRA And so on for a total of 49 lines. # 84 # Note: Some notes regarding these bumps The bumps have been binned in 5 categories ranging from 'please look at' till 'must fix'. Additionally, the integrated sum of all bumps, the squared sum of all bumps, and these latter two values normalized by the number of contacts are listed too for comparison purposes between, for example, small and large proteins. Total bump value: 5.771 Total bump value per residue: 0.057 Total number of bumps: 49 Total squared bump value: 1.135 Total number of bumps in the mildest bin: 44 Total number of bumps in the second bin: 5 Total number of bumps in the middle bin: 0 Total number of bumps in the fourth bin: 0 Total number of bumps in the worst bin: 0 # 85 # Note: Inside/outside distribution check The following list contains per-residue Z-scores describing how well the residue's observed accessibility fits the expected one. A positive Z-score indicates "more exposure than usual", whereas a negative Z-score means "more buried than usual". The absolute value of the Z-score must be used to judge the quality. Today WHAT CHECK saw no reason to complain. # 86 # Note: Inside/Outside residue distribution normal The distribution of residue types over the inside and the outside of the protein is normal. inside/outside RMS Z-score : 0.958 # 87 # Note: Inside/Outside RMS Z-score plot The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns. In the TeX file, a plot has been inserted here Chain identifier: A # 88 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Chain identifier: B # 89 # 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. 696 MET ( 292-) B - -6.07 264 MET ( 292-) A - -5.97 736 TYR ( 332-) B - -5.71 793 LYS ( 389-) B - -5.60 361 LYS ( 389-) A - -5.59 432 GLU ( 460-) A - -5.32 864 GLU ( 460-) B - -5.26 374 TRP ( 402-) A - -5.25 32 ARG ( 60-) A - -5.17 464 ARG ( 60-) B - -5.15 610 ARG ( 206-) B - -5.14 # 90 # Note: No series of residues with bad packing environment There are no stretches of three or more residues each having a packing score worse than -4.0. # 91 # Note: Structural average packing environment OK The structural average packing score is within normal ranges. Average for range 1 - 865 : 0.022 # 92 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing. In the TeX file, a plot has been inserted here Chain identifier: A # 93 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing. In the TeX file, a plot has been inserted here Chain identifier: B # 94 # 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. 336 ARG ( 364-) A - -2.89 768 ARG ( 364-) B - -2.79 # 95 # Note: No series of residues with abnormal new packing environment There are no stretches of four or more residues each having a packing Z-score worse than -1.75. ERROR. File not found: TAPEOUT.DAT ERROR. File not found: TAPEOUT.DAT # 96 # Note: Second generation quality Z-score plot The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing. In the TeX file, a plot has been inserted here Chain identifier: A # 97 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Chain identifier: B # 98 # Warning: No crystallisation information No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally. # 99 # Error: Water clusters without contacts with non-water atoms The water molecules listed in the table below are part of water molecule clusters that do not make contacts with non-waters. These water molecules are part of clusters that have a distance at least 1 Angstrom larger than the sum of the Van der Waals radii to the nearest non-solvent atom. Because these kinds of water clusters usually are not observed with X-ray diffraction their presence could indicate a refinement artifact. The number in brackets is the identifier of the water molecule in the input file. 881 HOH ( 931 ) A - O 881 HOH ( 933 ) A - O # 100 # Note: No waters need moving All water molecules are sufficiently close to the asymmetric unit given in the input file. # 101 # 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. 881 HOH ( 605 ) A - O 881 HOH ( 876 ) A - O 881 HOH ( 914 ) A - O 881 HOH ( 920 ) A - O 881 HOH ( 933 ) A - O 882 HOH ( 880 ) B - O 882 HOH ( 892 ) B - O 882 HOH ( 894 ) B - O 882 HOH ( 899 ) B - O 882 HOH ( 903 ) B - O # 102 # Error: His, Asn, Gln side chain flips Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors. 400 GLN ( 428-) A - 411 ASN ( 439-) A - 457 HIS ( 53-) B - 460 ASN ( 56-) B - 570 GLN ( 166-) B - 598 ASN ( 194-) B - 632 ASN ( 228-) B - 772 GLN ( 368-) B - # 103 # Note: Histidine type assignments For all complete HIS residues in the structure a tentative assignment to HIS-D (protonated on ND1), HIS-E (protonated on NE2), or HIS-H (protonated on both ND1 and NE2, positively charged) is made based on the hydrogen bond network. A second assignment is made based on which of the Engh and Huber [REF] histidine geometries fits best to the structure. In the table below all normal histidine residues are listed. The assignment based on the geometry of the residue is listed first, together with the RMS Z-score for the fit to the Engh and Huber parameters. For all residues where the H-bond assignment is different, the assignment is listed in the last columns, together with its RMS Z-score to the Engh and Huber parameters. As always, the RMS Z-scores should be close to 1.0 if the residues were restrained to the Engh and Huber parameters during refinement, and if enough (high resolution) data is available. Please note that because the differences between the geometries of the different types are small it is possible that the geometric assignment given here does not correspond to the type used in refinement. This is especially true if the RMS Z-scores are much higher than 1.0. If the two assignments differ, or the `geometry' RMS Z-score is high, it is advisable to verify the hydrogen bond assignment, check the HIS type used during the refinement and possibly adjust it. 25 HIS ( 53-) A - HIS-D 0.81 HIS-H 1.05 147 HIS ( 175-) A - HIS-E 0.69 HIS-D 1.26 161 HIS ( 189-) A - HIS-E 0.84 HIS-D 1.14 237 HIS ( 265-) A - HIS-E 0.70 HIS-D 0.89 282 HIS ( 310-) A - HIS-D 0.72 457 HIS ( 53-) B - HIS-D 0.63 579 HIS ( 175-) B - HIS-E 0.32 HIS-D 0.88 593 HIS ( 189-) B - HIS-E 0.59 HIS-H 0.94 669 HIS ( 265-) B - HIS-H 0.47 HIS-E 0.69 714 HIS ( 310-) B - HIS-D 0.70 # 104 # Warning: Buried unsatisfied hydrogen bond donors The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network. 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. 77 THR ( 105-) A - OG1 93 ASP ( 121-) A - N 109 GLN ( 137-) A - N 113 THR ( 141-) A - OG1 115 TRP ( 143-) A - NE1 160 THR ( 188-) A - OG1 172 THR ( 200-) A - OG1 208 ALA ( 236-) A - N 220 ASN ( 248-) A - N 232 ASP ( 260-) A - N 241 SER ( 269-) A - N 243 TYR ( 271-) A - OH 244 ILE ( 272-) A - N 261 VAL ( 289-) A - N 262 SER ( 290-) A - N And so on for a total of 38 lines. # 105 # Warning: Buried unsatisfied hydrogen bond acceptors The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network. 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. 72 ASP ( 100-) A - OD1 454 GLU ( 50-) B - OE1 461 ASN ( 57-) B - OD1 504 ASP ( 100-) B - OD1 669 HIS ( 265-) B - ND1 # 106 # Note: Some notes regarding these donors and acceptors The donors and acceptors have been counted, also as function of their accessibility. The buried donors and acceptors have been binned in five categories ranging from not forming any hydrogen bond till forming a poor till perfect hydrogen bond. Obviously, the buried donors and acceptors with no or just a poor hydrogen bond should be a topic of concern. As every protein contains more acceptors than donors, unsatisfied donors are more in need of attention than unsatisfied acceptors. Total number of donors: 1296 - of which buried: 752 Total number of acceptors: 1376 - of which buried: 648 Total number of donor+acceptors: 200 (e.g. the Ser Ogamma that can donate and accept) - of which buried: 58 Buried donors: 752 - without H-bond: 37 - essentially without H-bond: 0 - with only a very poor H-bond: 1 - with a poor H-bond: 13 - with a H-bond: 701 Buried acceptors: 648 - without H-bond: 76 - essentially without H-bond: 0 - with only a very poor H-bond: 3 - with a poor H-bond: 16 - with a H-bond: 553 # 107 # Note: Content of the PDB file as interpreted by WHAT CHECK Content of the PDB file as interpreted by WHAT CHECK. WHAT CHECK has read your PDB file, and stored it internally in what is called 'the soup'. The content of this soup is listed here. An extensive explanation of all frequently used WHAT CHECK output formats can be found at swift.cmbi.ru.nl. Look under output formats. A course on reading this 'Molecules' table is part of the WHAT CHECK website. 1 1 ( 29) 433 ( 461) A Protein /zata/tempdir/7n6... 2 434 ( 30) 865 ( 461) B Protein /zata/tempdir/7n6... 3 866 ( 528) 866 ( 528) B XYP <= /zata/tempdir/7n6... 4 867 ( 529) 867 ( 529) C XYP <- /zata/tempdir/7n6... 5 868 ( 528) 868 ( 528) E XYP <- /zata/tempdir/7n6... 6 869 ( 529) 869 ( 529) E XYP <- /zata/tempdir/7n6... 7 870 ( 501) 870 ( 501) A CL /zata/tempdir/7n6... 8 871 ( 502) 871 ( 502) A CL /zata/tempdir/7n6... 9 872 ( 503) 872 ( 503) A CL /zata/tempdir/7n6... 10 873 ( 504) 873 ( 504) A CL /zata/tempdir/7n6... 11 874 ( 505) 874 ( 505) A CL /zata/tempdir/7n6... 12 875 ( 506) 875 ( 506) A CL /zata/tempdir/7n6... 13 876 ( 501) 876 ( 501) B CL /zata/tempdir/7n6... 14 877 ( 502) 877 ( 502) B CL /zata/tempdir/7n6... 15 878 ( 503) 878 ( 503) B CL /zata/tempdir/7n6... 16 879 ( 504) 879 ( 504) B CL /zata/tempdir/7n6... 17 880 ( 505) 880 ( 505) B CL /zata/tempdir/7n6... 18 881 ( HOH ) 881 ( HOH ) A water ( 327) /zata/tempdir/7n6... 19 882 ( HOH ) 882 ( HOH ) B water ( 297) /zata/tempdir/7n6... # 108 # Note: Summary report This is an overall summary of the quality of the structure as compared with current reliable structures. Numbers in brackets are the average and standard deviation observed for a large number of files determined with a similar resolution. The second table mostly gives an impression of how well the model conforms to common refinement restraint values. These numbers are less than 1.0 if the spread in data is too little, and larger than 1.0 when the spread is too large. The former does not need to be a problem, the latter always is bad. Structure Z-scores, positive is better than average: Resolution read from PDB file : 1.500 1st generation packing quality : 1.305 ( ( 0.0, 2.5)) 2nd generation packing quality : -0.602 ( ( -1.0, 1.4)) Ramachandran plot appearance : -3.208 (poor ( -0.2, 1.2)) chi-1/chi-2 rotamer normality : -1.528 ( ( -1.0, 1.3)) Backbone conformation : -0.634 ( ( -0.1, 2.6)) Inside/Outside distribution : 0.958 RMS Z-scores, should be close to 1.0: Bond lengths : 0.502 (tight) Bond angles : 0.775 Omega angle restraints : 1.154 Side chain planarity : 0.985 Improper dihedral distribution : 0.826 B-factor distribution : 0.584 # 109 # Note: Introduction to refinement recommendations First, be aware that the recommendations for crystallographers listed below are produced by a computer program that was written by a guy who got his PhD in NMR... We have tried to convert the messages written in this report into a small set of things you can do with your refinement software to get a better structure. The things you should do first are listed first. And in some cases you should first fix that problem, then refine a bit further, and then run WHAT CHECK again before looking at other problems. If, for example, WHAT CHECK has found a problem with the SCALE and CRYST cards, then you must first fix that problem, refine the structure a bit further, and run WHAT CHECK again because errors in the SCALE and or CRYST card can lead to many problems elsewhere in the validation process. It is also important to keep in mind that WHAT CHECK is software and that it occasionally totally misunderstands what is the cause of a problem. But, if WHAT CHECK lists a problem there normally is a problem albeit that it not always is the actual problem that gets listed. # 110 # Note: Matthews coefficient problem WHAT CHECK detected a Matthews coefficient problem. Most times this is an administrative problem caused by typing the wrong cell multiplicity number on the CRYST card (or not typing it at all). Occasionally it is caused by typing the wrong space group on the CRYST card. You better fix this problem, but normally this problem does not cause WHAT CHECK to give any erroneous error messages further down in the report. # 111 # Error: Bumps in your structure Upon analysing the bumps in your structure, WHAT CHECK got a bit worried. Sometimes this means that you have forgotten to lower the occupancy of overlapping ligands, residues, or water molecules. But, whatever is the origin of this problem, you have to analyse it and fix it. # 112 # Note: Bond length variabilty Z-score low Even with a resolution better than 1.5 Angstrom, you have enough data to allow for more bond length variability that we observed (less than 0.75). You might get a bit better results if you restrain the bond lengths a bit less to the target values. # 113 # Note: His, Asn, Gln side chain flips. His, Asn, and Gln have an asymmetry in their side chain that is hard to detect unless you have data at much better than 1.0 Angstrom resolution. WHAT CHECK thinks that your structure contains His, Asn, or Gln residues that will make better hydrogen bonds when flipped around their chi-2, chi-2, or chi-3 side chain torsion angle, respectively. You better check these Asn, His, and Gln residues, and if you use a refinement program that includes molecular dynamics, then you must (after the flips were made) refine a bit further before running WHAT CHECK again. # 114 # Note: Free floating waters Your structure contains a few water molecules that make no hydrogen bonds at all. These waters must be removed, and you must then refine a bit further before running WHAT CHECK again. # 115 # Warning: Troublesome residues The residues listed in the table below need to be inspected This table is a very rough attempt to sort the residues according to how badly they need your attention. The idea is that when you sit in in front of the graphics screen and study the residues with the electron density present that you improve the structure most by dealing with the top residues in this list first. 736 TYR ( 332-) B - 12.41 696 MET ( 292-) B - 12.14 264 MET ( 292-) A - 11.93 793 LYS ( 389-) B - 11.21 361 LYS ( 389-) A - 11.19 432 GLU ( 460-) A - 10.64 864 GLU ( 460-) B - 10.52 374 TRP ( 402-) A - 10.50 610 ARG ( 206-) B - 10.36 32 ARG ( 60-) A - 10.34 464 ARG ( 60-) B - 10.30 726 PHE ( 322-) B - 4.77 294 PHE ( 322-) A - 4.51 818 PHE ( 414-) B - 4.44 93 ASP ( 121-) A - 4.37 And so on for a total of 58 lines. ============== 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 information) PDB facilities Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP, Vriend G. A series of PDB-related databanks for everyday needs. Nucleic Acids Research D364-368 Database issue (2015). 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) and R.Engh and R.Huber, International Tables for Crystallography (2001) 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). Peptide flips Touw WG, Joosten RP, Vriend G. Detection of trans-cis flips and peptide-plane flips in protein structures. Acta Crystallogr D Biological Crystallograhy 71, 1604-1614 (2015). 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). R.W.W. Hooft, C.Sander and G.Vriend, Objectively judging the quality of a protein structure from a Ramachandran plot CABIOS (1997), 13, 425--430. 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). Tau angle W.G.Touw and G.Vriend On the complexity of Engh and Huber refinement restraints: the angle tau as example. Acta Crystallogr D 66, 1341--1350 (2010). 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. ============== 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 information) PDB facilities Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP, Vriend G. A series of PDB-related databanks for everyday needs. Nucleic Acids Research D364-368 Database issue (2015). 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) and R.Engh and R.Huber, International Tables for Crystallography (2001) 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). Peptide flips Touw WG, Joosten RP, Vriend G. Detection of trans-cis flips and peptide-plane flips in protein structures. Acta Crystallogr D Biological Crystallograhy 71, 1604-1614 (2015). 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). R.W.W. Hooft, C.Sander and G.Vriend, Objectively judging the quality of a protein structure from a Ramachandran plot CABIOS (1997), 13, 425--430. 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). Tau angle W.G.Touw and G.Vriend On the complexity of Engh and Huber refinement restraints: the angle tau as example. Acta Crystallogr D 66, 1341--1350 (2010). 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.