************************************************************************ ********** REPORT OF PROTEIN ANALYSIS by the WHAT IF program ********** ************************************************************************ Date : 2012-05-26 This report was created by WHAT IF version 20120321-1556 This document is a WHAT_CHECK-report that holds the findings of the WHAT IF program during the analysis of 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. ERROR. C1A ( C1A) does not belong in NAG ( 166) 0 ERROR. C2A ( C2A) does not belong in NAG ( 166) 0 ERROR. C3A ( C3A) does not belong in NAG ( 166) 0 ERROR. C4A ( C4A) does not belong in NAG ( 166) 0 ERROR. C5A ( C5A) does not belong in NAG ( 166) 0 ERROR. C6A ( C6A) does not belong in NAG ( 166) 0 ERROR. C7A ( C7A) does not belong in NAG ( 166) 0 ERROR. C8A ( C8A) does not belong in NAG ( 166) 0 ERROR. N2A ( N2A) does not belong in NAG ( 166) 0 ERROR. O3A ( O3A) does not belong in NAG ( 166) 0 ERROR. O4A ( O4A) does not belong in NAG ( 166) 0 ERROR. O5A ( O5A) does not belong in NAG ( 166) 0 ERROR. O6A ( O6A) does not belong in NAG ( 166) 0 ERROR. O7A ( O7A) does not belong in NAG ( 166) 0 ERROR. C1B ( C1B) does not belong in NAG ( 166) 0 ERROR. C2B ( C2B) does not belong in NAG ( 166) 0 ERROR. C3B ( C3B) does not belong in NAG ( 166) 0 ERROR. C4B ( C4B) does not belong in NAG ( 166) 0 ERROR. C5B ( C5B) does not belong in NAG ( 166) 0 ERROR. C6B ( C6B) does not belong in NAG ( 166) 0 ERROR. C7B ( C7B) does not belong in NAG ( 166) 0 ERROR. C8B ( C8B) does not belong in NAG ( 166) 0 ERROR. N2B ( N2B) does not belong in NAG ( 166) 0 ERROR. O3B ( O3B) does not belong in NAG ( 166) 0 ERROR. O4B ( O4B) does not belong in NAG ( 166) 0 ERROR. O5B ( O5B) does not belong in NAG ( 166) 0 ERROR. O6B ( O6B) does not belong in NAG ( 166) 0 ERROR. O7B ( O7B) does not belong in NAG ( 166) 0 ERROR. C1C ( C1C) does not belong in NAG ( 166) 0 ERROR. C2C ( C2C) does not belong in NAG ( 166) 0 ERROR. C3C ( C3C) does not belong in NAG ( 166) 0 ERROR. C4C ( C4C) does not belong in NAG ( 166) 0 ERROR. C5C ( C5C) does not belong in NAG ( 166) 0 ERROR. C6C ( C6C) does not belong in NAG ( 166) 0 ERROR. C7C ( C7C) does not belong in NAG ( 166) 0 ERROR. C8C ( C8C) does not belong in NAG ( 166) 0 ERROR. OC ( OC ) does not belong in NAG ( 166) 0 ERROR. O3C ( O3C) does not belong in NAG ( 166) 0 ERROR. O4C ( O4C) does not belong in NAG ( 166) 0 ERROR. O6C ( O6C) does not belong in NAG ( 166) 0 ERROR. O7C ( O7C) does not belong in NAG ( 166) 0 ERROR. N2C ( N2C) does not belong in NAG ( 166) 0 ERROR. O1L ( O1L) does not belong in NAG ( 166) 0 ======================================================================== ==== Compound code /home/whatif/httpd/htdocs/servers/tmp//tmpbVzYpx/====L1.fil ======================================================================== # 1 # Error: Missing unit cell information No SCALE matrix is given in the PDB file. # 2 # Error: Missing symmetry information Problem: No CRYST1 card is given in the PDB file. SYMMETRY will be unavailable for this molecule. # 3 # Warning: Chain identifier inconsistency WHAT CHECK believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT CHECK does not care about the chain identifiers of water molecules. 1 MET ( 1-) A 2 PRO ( 2-) A 3 PRO ( 3-) A 4 SER ( 4-) A 5 LEU ( 5-) A 6 ARG ( 6-) A 7 LYS ( 7-) A 8 ALA ( 8-) A 9 VAL ( 9-) A 10 ALA ( 10-) A 11 ALA ( 11-) A 12 ALA ( 12-) A 13 ILE ( 13-) A 14 GLY ( 14-) A 15 GLY ( 15-) A 16 GLY ( 16-) A 17 ALA ( 17-) A 18 ILE ( 18-) A 19 ALA ( 19-) A 20 ILE ( 20-) A 21 ALA ( 21-) A 22 SER ( 22-) A 23 VAL ( 23-) A 24 LEU ( 24-) A 25 ILE ( 25-) A 26 THR ( 26-) A 27 GLY ( 27-) A 28 PRO ( 28-) A 29 SER ( 29-) A 30 GLY ( 30-) A 31 ASN ( 31-) A 32 ASP ( 32-) A 33 GLY ( 33-) A 34 LEU ( 34-) A 35 GLU ( 35-) A 36 GLY ( 36-) A 37 VAL ( 37-) A 38 SER ( 38-) A 39 TYR ( 39-) A 40 ILE ( 40-) A 41 PRO ( 41-) A 42 TYR ( 42-) A 43 LYS ( 43-) A 44 ASP ( 44-) A 45 ILE ( 45-) A 46 VAL ( 46-) A 47 GLY ( 47-) A 48 VAL ( 48-) A 49 TRP ( 49-) A 50 THR ( 50-) A 51 VAL ( 51-) A 52 CYS ( 52-) A 53 HIS ( 53-) A 54 GLY ( 54-) A 55 HIS ( 55-) A 56 THR ( 56-) A 57 GLY ( 57-) A 58 LYS ( 58-) A 59 ASP ( 59-) A 60 ILE ( 60-) A 61 MET ( 61-) A 62 LEU ( 62-) A 63 GLY ( 63-) A 64 LYS ( 64-) A 65 THR ( 65-) A 66 TYR ( 66-) A 67 THR ( 67-) A 68 LYS ( 68-) A 69 ALA ( 69-) A 70 GLU ( 70-) A 71 CYS ( 71-) A 72 LYS ( 72-) A 73 ALA ( 73-) A 74 LEU ( 74-) A 75 LEU ( 75-) A 76 ASN ( 76-) A 77 LYS ( 77-) A 78 ASP ( 78-) A 79 LEU ( 79-) A 80 ALA ( 80-) A 81 THR ( 81-) A 82 VAL ( 82-) A 83 ALA ( 83-) A 84 ARG ( 84-) A 85 GLN ( 85-) A 86 ILE ( 86-) A 87 ASN ( 87-) A 88 PRO ( 88-) A 89 TYR ( 89-) A 90 ILE ( 90-) A 91 LYS ( 91-) A 92 VAL ( 92-) A 93 ASP ( 93-) A 94 ILE ( 94-) A 95 PRO ( 95-) A 96 GLU ( 96-) A 97 THR ( 97-) A 98 MET ( 98-) A 99 ARG ( 99-) A 100 GLY ( 100-) A 101 ALA ( 101-) A 102 LEU ( 102-) A 103 TYR ( 103-) A 104 SER ( 104-) A 105 LEU ( 105-) A 106 LEU ( 106-) A 107 TYR ( 107-) A 108 ASN ( 108-) A 109 VAL ( 109-) A 110 GLY ( 110-) A 111 ALA ( 111-) A 112 GLY ( 112-) A 113 ASN ( 113-) A 114 PHE ( 114-) A 115 ARG ( 115-) A 116 THR ( 116-) A 117 SER ( 117-) A 118 THR ( 118-) A 119 LEU ( 119-) A 120 LEU ( 120-) A 121 ARG ( 121-) A 122 LYS ( 122-) A 123 ILE ( 123-) A 124 ASN ( 124-) A 125 GLN ( 125-) A 126 GLY ( 126-) A 127 ASP ( 127-) A 128 ILE ( 128-) A 129 LYS ( 129-) A 130 GLY ( 130-) A 131 ALA ( 131-) A 132 CYS ( 132-) A 133 ASP ( 133-) A 134 GLN ( 134-) A 135 LEU ( 135-) A 136 ARG ( 136-) A 137 ARG ( 137-) A 138 TRP ( 138-) A 139 THR ( 139-) A 140 TYR ( 140-) A 141 ALA ( 141-) A 142 GLY ( 142-) A 143 GLY ( 143-) A 144 LYS ( 144-) A 145 GLN ( 145-) A 146 TRP ( 146-) A 147 LYS ( 147-) A 148 GLY ( 148-) A 149 LEU ( 149-) A 150 MET ( 150-) A 151 THR ( 151-) A 152 ARG ( 152-) A 153 ARG ( 153-) A 154 GLU ( 154-) A 155 ILE ( 155-) A 156 GLU ( 156-) A 157 ARG ( 157-) A 158 GLU ( 158-) A 159 ILE ( 159-) A 160 CYS ( 160-) A 161 LEU ( 161-) A 162 TRP ( 162-) A 163 GLY ( 163-) A 164 GLN ( 164-) A 165 GLN ( 165-) A 166 NAG ( 166-) A 167 GLN ( 165-) A # 4 # Note: No strange inter-chain connections detected No covalent bonds have been detected between molecules with non-identical chain identifiers. Id: INTCNEU # 5 # Note: No duplicate atom names in ligands All atom names in ligands (if any) seem adequately unique. # 6 # Note: In all cases the primary alternate atom was used WHAT CHECK saw no need to make any alternate atom corrections (which means they are all correct, or there are none). Residue: 62 LEU ( 62-) A (Prp= 0.00) Atom X Y Z Acc B WT VdW Colr AtOK Val N 39.7 32.0 21.0 0.0196.0 1.0 1.7 340 + 0.00 CA 39.2 32.8 19.9 0.0196.0 1.0 1.8 240 + 0.00 C 39.3 34.3 20.2 0.0196.0 1.0 1.8 240 + 0.00 O 39.5 34.9 19.1 0.0196.0 1.0 1.4 120 + 0.00 CB 37.8 32.4 19.5 0.0196.0 1.0 1.8 240 + 0.00 CG 37.2 33.3 18.4 0.0196.0 1.0 1.8 240 + 0.00 CD1 38.0 33.1 17.1 0.0196.0 1.0 1.8 240 + 0.00 CD2 35.7 33.2 18.3 0.0196.0 1.0 1.8 240 + 0.00 Residue: 63 GLY ( 63-) A (Prp= 0.00) Atom X Y Z Acc B WT VdW Colr AtOK Val N 39.1 35.1 21.4 0.0307.1 1.0 1.7 340 + 0.00 CA 39.1 36.1 20.5 0.0307.1 1.0 1.8 240 + 0.00 C 40.5 36.5 21.0 0.0307.1 1.0 1.8 240 + 0.00 O 40.9 37.7 20.9 0.0307.1 1.0 1.4 120 + 0.00 Delete overlapping entity 63 GLY ( 63-) A # 7 # Warning: Overlapping residues or molecules This molecule or residue contains atoms that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued. Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the 'least important' of the two overlapping entities has been deleted before the validation continued. Obviously, 'least important' is a matter of definition where you and WHAT CHECK can have differences of opinion. If you want to validate both situations, make it two PDB files, one for each entity. And fudge reality a bit by making the occupancy of the atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that both solutions are each internally consistent, and cope intelligently with groups bound to the entities, and waters that are either there or not depending on the entity used. 63 GLY ( 63-) A Overlapping entity removed: 63 GLY ( 63-) A # 8 # 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). # 9 # Note: No attached groups interfere with hydrogen bond calculations It seems there are no sugars, lipids, etc., bound (or very close) to atoms that otherwise could form hydrogen bonds. # 10 # 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. # 11 # 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 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. # 12 # Note: All residues have a complete backbone. No residues have missing backbone atoms. # 13 # Note: No C-alpha only residues There are no residues that consist of only an alpha carbon atom. # 14 # Note: Non-canonical residues WHAT CHECK has not detected any non-canonical residue(s). # 15 # 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 ( 1) 62 ( 62) A Protein checkset 2 63 ( 64) 164 ( 165) A Protein checkset 3 165 ( 166) 165 ( 166) A Sugar checkset 4 166 ( 165) 166 ( 165) A Q O2 <- 164 checkset # 16 # Note: Some notes regarding the PDB file contents The numbers and remarks listed below have no explicit validation purpose, they are merely meant for the crystallographer or NMR spectroscopists to perhaps pinpoint something unexpected. See the WHAT CHECK course [REF] for an explanation of terms like 'poor', 'missing', etcetera (in case those words pop up in the lines underneath this message). The total number of amino acids found is 164 of which 103 have poor or missing atoms Number of (recognized) sugars: 1 FMT1551O # 17 # 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 - 62 MPPSLRKAVAAAIGGGAIAIASVLITGPSGNDGLEGVSYIPYKDIVGVWTVCHGHTGKDIML ( 1)-( 62) HHHHH TTT TTTTT TT333 HHHHHHHHHHHHTT TT SS TTT SS 70 80 90 100 110 120 | | | | | | 63 - 122 KTYTKAECKALLNKDLATVARQINPYIKVDIPETMRGALYSLLYNVGAGNFRTSTLLRKI ( 64)-( 123) TTTTSS T TT TTSST3333 TT HHHHHHHHHHHHTTT3333 HHHHHT 130 140 150 160 | | | | 123 - 164 NQGDIKGACDQLRRWTYAGGKQWKGLMTRREIEREICLWGQQ ( 124)-( 165) T TTTT HHHH T TT # 18 # Note: No rounded coordinates detected No significant rounding of atom coordinates has been detected. # 19 # Warning: Artificial side chains detected At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined. 62 LEU ( 62-) A 121 LYS ( 122-) A 159 CYS ( 160-) A 160 LEU ( 161-) A 161 TRP ( 162-) A # 20 # Warning: Unexpected atoms encountered While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about. # 21 # 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'. 165 NAG ( 166-) A O4 165 NAG ( 166-) A C4 165 NAG ( 166-) A C1 165 NAG ( 166-) A O5 165 NAG ( 166-) A C5 165 NAG ( 166-) A C6 165 NAG ( 166-) A O6 165 NAG ( 166-) A C3 165 NAG ( 166-) A O3 165 NAG ( 166-) A C2 165 NAG ( 166-) A N2 165 NAG ( 166-) A C7 165 NAG ( 166-) A O7 165 NAG ( 166-) A C8 # 22 # Warning: B-factors outside the range 0.0 - 100.0 In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed. 6 ARG ( 6-) A High 13 ILE ( 13-) A High 14 GLY ( 14-) A High 17 ALA ( 17-) A High 18 ILE ( 18-) A High 20 ILE ( 20-) A High 24 LEU ( 24-) A High 25 ILE ( 25-) A High 26 THR ( 26-) A High 28 PRO ( 28-) A High 34 LEU ( 34-) A High 35 GLU ( 35-) A High 37 VAL ( 37-) A High 38 SER ( 38-) A High 39 TYR ( 39-) A High 40 ILE ( 40-) A High 41 PRO ( 41-) A High 42 TYR ( 42-) A High 43 LYS ( 43-) A High 44 ASP ( 44-) A High 45 ILE ( 45-) A High 46 VAL ( 46-) A High 49 TRP ( 49-) A High 50 THR ( 50-) A High 51 VAL ( 51-) A High 53 HIS ( 53-) A High 55 HIS ( 55-) A High 56 THR ( 56-) A High 57 GLY ( 57-) A High 58 LYS ( 58-) A High 60 ILE ( 60-) A High 61 MET ( 61-) A High 62 LEU ( 62-) A High 63 LYS ( 64-) A High 64 THR ( 65-) A High 65 TYR ( 66-) A High 67 LYS ( 68-) A High 68 ALA ( 69-) A High 69 GLU ( 70-) A High 71 LYS ( 72-) A High 72 ALA ( 73-) A High 73 LEU ( 74-) A High 74 LEU ( 75-) A High 75 ASN ( 76-) A High 76 LYS ( 77-) A High 77 ASP ( 78-) A High 78 LEU ( 79-) A High 80 THR ( 81-) A High 81 VAL ( 82-) A High 83 ARG ( 84-) A High 85 ILE ( 86-) A High 87 PRO ( 88-) A High 88 TYR ( 89-) A High 89 ILE ( 90-) A High 90 LYS ( 91-) A High 93 ILE ( 94-) A High 94 PRO ( 95-) A High 96 THR ( 97-) A High 97 MET ( 98-) A High 98 ARG ( 99-) A High 104 LEU ( 105-) A High 105 LEU ( 106-) A High 106 TYR ( 107-) A High 112 ASN ( 113-) A High 114 ARG ( 115-) A High 115 THR ( 116-) A High 117 THR ( 118-) A High 118 LEU ( 119-) A High 119 LEU ( 120-) A High 120 ARG ( 121-) A High 121 LYS ( 122-) A High 122 ILE ( 123-) A High 123 ASN ( 124-) A High 124 GLN ( 125-) A High 125 GLY ( 126-) A High 126 ASP ( 127-) A High 127 ILE ( 128-) A High 128 LYS ( 129-) A High 129 GLY ( 130-) A High 130 ALA ( 131-) A High 131 CYS ( 132-) A High 132 ASP ( 133-) A High 133 GLN ( 134-) A High 135 ARG ( 136-) A High 136 ARG ( 137-) A High 143 LYS ( 144-) A High 144 GLN ( 145-) A High 145 TRP ( 146-) A High 146 LYS ( 147-) A High 148 LEU ( 149-) A High 149 MET ( 150-) A High 150 THR ( 151-) A High 151 ARG ( 152-) A High 152 ARG ( 153-) A High 153 GLU ( 154-) A High 154 ILE ( 155-) A High 155 GLU ( 156-) A High 156 ARG ( 157-) A High 157 GLU ( 158-) A High 160 LEU ( 161-) A High 161 TRP ( 162-) A High 162 GLY ( 163-) A High 163 GLN ( 164-) A High # 23 # Note: No C-terminal nitrogen detected The PDB indicates that a residue is not the true C-terminus by including only the backbone N of the next residue. This has not been observed in this PDB file. # 24 # Note: C-terminus capping The residues listed in the table below either are pseudo C-terminal residues, or have two groups attached of which neither is the normal C-terminal O. In this table REAL means that the C-terminal residue is likely to be the real C-terminus of its chain; OX means that an incorrect second oxygen (OXT) was detected that should not be there; -O indicates that the 'normal' oxygen (i.e. not the OXT) is missing; OT indicates the detection of any other capping group. C-terminal nitrogen atoms, if any, have already been dealt with in a previous check and are indicated here by -N. PSEUDO means that this is the last visible residue in the chain, but not the real C-terminus, i.e. all residues after this one are missing in this chain. BREAK means that this is the last residue before a chain-break, i.e. the chain continues but after this residue a number of residues is missing. In case a break is observed the number of residues that seems to be missing is shown in brackets. OK means that given the status (REAL, PSEUDO, BREAK), no problems were found. 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. 62 LEU ( 62-) A : Unknown problem 164 GLN ( 165-) A : Unknown problem # 25 # Note: No OXT found in the middle of chains No OXT groups were found in the middle of protein chains. # 26 # 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. # 27 # Note: Valine nomenclature OK No errors were detected in valine nomenclature. # 28 # Note: Threonine nomenclature OK No errors were detected in threonine nomenclature. # 29 # Note: Isoleucine nomenclature OK No errors were detected in isoleucine nomenclature. # 30 # Note: Leucine nomenclature OK No errors were detected in leucine nomenclature. # 31 # Note: Arginine nomenclature OK No errors were detected in arginine nomenclature. # 32 # Note: Tyrosine torsion conventions OK No errors were detected in tyrosine torsion angle conventions. # 33 # Note: Phenylalanine torsion conventions OK No errors were detected in phenylalanine torsion angle conventions. # 34 # Note: Aspartic acid torsion conventions OK No errors were detected in aspartic acid torsion angle conventions. # 35 # Note: Glutamic acid torsion conventions OK No errors were detected in glutamic acid torsion angle conventions. # 36 # Note: Phosphate group names OK in DNA/RNA No errors were detected in nucleic acid phosphate group naming conventions. # 37 # 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. # 38 # 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]). # 39 # Note: Normal bond length variability Bond lengths were found to deviate normally from the standard bond lengths (values for Protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). RMS Z-score for bond lengths: 1.006 RMS-deviation in bond distances: 0.020 # 40 # 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. 19 ALA ( 19-) A -C N CA 114.36 -4.1 31 ASN ( 31-) A CA CB CG 108.28 -4.3 35 GLU ( 35-) A CB CG CD 105.72 -4.0 41 PRO ( 41-) A -CA -C N 124.43 5.0 42 TYR ( 42-) A CA CB CG 103.03 -5.6 59 ASP ( 59-) A CA CB CG 107.79 -4.8 61 MET ( 61-) A CG SD CE 90.54 -4.7 62 LEU ( 62-) A CA C O 108.09 -7.5 75 ASN ( 76-) A CA CB CG 108.22 -4.4 77 ASP ( 78-) A CA CB CG 108.32 -4.3 86 ASN ( 87-) A CA CB CG 107.94 -4.7 87 PRO ( 88-) A C CA CB 118.33 4.3 92 ASP ( 93-) A CA CB CG 108.45 -4.2 94 PRO ( 95-) A -CA -C N 126.40 6.3 95 GLU ( 96-) A CB CG CD 105.21 -4.3 107 ASN ( 108-) A CA CB CG 108.37 -4.2 113 PHE ( 114-) A CA CB CG 108.66 -5.1 115 THR ( 116-) A N CA CB 117.61 4.2 126 ASP ( 127-) A CA CB CG 108.44 -4.2 131 CYS ( 132-) A -C N CA 129.41 4.3 131 CYS ( 132-) A N CA C 96.36 -5.3 132 ASP ( 133-) A -C N CA 114.26 -4.1 139 TYR ( 140-) A CA CB CG 104.07 -5.0 145 TRP ( 146-) A -C N CA 114.38 -4.1 # 41 # 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: 1.310 RMS-deviation in bond angles: 2.465 # 42 # 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. # 43 # Warning: Chirality deviations detected The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations. Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks. Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value. 28 PRO ( 28-) A N -7.2 -25.99 -2.48 41 PRO ( 41-) A N 7.1 20.76 -2.48 94 PRO ( 95-) A N -6.1 -22.55 -2.48 The average deviation= 1.203 # 44 # 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 : 1.114 # 45 # Error: Tau angle problems The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value. 131 CYS ( 132-) A 5.82 # 46 # Warning: High tau angle deviations The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, 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 : 1.634 # 47 # Note: Side chain planarity OK All of the side chains of residues that have an intact planar group are planar within expected RMS deviations. # 48 # 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. Ramachandran Z-score : -2.999 # 49 # Note: Ramachandran Z-score OK The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is within expected ranges for well-refined structures. Ramachandran Z-score : -2.999 # 50 # 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. 56 THR ( 56-) A -3.2 45 ILE ( 45-) A -2.8 131 CYS ( 132-) A -2.3 61 MET ( 61-) A -2.1 # 51 # 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. 24 LEU ( 24-) A Poor phi/psi 29 SER ( 29-) A Poor phi/psi 45 ILE ( 45-) A Poor phi/psi 56 THR ( 56-) A Poor phi/psi 58 LYS ( 58-) A Poor phi/psi 61 MET ( 61-) A Poor phi/psi 68 ALA ( 69-) A omega poor 73 LEU ( 74-) A Poor phi/psi 83 ARG ( 84-) A Poor phi/psi 128 LYS ( 129-) A Poor phi/psi 131 CYS ( 132-) A Poor phi/psi 132 ASP ( 133-) A Poor phi/psi 144 GLN ( 145-) A Poor phi/psi 146 LYS ( 147-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -3.640 # 52 # Warning: chi-1/chi-2 angle correlation Z-score low The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low. chi-1/chi-2 correlation Z-score : -3.640 # 53 # 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. 150 THR ( 151-) A 0.36 137 TRP ( 138-) A 0.36 # 54 # 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) is indicated! 19 ALA ( 19-) A 0 20 ILE ( 20-) A 0 28 PRO ( 28-) A H 0 45 ILE ( 45-) A 0 55 HIS ( 55-) A 0 56 THR ( 56-) A 0 58 LYS ( 58-) A 0 61 MET ( 61-) A 0 62 LEU ( 62-) A 0 63 LYS ( 64-) A 0 64 THR ( 65-) A 0 69 GLU ( 70-) A 0 73 LEU ( 74-) A 0 80 THR ( 81-) A 0 128 LYS ( 129-) A 0 130 ALA ( 131-) A 0 131 CYS ( 132-) A 0 132 ASP ( 133-) A 0 133 GLN ( 134-) A 0 143 LYS ( 144-) A 0 144 GLN ( 145-) A 0 145 TRP ( 146-) A 0 146 LYS ( 147-) A 0 163 GLN ( 164-) A 0 25 ILE ( 25-) A 1 72 ALA ( 73-) A 1 82 ALA ( 83-) A 1 83 ARG ( 84-) A S 1 127 ILE ( 128-) A 1 17 ALA ( 17-) A 2 46 VAL ( 46-) A 2 136 ARG ( 137-) A 2 # 55 # Error: Backbone conformation Z-score very low A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is very unusual. Backbone conformation Z-score : -4.451 Omega average and std. deviation= 181.231 3.892 Significant deviations from expected 5.5!!! # 56 # Warning: Omega angles too tightly restrained The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees. Standard deviation of omega values : 3.892 # 57 # Note: PRO puckering amplitude OK Puckering amplitudes for all PRO residues are within normal ranges. # 58 # 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]. 2 PRO ( 2-) A -123.3 half-chair C-delta/C-gamma (-126 degrees) 28 PRO ( 28-) A 119.0 half-chair C-beta/C-alpha (126 degrees) 41 PRO ( 41-) A -57.0 half-chair C-beta/C-alpha (-54 degrees) 87 PRO ( 88-) A -123.4 half-chair C-delta/C-gamma (-126 degrees) 94 PRO ( 95-) A 109.6 envelop C-beta (108 degrees) # 59 # Note: Backbone oxygen evaluation OK All residues for which the local backbone conformation could be found in the WHAT CHECK database have a normal backbone oxygen position. # 60 # Note: Peptide bond conformations There are not enough (intact) amino acids in the file to analyse peptide bond conformations. # 61 # 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. 61 MET ( 61-) A SD <-> 88 TYR ( 89-) A CB 0.33 3.07 INTRA BF 97 MET ( 98-) A SD <-> 101 LEU ( 102-) A CD2 0.33 3.07 INTRA BL 61 MET ( 61-) A SD <-> 96 THR ( 97-) A CB 0.33 3.07 INTRA BF 61 MET ( 61-) A SD <-> 88 TYR ( 89-) A CD2 0.32 3.08 INTRA BF 1 MET ( 1-) A SD <-> 91 VAL ( 92-) A CG2 0.32 3.08 INTRA BL 126 ASP ( 127-) A C <-> 137 TRP ( 138-) A NE1 0.31 2.79 INTRA BF 70 CYS ( 71-) A SG <-> 85 ILE ( 86-) A CB 0.30 3.10 INTRA BF 97 MET ( 98-) A SD <-> 101 LEU ( 102-) A CG 0.29 3.11 INTRA BL 131 CYS ( 132-) A N <-> 136 ARG ( 137-) A CZ 0.28 2.82 INTRA BF 48 VAL ( 48-) A CG1 <-> 90 LYS ( 91-) A N 0.28 2.82 INTRA BL 130 ALA ( 131-) A N <-> 136 ARG ( 137-) A CG 0.28 2.82 INTRA BF 121 LYS ( 122-) A N <-> 134 LEU ( 135-) A CD1 0.27 2.83 INTRA BF 4 SER ( 4-) A N <-> 49 TRP ( 49-) A CE3 0.27 2.83 INTRA BF 131 CYS ( 132-) A SG <-> 132 ASP ( 133-) A N 0.27 2.93 INTRA BF 78 LEU ( 79-) A CD1 <-> 80 THR ( 81-) A CG2 0.27 2.93 INTRA BF 49 TRP ( 49-) A CH2 <-> 91 VAL ( 92-) A N 0.27 2.83 INTRA BF 128 LYS ( 129-) A N <-> 135 ARG ( 136-) A CD 0.27 2.83 INTRA BF 20 ILE ( 20-) A CG1 <-> 25 ILE ( 25-) A CG1 0.27 2.93 INTRA BF 43 LYS ( 43-) A CE <-> 63 LYS ( 64-) A CG 0.27 2.93 INTRA BF 61 MET ( 61-) A N <-> 89 ILE ( 90-) A CD1 0.27 2.83 INTRA BF 61 MET ( 61-) A CE <-> 96 THR ( 97-) A CB 0.27 2.93 INTRA BF 83 ARG ( 84-) A CZ <-> 95 GLU ( 96-) A CD 0.27 2.93 INTRA BF 6 ARG ( 6-) A CD <-> 11 ALA ( 11-) A N 0.26 2.84 INTRA BF 49 TRP ( 49-) A CG <-> 89 ILE ( 90-) A CG2 0.26 2.94 INTRA BF 120 ARG ( 121-) A CG <-> 132 ASP ( 133-) A CG 0.26 2.94 INTRA BF 38 SER ( 38-) A CB <-> 136 ARG ( 137-) A NE 0.26 2.84 INTRA BF 72 ALA ( 73-) A CB <-> 74 LEU ( 75-) A CD2 0.26 2.94 INTRA BF 6 ARG ( 6-) A CB <-> 46 VAL ( 46-) A CG1 0.26 2.94 INTRA BF 23 VAL ( 23-) A CG1 <-> 97 MET ( 98-) A CG 0.26 2.94 INTRA BL 65 TYR ( 66-) A CE2 <-> 67 LYS ( 68-) A CB 0.26 2.94 INTRA BF 128 LYS ( 129-) A N <-> 135 ARG ( 136-) A CG 0.26 2.84 INTRA BF 60 ILE ( 60-) A CD1 <-> 66 THR ( 67-) A CG2 0.26 2.94 INTRA BL 18 ILE ( 18-) A CG2 <-> 22 SER ( 22-) A CB 0.26 2.94 INTRA BL 4 SER ( 4-) A N <-> 49 TRP ( 49-) A CZ3 0.26 2.84 INTRA BF 71 LYS ( 72-) A CB <-> 80 THR ( 81-) A CG2 0.26 2.94 INTRA BF 38 SER ( 38-) A CB <-> 136 ARG ( 137-) A CZ 0.26 2.94 INTRA BF 35 GLU ( 35-) A CB <-> 130 ALA ( 131-) A CB 0.26 2.94 INTRA BF 49 TRP ( 49-) A CA <-> 89 ILE ( 90-) A CG2 0.26 2.94 INTRA BF 130 ALA ( 131-) A CB <-> 136 ARG ( 137-) A CD 0.26 2.94 INTRA BF 6 ARG ( 6-) A CD <-> 10 ALA ( 10-) A CB 0.26 2.94 INTRA BF 119 LEU ( 120-) A CB <-> 131 CYS ( 132-) A CB 0.26 2.94 INTRA BF 13 ILE ( 13-) A CG1 <-> 145 TRP ( 146-) A CZ3 0.26 2.94 INTRA BF 36 GLY ( 36-) A CA <-> 39 TYR ( 39-) A CE2 0.26 2.94 INTRA BF 60 ILE ( 60-) A CG1 <-> 85 ILE ( 86-) A CD1 0.26 2.94 INTRA BF 31 ASN ( 31-) A CB <-> 35 GLU ( 35-) A CD 0.25 2.95 INTRA BL 70 CYS ( 71-) A CB <-> 88 TYR ( 89-) A CE1 0.25 2.95 INTRA BL 43 LYS ( 43-) A CD <-> 115 THR ( 116-) A CG2 0.25 2.95 INTRA BF 44 ASP ( 44-) A CB <-> 50 THR ( 50-) A CG2 0.25 2.95 INTRA BF 42 TYR ( 42-) A CB <-> 119 LEU ( 120-) A CD2 0.25 2.95 INTRA BF 70 CYS ( 71-) A C <-> 80 THR ( 81-) A CG2 0.25 2.95 INTRA BF 128 LYS ( 129-) A C <-> 135 ARG ( 136-) A CD 0.25 2.95 INTRA BF 131 CYS ( 132-) A CA <-> 136 ARG ( 137-) A NH2 0.25 2.85 INTRA BF 34 LEU ( 34-) A CD1 <-> 129 GLY ( 130-) A CA 0.25 2.95 INTRA BL 78 LEU ( 79-) A CD2 <-> 80 THR ( 81-) A CG2 0.25 2.95 INTRA BF 37 VAL ( 37-) A CG1 <-> 139 TYR ( 140-) A CB 0.25 2.95 INTRA BL 40 ILE ( 40-) A CG2 <-> 62 LEU ( 62-) A CD1 0.25 2.95 INTRA BF 93 ILE ( 94-) A CB <-> 96 THR ( 97-) A CG2 0.25 2.95 INTRA BF 120 ARG ( 121-) A CG <-> 132 ASP ( 133-) A CB 0.25 2.95 INTRA BF 32 ASP ( 32-) A CG <-> 34 LEU ( 34-) A CD2 0.25 2.95 INTRA BL 49 TRP ( 49-) A CH2 <-> 91 VAL ( 92-) A CG2 0.25 2.95 INTRA BF 38 SER ( 38-) A CB <-> 136 ARG ( 137-) A NH2 0.25 2.85 INTRA BF 34 LEU ( 34-) A C <-> 136 ARG ( 137-) A CD 0.25 2.95 INTRA BF 12 ALA ( 12-) A CB <-> 146 LYS ( 147-) A CE 0.25 2.95 INTRA BF 51 VAL ( 51-) A CB <-> 58 LYS ( 58-) A CE 0.25 2.95 INTRA BF 18 ILE ( 18-) A CD1 <-> 23 VAL ( 23-) A CA 0.25 2.95 INTRA BL 42 TYR ( 42-) A CE1 <-> 119 LEU ( 120-) A CD1 0.25 2.95 INTRA BF 61 MET ( 61-) A SD <-> 88 TYR ( 89-) A CA 0.25 3.15 INTRA BF 83 ARG ( 84-) A CZ <-> 95 GLU ( 96-) A CG 0.25 2.95 INTRA BF 9 VAL ( 9-) A CG2 <-> 146 LYS ( 147-) A CB 0.24 2.96 INTRA BF 36 GLY ( 36-) A CA <-> 39 TYR ( 39-) A CD2 0.24 2.96 INTRA BF 39 TYR ( 39-) A CE1 <-> 40 ILE ( 40-) A CG2 0.24 2.96 INTRA BF 9 VAL ( 9-) A CG1 <-> 144 GLN ( 145-) A CD 0.24 2.96 INTRA BF 102 TYR ( 103-) A CE2 <-> 106 TYR ( 107-) A CE1 0.24 2.96 INTRA BL 130 ALA ( 131-) A C <-> 136 ARG ( 137-) A NE 0.24 2.86 INTRA BF 70 CYS ( 71-) A SG <-> 85 ILE ( 86-) A CG1 0.24 3.16 INTRA BF 35 GLU ( 35-) A CA <-> 136 ARG ( 137-) A NH1 0.24 2.86 INTRA BF 83 ARG ( 84-) A NH1 <-> 88 TYR ( 89-) A CE1 0.24 2.86 INTRA BF 83 ARG ( 84-) A CD <-> 98 ARG ( 99-) A NH2 0.23 2.87 INTRA BF 42 TYR ( 42-) A CG <-> 119 LEU ( 120-) A CD2 0.23 2.97 INTRA BF 9 VAL ( 9-) A CG1 <-> 144 GLN ( 145-) A NE2 0.23 2.87 INTRA BF 6 ARG ( 6-) A NE <-> 10 ALA ( 10-) A CB 0.23 2.87 INTRA BF 136 ARG ( 137-) A CB <-> 139 TYR ( 140-) A CD2 0.23 2.97 INTRA BF 131 CYS ( 132-) A CB <-> 136 ARG ( 137-) A NH2 0.23 2.87 INTRA BF 127 ILE ( 128-) A CD1 <-> 135 ARG ( 136-) A NE 0.23 2.87 INTRA BF 95 GLU ( 96-) A CG <-> 98 ARG ( 99-) A NH2 0.23 2.87 INTRA BF 7 LYS ( 7-) A CE <-> 144 GLN ( 145-) A NE2 0.23 2.87 INTRA BF 130 ALA ( 131-) A CB <-> 136 ARG ( 137-) A NH1 0.23 2.87 INTRA BF 131 CYS ( 132-) A SG <-> 134 LEU ( 135-) A CB 0.22 3.18 INTRA BF 83 ARG ( 84-) A NH1 <-> 95 GLU ( 96-) A CD 0.22 2.88 INTRA BF 130 ALA ( 131-) A C <-> 136 ARG ( 137-) A CZ 0.22 2.98 INTRA BF 62 LEU ( 62-) A C <-> 63 LYS ( 64-) A N 0.21 2.69 INTRA BF 60 ILE ( 60-) A CG2 <-> 89 ILE ( 90-) A CD1 0.21 2.99 INTRA BF 71 LYS ( 72-) A N <-> 80 THR ( 81-) A CG2 0.21 2.89 INTRA BF 48 VAL ( 48-) A CG1 <-> 89 ILE ( 90-) A C 0.21 2.99 INTRA BF 3 PRO ( 3-) A CA <-> 49 TRP ( 49-) A CD2 0.21 2.99 INTRA BF 59 ASP ( 59-) A CG <-> 63 LYS ( 64-) A CE 0.20 3.00 INTRA BF 38 SER ( 38-) A C <-> 41 PRO ( 41-) A CD 0.20 3.00 INTRA BF 83 ARG ( 84-) A CG <-> 84 GLN ( 85-) A N 0.20 2.80 INTRA BF 35 GLU ( 35-) A CA <-> 130 ALA ( 131-) A CB 0.20 3.00 INTRA BF 128 LYS ( 129-) A CA <-> 135 ARG ( 136-) A CD 0.20 3.00 INTRA BF 51 VAL ( 51-) A CG1 <-> 58 LYS ( 58-) A NZ 0.20 2.90 INTRA BF 131 CYS ( 132-) A CA <-> 136 ARG ( 137-) A CZ 0.19 3.01 INTRA BF 43 LYS ( 43-) A NZ <-> 115 THR ( 116-) A CG2 0.19 2.91 INTRA BF 43 LYS ( 43-) A CE <-> 63 LYS ( 64-) A CD 0.19 3.01 INTRA BF 132 ASP ( 133-) A CG <-> 133 GLN ( 134-) A N 0.19 2.81 INTRA BF 20 ILE ( 20-) A CG2 <-> 21 ALA ( 21-) A N 0.19 2.81 INTRA BF 143 LYS ( 144-) A NZ <-> 146 LYS ( 147-) A C 0.19 2.91 INTRA BF 12 ALA ( 12-) A CB <-> 146 LYS ( 147-) A NZ 0.19 2.91 INTRA BF 140 ALA ( 141-) A CA <-> 146 LYS ( 147-) A NZ 0.19 2.91 INTRA BF 10 ALA ( 10-) A CA <-> 13 ILE ( 13-) A CD1 0.18 3.02 INTRA BF 26 THR ( 26-) A C <-> 28 PRO ( 28-) A CD 0.18 3.02 INTRA BF 61 MET ( 61-) A CG <-> 62 LEU ( 62-) A N 0.18 2.82 INTRA BF 146 LYS ( 147-) A CG <-> 147 GLY ( 148-) A N 0.18 2.82 INTRA BF 9 VAL ( 9-) A CG1 <-> 10 ALA ( 10-) A N 0.18 2.82 INTRA BL 58 LYS ( 58-) A NZ <-> 60 ILE ( 60-) A CG1 0.18 2.92 INTRA BF 96 THR ( 97-) A CG2 <-> 97 MET ( 98-) A N 0.18 2.82 INTRA BL 74 LEU ( 75-) A CD2 <-> 75 ASN ( 76-) A N 0.18 2.82 INTRA BF 25 ILE ( 25-) A CD1 <-> 26 THR ( 26-) A N 0.18 2.82 INTRA BF 92 ASP ( 93-) A CG <-> 94 PRO ( 95-) A CD 0.18 3.02 INTRA BF 120 ARG ( 121-) A CB <-> 132 ASP ( 133-) A CG 0.18 3.02 INTRA BF 6 ARG ( 6-) A CD <-> 7 LYS ( 7-) A N 0.18 2.82 INTRA BF 144 GLN ( 145-) A CG <-> 145 TRP ( 146-) A N 0.18 2.82 INTRA BF 117 THR ( 118-) A CG2 <-> 118 LEU ( 119-) A N 0.18 2.82 INTRA BF 81 VAL ( 82-) A CG2 <-> 82 ALA ( 83-) A N 0.18 2.82 INTRA BL 126 ASP ( 127-) A CG <-> 127 ILE ( 128-) A N 0.18 2.82 INTRA BF 35 GLU ( 35-) A CG <-> 36 GLY ( 36-) A N 0.17 2.83 INTRA BL 110 ALA ( 111-) A C <-> 112 ASN ( 113-) A ND2 0.17 2.93 INTRA BL 163 GLN ( 164-) A CD <-> 164 GLN ( 165-) A N 0.17 2.83 INTRA BF 1 MET ( 1-) A CG <-> 2 PRO ( 2-) A CD 0.17 3.03 INTRA BL 85 ILE ( 86-) A CG2 <-> 86 ASN ( 87-) A N 0.17 2.83 INTRA BF 107 ASN ( 108-) A CG <-> 108 VAL ( 109-) A N 0.17 2.83 INTRA BL 61 MET ( 61-) A CB <-> 62 LEU ( 62-) A N 0.16 2.54 INTRA BF 59 ASP ( 59-) A C <-> 60 ILE ( 60-) A CD1 0.15 2.95 INTRA BL 71 LYS ( 72-) A CA <-> 80 THR ( 81-) A CG2 0.15 3.05 INTRA BF 112 ASN ( 113-) A ND2 <-> 113 PHE ( 114-) A CD2 0.15 2.95 INTRA BL 39 TYR ( 39-) A CZ <-> 40 ILE ( 40-) A CG2 0.15 3.05 INTRA BF 78 LEU ( 79-) A CD2 <-> 80 THR ( 81-) A N 0.15 2.95 INTRA BF 83 ARG ( 84-) A NE <-> 95 GLU ( 96-) A CG 0.15 2.95 INTRA BF 126 ASP ( 127-) A C <-> 137 TRP ( 138-) A CD1 0.15 3.05 INTRA BF 131 CYS ( 132-) A SG <-> 132 ASP ( 133-) A OD1 0.14 2.86 INTRA BF 56 THR ( 56-) A CG2 <-> 57 GLY ( 57-) A N 0.14 2.86 INTRA BF 93 ILE ( 94-) A N <-> 94 PRO ( 95-) A CD 0.14 2.86 INTRA BF 42 TYR ( 42-) A CD1 <-> 119 LEU ( 120-) A CD1 0.13 3.07 INTRA BF 42 TYR ( 42-) A CZ <-> 119 LEU ( 120-) A CD1 0.13 3.07 INTRA BF 9 VAL ( 9-) A CG2 <-> 145 TRP ( 146-) A C 0.12 3.08 INTRA BF 13 ILE ( 13-) A CG2 <-> 146 LYS ( 147-) A CA 0.12 3.08 INTRA BF 20 ILE ( 20-) A C <-> 25 ILE ( 25-) A CG1 0.12 3.08 INTRA BF 60 ILE ( 60-) A CG2 <-> 61 MET ( 61-) A N 0.12 2.88 INTRA BF 25 ILE ( 25-) A CG1 <-> 26 THR ( 26-) A N 0.12 2.88 INTRA BF 120 ARG ( 121-) A CA <-> 132 ASP ( 133-) A CG 0.12 3.08 INTRA BF 161 TRP ( 162-) A CG <-> 162 GLY ( 163-) A N 0.11 2.89 INTRA BF 60 ILE ( 60-) A CG1 <-> 85 ILE ( 86-) A CG1 0.11 3.09 INTRA BF 40 ILE ( 40-) A N <-> 41 PRO ( 41-) A CD 0.11 2.89 INTRA BF 49 TRP ( 49-) A CD1 <-> 89 ILE ( 90-) A CG2 0.11 3.09 INTRA BF 61 MET ( 61-) A CA <-> 89 ILE ( 90-) A CD1 0.11 3.09 INTRA BF 119 LEU ( 120-) A CG <-> 136 ARG ( 137-) A NH2 0.11 2.99 INTRA BF 140 ALA ( 141-) A CA <-> 146 LYS ( 147-) A CE 0.11 3.09 INTRA BF 85 ILE ( 86-) A CA <-> 88 TYR ( 89-) A CD1 0.11 3.09 INTRA BF 115 THR ( 116-) A O <-> 119 LEU ( 120-) A N 0.11 2.59 INTRA BF 41 PRO ( 41-) A CD <-> 42 TYR ( 42-) A N 0.11 2.89 INTRA BF 6 ARG ( 6-) A CZ <-> 10 ALA ( 10-) A CB 0.11 3.09 INTRA BF 75 ASN ( 76-) A ND2 <-> 77 ASP ( 78-) A N 0.10 2.75 INTRA BF 128 LYS ( 129-) A O <-> 137 TRP ( 138-) A NE1 0.10 2.60 INTRA BF 3 PRO ( 3-) A CA <-> 49 TRP ( 49-) A CE3 0.10 3.10 INTRA BF 61 MET ( 61-) A SD <-> 96 THR ( 97-) A OG1 0.10 2.90 INTRA BF 54 GLY ( 54-) A C <-> 56 THR ( 56-) A N 0.10 2.80 INTRA BF 70 CYS ( 71-) A SG <-> 85 ILE ( 86-) A CA 0.10 3.30 INTRA BF 51 VAL ( 51-) A CG1 <-> 58 LYS ( 58-) A CE 0.10 3.10 INTRA BF 86 ASN ( 87-) A N <-> 87 PRO ( 88-) A CD 0.10 2.90 INTRA BL 131 CYS ( 132-) A N <-> 136 ARG ( 137-) A NH1 0.09 2.76 INTRA BF 41 PRO ( 41-) A CG <-> 42 TYR ( 42-) A N 0.09 2.91 INTRA BF 121 LYS ( 122-) A C <-> 134 LEU ( 135-) A CD1 0.09 3.11 INTRA BF 104 LEU ( 105-) A CD2 <-> 110 ALA ( 111-) A N 0.09 3.01 INTRA BL 37 VAL ( 37-) A CG1 <-> 38 SER ( 38-) A N 0.09 2.91 INTRA BL 1 MET ( 1-) A CG <-> 2 PRO ( 2-) A N 0.09 2.91 INTRA BL 87 PRO ( 88-) A CB <-> 95 GLU ( 96-) A CD 0.09 3.11 INTRA BL 130 ALA ( 131-) A C <-> 136 ARG ( 137-) A CD 0.09 3.11 INTRA BF 148 LEU ( 149-) A CD1 <-> 149 MET ( 150-) A N 0.08 2.92 INTRA BF 44 ASP ( 44-) A OD2 <-> 47 GLY ( 47-) A N 0.08 2.62 INTRA BF 60 ILE ( 60-) A CG2 <-> 85 ILE ( 86-) A CD1 0.08 3.12 INTRA BF 126 ASP ( 127-) A CB <-> 137 TRP ( 138-) A CE2 0.08 3.12 INTRA BF 61 MET ( 61-) A CB <-> 88 TYR ( 89-) A O 0.08 2.72 INTRA BF 144 GLN ( 145-) A O <-> 146 LYS ( 147-) A N 0.08 2.62 INTRA BF 29 SER ( 29-) A CB <-> 104 LEU ( 105-) A CD1 0.08 3.12 INTRA BL 7 LYS ( 7-) A O <-> 11 ALA ( 11-) A N 0.08 2.62 INTRA BL 31 ASN ( 31-) A CG <-> 35 GLU ( 35-) A CD 0.08 3.12 INTRA BL 56 THR ( 56-) A CG2 <-> 65 TYR ( 66-) A CE1 0.07 3.13 INTRA BF 10 ALA ( 10-) A O <-> 19 ALA ( 19-) A CB 0.07 2.73 INTRA BL 115 THR ( 116-) A O <-> 119 LEU ( 120-) A CD2 0.07 2.73 INTRA BF 161 TRP ( 162-) A CD1 <-> 162 GLY ( 163-) A N 0.07 2.93 INTRA BF 132 ASP ( 133-) A OD1 <-> 134 LEU ( 135-) A N 0.07 2.63 INTRA BF 112 ASN ( 113-) A CG <-> 113 PHE ( 114-) A N 0.07 2.93 INTRA BL 34 LEU ( 34-) A O <-> 136 ARG ( 137-) A CD 0.07 2.73 INTRA BF 37 VAL ( 37-) A O <-> 40 ILE ( 40-) A CG1 0.07 2.73 INTRA BL 37 VAL ( 37-) A O <-> 41 PRO ( 41-) A CD 0.07 2.73 INTRA BF 48 VAL ( 48-) A CG1 <-> 89 ILE ( 90-) A CA 0.07 3.13 INTRA BF 9 VAL ( 9-) A O <-> 13 ILE ( 13-) A CD1 0.07 2.73 INTRA BF 48 VAL ( 48-) A CG1 <-> 90 LYS ( 91-) A O 0.06 2.74 INTRA BL 13 ILE ( 13-) A O <-> 19 ALA ( 19-) A CB 0.06 2.74 INTRA BF 101 LEU ( 102-) A O <-> 105 LEU ( 106-) A CD1 0.06 2.74 INTRA BL 121 LYS ( 122-) A O <-> 134 LEU ( 135-) A CD1 0.06 2.74 INTRA BF 34 LEU ( 34-) A O <-> 37 VAL ( 37-) A CG1 0.06 2.74 INTRA BL 86 ASN ( 87-) A CB <-> 87 PRO ( 88-) A CD 0.06 3.04 INTRA BL 90 LYS ( 91-) A CG <-> 92 ASP ( 93-) A O 0.06 2.74 INTRA BL 18 ILE ( 18-) A CB <-> 22 SER ( 22-) A CB 0.06 3.14 INTRA BL 50 THR ( 50-) A CG2 <-> 61 MET ( 61-) A O 0.06 2.74 INTRA BF 164 GLN ( 165-) A CG <-> 166 GLN ( 165-) A O'' 0.06 2.74 INTRA BL 93 ILE ( 94-) A O <-> 96 THR ( 97-) A CG2 0.06 2.74 INTRA BF 12 ALA ( 12-) A O <-> 20 ILE ( 20-) A CG2 0.06 2.74 INTRA BF 32 ASP ( 32-) A OD2 <-> 34 LEU ( 34-) A CD2 0.06 2.74 INTRA BL 23 VAL ( 23-) A N <-> 24 LEU ( 24-) A N 0.06 2.54 INTRA BF 83 ARG ( 84-) A NE <-> 98 ARG ( 99-) A NH2 0.06 2.79 INTRA BF 34 LEU ( 34-) A CB <-> 136 ARG ( 137-) A CG 0.06 3.14 INTRA BF 18 ILE ( 18-) A O <-> 23 VAL ( 23-) A CG2 0.06 2.74 INTRA BL 39 TYR ( 39-) A O <-> 43 LYS ( 43-) A CG 0.06 2.74 INTRA BF 114 ARG ( 115-) A O <-> 117 THR ( 118-) A CG2 0.06 2.74 INTRA BL 36 GLY ( 36-) A O <-> 39 TYR ( 39-) A CD2 0.06 2.74 INTRA BF 48 VAL ( 48-) A O <-> 89 ILE ( 90-) A CD1 0.06 2.74 INTRA BF 61 MET ( 61-) A CG <-> 88 TYR ( 89-) A CB 0.06 3.14 INTRA BF 41 PRO ( 41-) A CG <-> 42 TYR ( 42-) A CD1 0.06 3.14 INTRA BF 13 ILE ( 13-) A CD1 <-> 145 TRP ( 146-) A CH2 0.06 3.14 INTRA BF 31 ASN ( 31-) A CB <-> 35 GLU ( 35-) A OE2 0.06 2.74 INTRA BL 59 ASP ( 59-) A CB <-> 63 LYS ( 64-) A CE 0.06 3.14 INTRA BF 83 ARG ( 84-) A CD <-> 95 GLU ( 96-) A OE2 0.06 2.74 INTRA BF 130 ALA ( 131-) A O <-> 136 ARG ( 137-) A NE 0.06 2.64 INTRA BF 20 ILE ( 20-) A O <-> 23 VAL ( 23-) A CB 0.06 2.74 INTRA BF 20 ILE ( 20-) A O <-> 25 ILE ( 25-) A CG1 0.05 2.75 INTRA BF 11 ALA ( 11-) A O <-> 19 ALA ( 19-) A CB 0.05 2.75 INTRA BL 40 ILE ( 40-) A CB <-> 62 LEU ( 62-) A CD1 0.05 3.15 INTRA BF 84 GLN ( 85-) A O <-> 88 TYR ( 89-) A CE1 0.05 2.75 INTRA BL 112 ASN ( 113-) A OD1 <-> 113 PHE ( 114-) A CE2 0.05 2.75 INTRA BL 67 LYS ( 68-) A CD <-> 77 ASP ( 78-) A O 0.05 2.75 INTRA BF 126 ASP ( 127-) A O <-> 137 TRP ( 138-) A CD1 0.05 2.75 INTRA BF 120 ARG ( 121-) A CB <-> 132 ASP ( 133-) A OD2 0.05 2.75 INTRA BF 31 ASN ( 31-) A CG <-> 35 GLU ( 35-) A OE2 0.05 2.75 INTRA BL 128 LYS ( 129-) A O <-> 135 ARG ( 136-) A CB 0.05 2.75 INTRA BF 117 THR ( 118-) A O <-> 120 ARG ( 121-) A CG 0.05 2.75 INTRA BF 5 LEU ( 5-) A CD1 <-> 45 ILE ( 45-) A O 0.05 2.75 INTRA BF 58 LYS ( 58-) A CG <-> 59 ASP ( 59-) A N 0.05 2.95 INTRA BF 6 ARG ( 6-) A O <-> 46 VAL ( 46-) A CG1 0.05 2.75 INTRA BF 36 GLY ( 36-) A O <-> 39 TYR ( 39-) A CE2 0.05 2.75 INTRA BF 41 PRO ( 41-) A O <-> 45 ILE ( 45-) A CG2 0.05 2.75 INTRA BF 60 ILE ( 60-) A CG2 <-> 88 TYR ( 89-) A CB 0.05 3.15 INTRA BL 70 CYS ( 71-) A O <-> 78 LEU ( 79-) A CD2 0.05 2.75 INTRA BF 64 THR ( 65-) A CB <-> 69 GLU ( 70-) A OE1 0.04 2.76 INTRA BF 43 LYS ( 43-) A CD <-> 115 THR ( 116-) A OG1 0.04 2.76 INTRA BF 83 ARG ( 84-) A NH1 <-> 95 GLU ( 96-) A OE1 0.04 2.66 INTRA BF 61 MET ( 61-) A SD <-> 88 TYR ( 89-) A C 0.04 3.36 INTRA BF 18 ILE ( 18-) A CG1 <-> 23 VAL ( 23-) A CG2 0.04 3.16 INTRA BL 40 ILE ( 40-) A CG1 <-> 41 PRO ( 41-) A N 0.04 2.96 INTRA BF 34 LEU ( 34-) A CD1 <-> 136 ARG ( 137-) A CG 0.04 3.16 INTRA BF 61 MET ( 61-) A CE <-> 88 TYR ( 89-) A O 0.04 2.76 INTRA BF 121 LYS ( 122-) A CG <-> 122 ILE ( 123-) A N 0.04 2.96 INTRA BF 120 ARG ( 121-) A NE <-> 132 ASP ( 133-) A OD2 0.04 2.66 INTRA BF 28 PRO ( 28-) A C <-> 30 GLY ( 30-) A N 0.04 2.86 INTRA BF 27 GLY ( 27-) A N <-> 31 ASN ( 31-) A O 0.04 2.66 INTRA BL 31 ASN ( 31-) A ND2 <-> 35 GLU ( 35-) A OE1 0.04 2.66 INTRA BL 15 GLY ( 15-) A N <-> 22 SER ( 22-) A OG 0.04 2.66 INTRA BL 27 GLY ( 27-) A N <-> 28 PRO ( 28-) A CD 0.04 2.96 INTRA BF 39 TYR ( 39-) A CD1 <-> 40 ILE ( 40-) A N 0.04 2.96 INTRA BF 27 GLY ( 27-) A O <-> 152 ARG ( 153-) A NH2 0.04 2.66 INTRA BF 29 SER ( 29-) A OG <-> 104 LEU ( 105-) A CD1 0.03 2.77 INTRA BL 83 ARG ( 84-) A CD <-> 95 GLU ( 96-) A CD 0.03 3.17 INTRA BF 60 ILE ( 60-) A N <-> 64 THR ( 65-) A O 0.03 2.67 INTRA BF 30 GLY ( 30-) A N <-> 152 ARG ( 153-) A NH2 0.03 2.82 INTRA BF 109 GLY ( 110-) A O <-> 112 ASN ( 113-) A ND2 0.03 2.67 INTRA BL 22 SER ( 22-) A N <-> 23 VAL ( 23-) A N 0.03 2.57 INTRA BL 18 ILE ( 18-) A CB <-> 22 SER ( 22-) A C 0.03 3.17 INTRA BL 85 ILE ( 86-) A O <-> 88 TYR ( 89-) A CD1 0.03 2.77 INTRA BF 40 ILE ( 40-) A CD1 <-> 46 VAL ( 46-) A CG2 0.03 3.17 INTRA BL 36 GLY ( 36-) A C <-> 39 TYR ( 39-) A CD2 0.03 3.17 INTRA BF 67 LYS ( 68-) A NZ <-> 68 ALA ( 69-) A CB 0.02 2.98 INTRA BF 132 ASP ( 133-) A CB <-> 133 GLN ( 134-) A N 0.02 2.68 INTRA BF 110 ALA ( 111-) A C <-> 112 ASN ( 113-) A N 0.02 2.88 INTRA BL 14 GLY ( 14-) A CA <-> 22 SER ( 22-) A OG 0.02 2.78 INTRA BL 147 GLY ( 148-) A N <-> 148 LEU ( 149-) A N 0.02 2.58 INTRA BF 18 ILE ( 18-) A CB <-> 23 VAL ( 23-) A N 0.02 3.08 INTRA BL 25 ILE ( 25-) A CD1 <-> 33 GLY ( 33-) A CA 0.02 3.18 INTRA BF 108 VAL ( 109-) A CG1 <-> 112 ASN ( 113-) A N 0.02 3.08 INTRA BL 56 THR ( 56-) A CG2 <-> 65 TYR ( 66-) A OH 0.02 2.78 INTRA BF 25 ILE ( 25-) A C <-> 28 PRO ( 28-) A CD 0.02 3.18 INTRA BF 102 TYR ( 103-) A CE2 <-> 106 TYR ( 107-) A OH 0.02 2.78 INTRA BL 21 ALA ( 21-) A O <-> 24 LEU ( 24-) A N 0.02 2.68 INTRA BF 38 SER ( 38-) A OG <-> 139 TYR ( 140-) A CZ 0.02 2.78 INTRA BL 82 ALA ( 83-) A CB <-> 88 TYR ( 89-) A OH 0.01 2.79 INTRA BL 26 THR ( 26-) A CG2 <-> 150 THR ( 151-) A OG1 0.01 2.79 INTRA BF 119 LEU ( 120-) A C <-> 120 ARG ( 121-) A C 0.01 2.79 INTRA BF 41 PRO ( 41-) A O <-> 45 ILE ( 45-) A N 0.01 2.69 INTRA BF 15 GLY ( 15-) A C <-> 16 GLY ( 16-) A C 0.01 2.79 INTRA BL 31 ASN ( 31-) A OD1 <-> 104 LEU ( 105-) A CG 0.01 2.79 INTRA BL 85 ILE ( 86-) A C <-> 88 TYR ( 89-) A CD1 0.01 3.19 INTRA BF 38 SER ( 38-) A OG <-> 119 LEU ( 120-) A CD1 0.01 2.79 INTRA BF 131 CYS ( 132-) A SG <-> 134 LEU ( 135-) A C 0.01 3.39 INTRA BF 22 SER ( 22-) A C <-> 24 LEU ( 24-) A N 0.01 2.89 INTRA BF 118 LEU ( 119-) A C <-> 120 ARG ( 121-) A N 0.01 2.89 INTRA BF 61 MET ( 61-) A CE <-> 96 THR ( 97-) A OG1 0.01 2.79 INTRA BF 108 VAL ( 109-) A CG1 <-> 111 GLY ( 112-) A C 0.01 3.19 INTRA BL 83 ARG ( 84-) A NE <-> 95 GLU ( 96-) A CD 0.01 3.09 INTRA BF 39 TYR ( 39-) A CG <-> 40 ILE ( 40-) A N 0.01 2.99 INTRA BF 60 ILE ( 60-) A CG2 <-> 89 ILE ( 90-) A CG1 0.01 3.19 INTRA BF 144 GLN ( 145-) A CB <-> 145 TRP ( 146-) A N 0.01 2.69 INTRA BF 38 SER ( 38-) A O <-> 41 PRO ( 41-) A CD 0.01 2.79 INTRA BF # 62 # Note: Some notes regarding these bumps The bumps have been binned in 5 categories ranging from 'should deal with' 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: 41.758 Total bump value per residue: 1.830 Total number of bumps: 302 Total squared bump value: 8.412 Total number of bumps in the mildest bin: 246 Total number of bumps in the second bin: 56 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 # 63 # Warning: Inside/Outside residue distribution unusual The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density. inside/outside RMS Z-score : 1.231 1 MET ( 1) : -6.604 55 HIS ( 55) : -6.832 112 ASN ( 113) : -5.148 122 ILE ( 123) : -5.412 124 GLN ( 125) : -7.147 127 ILE ( 128) : -5.267 133 GLN ( 134) : -5.304 143 LYS ( 144) : -6.217 149 MET ( 150) : -6.676 151 ARG ( 152) : -5.775 152 ARG ( 153) : -6.419 156 ARG ( 157) : -6.046 160 LEU ( 161) : -6.764 163 GLN ( 164) : -7.890 164 GLN ( 165) : -7.882 # 64 # 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. 163 GLN ( 164-) A -7.89 124 GLN ( 125-) A -7.15 55 HIS ( 55-) A -6.83 160 LEU ( 161-) A -6.76 149 MET ( 150-) A -6.68 152 ARG ( 153-) A -6.42 143 LYS ( 144-) A -6.22 156 ARG ( 157-) A -6.05 151 ARG ( 152-) A -5.77 122 ILE ( 123-) A -5.41 133 GLN ( 134-) A -5.30 127 ILE ( 128-) A -5.27 112 ASN ( 113-) A -5.15 # 65 # Warning: Abnormal packing environment for sequential residues A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc. The table below lists the first and last residue in each stretch found, as well as the average residue score of the series. 28 PRO ( 28-) A 30 - GLY 30- ( A) -4.36 122 ILE ( 123-) A 124 - GLN 125- ( A) -5.75 158 ILE ( 159-) A 161 - TRP 162- ( A) -5.03 # 66 # Error: Abnormal average packing environment The average packing score for the structure is very low. A molecule is certain to be incorrect if the average packing score is below -3.0. Poorly refined molecules, very well energy minimized misthreaded molecules and low homology models give values between -2.0 and -3.0. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF]. Average for range 1 - 165 : -2.324 Number of ambiguities touching ambiguities: 0 # 67 # 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. 55 HIS ( 55-) A 75 ASN ( 76-) A # 68 # 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. 53 HIS ( 53-) A HIS-D 0.38 55 HIS ( 55-) A HIS-D 0.38 # 69 # 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. 10 ALA ( 10-) A N 20 ILE ( 20-) A N 22 SER ( 22-) A N 23 VAL ( 23-) A N 26 THR ( 26-) A N 49 TRP ( 49-) A N 50 THR ( 50-) A N 54 GLY ( 54-) A N 58 LYS ( 58-) A N 62 LEU ( 62-) A N 63 LYS ( 64-) A N 67 LYS ( 68-) A N 68 ALA ( 69-) A N 70 CYS ( 71-) A N 72 ALA ( 73-) A N 73 LEU ( 74-) A N 75 ASN ( 76-) A N 76 LYS ( 77-) A N 83 ARG ( 84-) A NE 83 ARG ( 84-) A NH1 84 GLN ( 85-) A N 86 ASN ( 87-) A N 88 TYR ( 89-) A OH 90 LYS ( 91-) A N 96 THR ( 97-) A N 108 VAL ( 109-) A N 112 ASN ( 113-) A ND2 115 THR ( 116-) A N 116 SER ( 117-) A N 121 LYS ( 122-) A N 128 LYS ( 129-) A N 130 ALA ( 131-) A N 131 CYS ( 132-) A N 136 ARG ( 137-) A N 136 ARG ( 137-) A NE 136 ARG ( 137-) A NH2 137 TRP ( 138-) A NE1 143 LYS ( 144-) A NZ 144 GLN ( 145-) A N 147 GLY ( 148-) A N 152 ARG ( 153-) A NE # 70 # 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. 69 GLU ( 70-) A OE1 95 GLU ( 96-) A OE1 # 71 # 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. Total number of donors: 242 of which buried: 105 Total number of acceptors: 236 of which buried: 72 Total number of donor+acceptors: 24 (donor+acceptor is e.g. the Ser Ogamma that can donate and accept) of which buried: 5 Buried donors: 105 without H-bond: 36 essentially without H-bond: 0 with only a very poor H-bond: 1 with a poor H-bond: 3 with a H-bond: 65 Buried acceptors: 72 without H-bond: 27 essentially without H-bond: 0 with only a very poor H-bond: 2 with a poor H-bond: 1 with a H-bond: 42 # 72 # 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. # 73 # Note: No ions (of a type we can validate) in structure Since there are no ions in the structure of a type we can validate, this check will not be executed. Since there are no waters, the water check has been skipped. SOUP contains no water: # 74 # Warning: Possible wrong residue type The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue. 59 ASP ( 59-) A H-bonding suggests Asn; but Alt-Rotamer # 75 # 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 ( 1) 62 ( 62) A Protein checkset 2 63 ( 64) 164 ( 165) A Protein checkset 3 165 ( 166) 165 ( 166) A Sugar checkset 4 166 ( 165) 166 ( 165) A Q O2 <- 164 checkset # 76 # Note: Summary report for users of a structure This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations. 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 : -4.560 (poor) Ramachandran plot appearance : -2.999 chi-1/chi-2 rotamer normality : -3.640 (poor) Backbone conformation : -4.451 (bad) RMS Z-scores, should be close to 1.0: Bond lengths : 1.006 Bond angles : 1.310 Omega angle restraints : 0.708 (tight) Side chain planarity : 0.343 (tight) Improper dihedral distribution : 1.114 Inside/Outside distribution : 1.231 (unusual) # 77 # 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. # 78 # Note: No crippling problems detected Some problems can be so crippling that they negatively influence the validity of other validation steps. If such a problem is detected, it must be solved and some further refinemnet must be done before you can continue working with a new WHAT CHECK report. In this file such problems were not detected. You can therefore try to fix as many problems in one go as you want. # 79 # Note: No resolution information detected WHAT CHECK needs to know the resolution of your data to provide advice for the refinement process. This resolution information is needed because a Z-score that is very good at 1.0 Angstrom resolution might actually be a sign of over-refinement at 3.5 Angstrom, etcetera. So, take a look at the formats of REMARK 2 and/or REMARK 3 and put the resolution in ether of those 2. An example of a REMARK 2 card is: REMARK 2 RESOLUTION. 4.50 ANGSTROMS. ============== 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) 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). 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. /home/vriend/whatif/dbdata/pdbout2html After running WHAT IF's WHAT CHECK option many things have happened to the data structure that might not be optimal for many other options. FULCHK therefore is a so-called terminal option, i.e. after running the validation option, WHAT IF will restart without any coordinates in the soup; so the molecule you just checked got deleted together with anything else you might have had in the SOUP. Option not found, try:%NO For obvious reasons $ commands are not allowed in WWW scripts. WHAT IF detected a $ in a WWW script. The command will be listed below. If this command contains something that is potentially harmful to your environment, please mail G Vriend (Vriend@cmbi.kun.nl) which $ command was detected, and from where you got this script. Option:$/home/vriend/whatif/dbdata/pdbout2html ERROR. Trying to close non-opened log file ============== 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) 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). 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.