************************************************************************ ********** REPORT OF PROTEIN ANALYSIS by the WHAT IF program ********** ************************************************************************ Date : 2015-05-08 This report was created by WHAT IF version 20150422-1601 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. # 1 # Note: Introduction WHAT CHECK needs to read in 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 syyetry 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. # 2 # Error: Missing unit cell information No SCALE matrix is given in the PDB file. # 3 # Error: Missing symmetry information Problem: No CRYST1 card is given in the PDB file. SYMMETRY will be unavailable for this molecule. # 4 # 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 ASN ( 2-) A - 3 ILE ( 3-) A - 4 SER ( 4-) A - 5 GLN ( 5-) A - 6 ALA ( 6-) A - 7 GLY ( 7-) A - 8 ILE ( 8-) A - 9 ASN ( 9-) A - 10 LEU ( 10-) A - 11 ILE ( 11-) A - 12 LYS ( 12-) A - 13 SER ( 13-) A - 14 PHE ( 14-) A - 15 GLU ( 15-) A - 16 GLY ( 16-) A - 17 LEU ( 17-) A - 18 ARG ( 18-) A - 19 THR ( 19-) A - 20 LYS ( 20-) A - 21 ALA ( 21-) A - 22 TYR ( 22-) A - 23 LYS ( 23-) A - 24 ALA ( 24-) A - 25 VAL ( 25-) A - 26 PRO ( 26-) A - 27 THR ( 27-) A - 28 GLU ( 28-) A - 29 LYS ( 29-) A - 30 TYR ( 30-) A - 31 TYR ( 31-) A - 32 THR ( 32-) A - 33 ILE ( 33-) A - 34 GLY ( 34-) A - 35 TYR ( 35-) A - 36 GLY ( 36-) A - 37 HIS ( 37-) A - 38 TYR ( 38-) A - 39 GLY ( 39-) A - 40 SER ( 40-) A - 41 ASP ( 41-) A - 42 VAL ( 42-) A - 43 HIS ( 43-) A - 44 PRO ( 44-) A - 45 CYS ( 45-) A - 46 GLN ( 46-) A - 47 VAL ( 47-) A - 48 ILE ( 48-) A - 49 SER ( 49-) A - 50 GLU ( 50-) A - 51 GLU ( 51-) A - 52 LYS ( 52-) A - 53 ALA ( 53-) A - 54 GLU ( 54-) A - 55 LYS ( 55-) A - 56 LEU ( 56-) A - 57 LEU ( 57-) A - 58 ARG ( 58-) A - 59 ASP ( 59-) A - 60 ASP ( 60-) A - 61 VAL ( 61-) A - 62 GLN ( 62-) A - 63 GLU ( 63-) A - 64 PHE ( 64-) A - 65 VAL ( 65-) A - 66 ASP ( 66-) A - 67 GLY ( 67-) A - 68 VAL ( 68-) A - 69 ASP ( 69-) A - 70 LYS ( 70-) A - 71 LEU ( 71-) A - 72 LEU ( 72-) A - 73 LYS ( 73-) A - 74 VAL ( 74-) A - 75 ASP ( 75-) A - 76 VAL ( 76-) A - 77 THR ( 77-) A - 78 GLN ( 78-) A - 79 SER ( 79-) A - 80 GLN ( 80-) A - 81 PHE ( 81-) A - 82 ASP ( 82-) A - 83 ALA ( 83-) A - 84 LEU ( 84-) A - 85 VAL ( 85-) A - 86 SER ( 86-) A - 87 PHE ( 87-) A - 88 ALA ( 88-) A - 89 TYR ( 89-) A - 90 ASN ( 90-) A - 91 VAL ( 91-) A - 92 GLY ( 92-) A - 93 LEU ( 93-) A - 94 GLY ( 94-) A - 95 ALA ( 95-) A - 96 LEU ( 96-) A - 97 LYS ( 97-) A - 98 SER ( 98-) A - 99 SER ( 99-) A - 100 THR ( 100-) A - 101 LEU ( 101-) A - 102 LEU ( 102-) A - 103 GLN ( 103-) A - 104 TYR ( 104-) A - 105 LEU ( 105-) A - 106 ASN ( 106-) A - 107 ALA ( 107-) A - 108 GLY ( 108-) A - 109 ASN ( 109-) A - 110 PHE ( 110-) A - 111 GLN ( 111-) A - 112 LYS ( 112-) A - 113 ALA ( 113-) A - 114 ALA ( 114-) A - 115 ASN ( 115-) A - 116 GLU ( 116-) A - 117 PHE ( 117-) A - 118 LEU ( 118-) A - 119 LYS ( 119-) A - 120 TRP ( 120-) A - 121 ASN ( 121-) A - 122 LYS ( 122-) A - 123 SER ( 123-) A - 124 GLY ( 124-) A - 125 GLY ( 125-) A - 126 LYS ( 126-) A - 127 VAL ( 127-) A - 128 TYR ( 128-) A - 129 ASN ( 129-) A - 130 GLY ( 130-) A - 131 LEU ( 131-) A - 132 VAL ( 132-) A - 133 LYS ( 133-) A - 134 ARG ( 134-) A - 135 ARG ( 135-) A - 136 GLU ( 136-) A - 137 GLN ( 137-) A - 138 GLU ( 138-) A - 139 ARG ( 139-) A - 140 THR ( 140-) A - 141 LEU ( 141-) A - 142 PHE ( 142-) A - 143 LEU ( 143-) A - 144 THR ( 144-) A - 145 GLY ( 145-) A - 146 GLU ( 146-) A - 147 SER ( 147-) A - 148 LYS ( 148-) A - 149 ASN ( 149-) A - 150 VAL ( 150-) A - 151 SER ( 151-) A - 152 ARG ( 152-) A - 153 GLU ( 153-) A - 154 THR ( 154-) A - 155 SER ( 155-) A - 156 LYS ( 156-) A - 157 PRO ( 157-) A - 158 LYS ( 158-) A - 159 THR ( 159-) A - 160 SER ( 160-) A - 161 LYS ( 161-) A - 162 THR ( 162-) A - 163 ASN ( 163-) A - 164 THR ( 164-) A - 165 HIS ( 165-) A - 166 VAL ( 166-) A - 167 VAL ( 167-) A - 168 LYS ( 168-) A - 169 LYS ( 169-) A - 170 GLY ( 170-) A - 171 ASP ( 171-) A - 172 THR ( 172-) A - 173 LEU ( 173-) A - 174 SER ( 174-) A - 175 GLU ( 175-) A - 176 ILE ( 176-) A - 177 ALA ( 177-) A - 178 LYS ( 178-) A - 179 LYS ( 179-) A - 180 ILE ( 180-) A - 181 LYS ( 181-) A - 182 THR ( 182-) A - 183 SER ( 183-) A - 184 THR ( 184-) A - 185 LYS ( 185-) A - 186 THR ( 186-) A - 187 LEU ( 187-) A - 188 LEU ( 188-) A - 189 GLU ( 189-) A - 190 LEU ( 190-) A - 191 ASN ( 191-) A - 192 PRO ( 192-) A - 193 THR ( 193-) A - 194 ILE ( 194-) A - 195 LYS ( 195-) A - 196 ASN ( 196-) A - 197 PRO ( 197-) A - 198 ASN ( 198-) A - 199 LYS ( 199-) A - 200 ILE ( 200-) A - 201 TYR ( 201-) A - 202 VAL ( 202-) A - 203 GLY ( 203-) A - 204 GLN ( 204-) A - 205 ARG ( 205-) A - 206 ILE ( 206-) A - 207 ASN ( 207-) A - 208 VAL ( 208-) A - 209 GLY ( 209-) A - 210 GLY ( 210-) A - 211 SER ( 211-) A - 212 PRO ( 212-) A - 213 VAL ( 213-) A - 214 LYS ( 214-) A - 215 SER ( 215-) A - 216 THR ( 216-) A - 217 LEU ( 217-) A - 218 LYS ( 218-) A - 219 TYR ( 219-) A - 220 LYS ( 220-) A - 221 ILE ( 221-) A - 222 LYS ( 222-) A - 223 ARG ( 223-) A - 224 GLY ( 224-) A - 225 GLU ( 225-) A - 226 THR ( 226-) A - 227 LEU ( 227-) A - 228 THR ( 228-) A - 229 GLY ( 229-) A - 230 ILE ( 230-) A - 231 ALA ( 231-) A - 232 LYS ( 232-) A - 233 LYS ( 233-) A - 234 ASN ( 234-) A - 235 LYS ( 235-) A - 236 THR ( 236-) A - 237 THR ( 237-) A - 238 VAL ( 238-) A - 239 SER ( 239-) A - 240 GLN ( 240-) A - 241 LEU ( 241-) A - 242 MET ( 242-) A - 243 LYS ( 243-) A - 244 LEU ( 244-) A - 245 ASN ( 245-) A - 246 PRO ( 246-) A - 247 ASN ( 247-) A - 248 ILE ( 248-) A - 249 LYS ( 249-) A - 250 ASN ( 250-) A - 251 ALA ( 251-) A - 252 ASN ( 252-) A - 253 ASN ( 253-) A - 254 ILE ( 254-) A - 255 TYR ( 255-) A - 256 ALA ( 256-) A - 257 GLY ( 257-) A - 258 GLN ( 258-) A - 259 THR ( 259-) A - 260 ILE ( 260-) A - 261 ARG ( 261-) A - 262 LEU ( 262-) A - 263 LYS ( 263-) A - 264 NAG ( 264-) A - 265 LYS ( 263-) A - # 5 # Note: No strange inter-chain connections detected No covalent bonds have been detected between molecules with non-identical chain identifiers. # 6 # Note: No duplicate atom names in ligands All atom names in ligands (if any) seem adequately unique. # 7 # Note: In all cases the primary alternate atom was used WHAT CHECK saw no need to make any alternate atom corrections (which means they either are all correct, or there are none). # 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 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. # 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) 263 ( 263) A Protein checkset 2 264 ( 264) 264 ( 264) A Sugar checkset 3 265 ( 263) 265 ( 263) A K O2 <- 263 checkset \begin{note} \showsect{Some numbers...} Number of NMR MODELs skipped upon reading PDB file: 0 This is an X-ray structure. No MODELs found The total number of amino acids found is 263 of which 228 have poor or (essentially) missing atoms No nucleic acids observed in input file Number of (recognized) sugars: 1 of which one has poor or (essentially) missing atoms') No water observed in input file Residue numbers increase monotonously OK \end{note} # 16 # 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 MNISQAGINLIKSFEGLRTKAYKAVPTEKYYTIGYGHYGSDVHPCQVISEEKAEKLLRDD ( 1)-( 60) S B SS S HHHHHHSSSSS 70 80 90 100 110 120 | | | | | | 61 - 120 VQEFVDGVDKLLKVDVTQSQFDALVSFAYNVGLGALKSSTLLQYLNAGNFQKAANEFLKW ( 61)-( 120) S S TT TT S THHHHHHHHHHTTBS EE 130 140 150 160 170 180 | | | | | | 121 - 180 NKSGGKVYNGLVKRREQERTLFLTGESKNVSRETSKPKTSKTNTHVVKKGDTLSEIAKKI ( 121)-( 180)E TTS EEETTTTEE SBSS S SS BS S SS S GGGGGS SSTTTTHHHHH 190 200 210 220 230 240 | | | | | | 181 - 240 KTSTKTLLELNPTIKNPNKIYVGQRINVGGSPVKSTLKYKIKRGETLTGIAKKNKTTVSQ ( 181)-( 240)HHHHHTSS TTTTHHHHT TTHHHHTTTS SS SSSSSSSSS 250 260 | | 241 - 263 LMKLNPNIKNANNIYAGQTIRLK ( 241)-( 263) # 17 # Note: No rounded coordinates detected No significant rounding of atom coordinates has been detected. # 18 # 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. 58 ARG ( 58-) A - 62 GLN ( 62-) A - 96 LEU ( 96-) A - 214 LYS ( 214-) A - 222 LYS ( 222-) A - 255 TYR ( 255-) A - # 19 # 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. # 20 # 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'. 264 NAG ( 264-) A - O4 264 NAG ( 264-) A - C4 264 NAG ( 264-) A - C1 264 NAG ( 264-) A - O5 264 NAG ( 264-) A - C5 264 NAG ( 264-) A - C6 264 NAG ( 264-) A - O6 264 NAG ( 264-) A - C3 264 NAG ( 264-) A - O3 264 NAG ( 264-) A - C2 264 NAG ( 264-) A - N2 264 NAG ( 264-) A - C7 264 NAG ( 264-) A - O7 264 NAG ( 264-) A - C8 # 21 # 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. 2 ASN ( 2-) A - High 3 ILE ( 3-) A - High 4 SER ( 4-) A - High 5 GLN ( 5-) A - High 6 ALA ( 6-) A - High 7 GLY ( 7-) A - High 9 ASN ( 9-) A - High 10 LEU ( 10-) A - High 11 ILE ( 11-) A - High 12 LYS ( 12-) A - High 13 SER ( 13-) A - High 14 PHE ( 14-) A - High 15 GLU ( 15-) A - High 16 GLY ( 16-) A - High 17 LEU ( 17-) A - High 18 ARG ( 18-) A - High 19 THR ( 19-) A - High 20 LYS ( 20-) A - High 21 ALA ( 21-) A - High 22 TYR ( 22-) A - High 23 LYS ( 23-) A - High 24 ALA ( 24-) A - High 28 GLU ( 28-) A - High 29 LYS ( 29-) A - High 30 TYR ( 30-) A - High 31 TYR ( 31-) A - High 33 ILE ( 33-) A - High 34 GLY ( 34-) A - High 35 TYR ( 35-) A - High 36 GLY ( 36-) A - High 37 HIS ( 37-) A - High 38 TYR ( 38-) A - High 40 SER ( 40-) A - High 41 ASP ( 41-) A - High 43 HIS ( 43-) A - High 44 PRO ( 44-) A - High 45 CYS ( 45-) A - High 46 GLN ( 46-) A - High 47 VAL ( 47-) A - High 48 ILE ( 48-) A - High 49 SER ( 49-) A - High 50 GLU ( 50-) A - High 51 GLU ( 51-) A - High 52 LYS ( 52-) A - High 53 ALA ( 53-) A - High 54 GLU ( 54-) A - High 55 LYS ( 55-) A - High 56 LEU ( 56-) A - High 57 LEU ( 57-) A - High 58 ARG ( 58-) A - High 59 ASP ( 59-) A - High 60 ASP ( 60-) A - High 62 GLN ( 62-) A - High 63 GLU ( 63-) A - High 64 PHE ( 64-) A - High 65 VAL ( 65-) A - High 66 ASP ( 66-) A - High 69 ASP ( 69-) A - High 70 LYS ( 70-) A - High 71 LEU ( 71-) A - High 72 LEU ( 72-) A - High 73 LYS ( 73-) A - High 75 ASP ( 75-) A - High 77 THR ( 77-) A - High 78 GLN ( 78-) A - High 79 SER ( 79-) A - High 80 GLN ( 80-) A - High 81 PHE ( 81-) A - High 82 ASP ( 82-) A - High 83 ALA ( 83-) A - High 84 LEU ( 84-) A - High 85 VAL ( 85-) A - High 86 SER ( 86-) A - High 87 PHE ( 87-) A - High 88 ALA ( 88-) A - High 89 TYR ( 89-) A - High 90 ASN ( 90-) A - High 91 VAL ( 91-) A - High 93 LEU ( 93-) A - High 94 GLY ( 94-) A - High 95 ALA ( 95-) A - High 96 LEU ( 96-) A - High 97 LYS ( 97-) A - High 98 SER ( 98-) A - High 99 SER ( 99-) A - High 100 THR ( 100-) A - High 101 LEU ( 101-) A - High 102 LEU ( 102-) A - High 103 GLN ( 103-) A - High 104 TYR ( 104-) A - High 105 LEU ( 105-) A - High 106 ASN ( 106-) A - High 107 ALA ( 107-) A - High 108 GLY ( 108-) A - High 109 ASN ( 109-) A - High 110 PHE ( 110-) A - High 111 GLN ( 111-) A - High 112 LYS ( 112-) A - High 113 ALA ( 113-) A - High 114 ALA ( 114-) A - High 115 ASN ( 115-) A - High 116 GLU ( 116-) A - High 117 PHE ( 117-) A - High 118 LEU ( 118-) A - High 119 LYS ( 119-) A - High 122 LYS ( 122-) A - High 126 LYS ( 126-) A - High 127 VAL ( 127-) A - High 128 TYR ( 128-) A - High 129 ASN ( 129-) A - High 131 LEU ( 131-) A - High 132 VAL ( 132-) A - High 133 LYS ( 133-) A - High 134 ARG ( 134-) A - High 135 ARG ( 135-) A - High 136 GLU ( 136-) A - High 137 GLN ( 137-) A - High 138 GLU ( 138-) A - High 139 ARG ( 139-) A - High 140 THR ( 140-) A - High 141 LEU ( 141-) A - High 142 PHE ( 142-) A - High 143 LEU ( 143-) A - High 146 GLU ( 146-) A - High 147 SER ( 147-) A - High 148 LYS ( 148-) A - High 149 ASN ( 149-) A - High 150 VAL ( 150-) A - High 151 SER ( 151-) A - High 152 ARG ( 152-) A - High 153 GLU ( 153-) A - High 154 THR ( 154-) A - High 155 SER ( 155-) A - High 156 LYS ( 156-) A - High 157 PRO ( 157-) A - High 158 LYS ( 158-) A - High 159 THR ( 159-) A - High 160 SER ( 160-) A - High 161 LYS ( 161-) A - High 162 THR ( 162-) A - High 166 VAL ( 166-) A - High 167 VAL ( 167-) A - High 168 LYS ( 168-) A - High 169 LYS ( 169-) A - High 170 GLY ( 170-) A - High 171 ASP ( 171-) A - High 172 THR ( 172-) A - High 173 LEU ( 173-) A - High 174 SER ( 174-) A - High 175 GLU ( 175-) A - High 176 ILE ( 176-) A - High 178 LYS ( 178-) A - High 179 LYS ( 179-) A - High 180 ILE ( 180-) A - High 181 LYS ( 181-) A - High 182 THR ( 182-) A - High 183 SER ( 183-) A - High 184 THR ( 184-) A - High 185 LYS ( 185-) A - High 186 THR ( 186-) A - High 187 LEU ( 187-) A - High 188 LEU ( 188-) A - High 189 GLU ( 189-) A - High 190 LEU ( 190-) A - High 191 ASN ( 191-) A - High 192 PRO ( 192-) A - High 193 THR ( 193-) A - High 194 ILE ( 194-) A - High 195 LYS ( 195-) A - High 196 ASN ( 196-) A - High 197 PRO ( 197-) A - High 198 ASN ( 198-) A - High 199 LYS ( 199-) A - High 200 ILE ( 200-) A - High 201 TYR ( 201-) A - High 202 VAL ( 202-) A - High 203 GLY ( 203-) A - High 204 GLN ( 204-) A - High 205 ARG ( 205-) A - High 206 ILE ( 206-) A - High 207 ASN ( 207-) A - High 208 VAL ( 208-) A - High 212 PRO ( 212-) A - High 213 VAL ( 213-) A - High 214 LYS ( 214-) A - High 215 SER ( 215-) A - High 216 THR ( 216-) A - High 218 LYS ( 218-) A - High 219 TYR ( 219-) A - High 220 LYS ( 220-) A - High 221 ILE ( 221-) A - High 222 LYS ( 222-) A - High 223 ARG ( 223-) A - High 225 GLU ( 225-) A - High 226 THR ( 226-) A - High 227 LEU ( 227-) A - High 228 THR ( 228-) A - High 229 GLY ( 229-) A - High 230 ILE ( 230-) A - High 231 ALA ( 231-) A - High 232 LYS ( 232-) A - High 233 LYS ( 233-) A - High 234 ASN ( 234-) A - High 235 LYS ( 235-) A - High 236 THR ( 236-) A - High 237 THR ( 237-) A - High 239 SER ( 239-) A - High 240 GLN ( 240-) A - High 241 LEU ( 241-) A - High 242 MET ( 242-) A - High 243 LYS ( 243-) A - High 244 LEU ( 244-) A - High 245 ASN ( 245-) A - High 247 ASN ( 247-) A - High 248 ILE ( 248-) A - High 249 LYS ( 249-) A - High 250 ASN ( 250-) A - High 251 ALA ( 251-) A - High 252 ASN ( 252-) A - High 253 ASN ( 253-) A - High 254 ILE ( 254-) A - High 255 TYR ( 255-) A - High 256 ALA ( 256-) A - High 257 GLY ( 257-) A - High 258 GLN ( 258-) A - High 259 THR ( 259-) A - High 260 ILE ( 260-) A - High 261 ARG ( 261-) A - High # 22 # 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. # 23 # 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. 263 LYS ( 263-) A - : Unknown problem # 24 # Note: No OXT found in the middle of chains No OXT groups were found in the middle of protein chains. # 25 # 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. # 26 # Note: Valine nomenclature OK No errors were detected in valine nomenclature. # 27 # Note: Threonine nomenclature OK No errors were detected in threonine nomenclature. # 28 # Note: Isoleucine nomenclature OK No errors were detected in isoleucine nomenclature. # 29 # Note: Leucine nomenclature OK No errors were detected in leucine nomenclature. # 30 # Note: Arginine nomenclature OK No errors were detected in arginine nomenclature. # 31 # Note: Tyrosine torsion conventions OK No errors were detected in tyrosine torsion angle conventions. # 32 # Note: Phenylalanine torsion conventions OK No errors were detected in phenylalanine torsion angle conventions. # 33 # Note: Aspartic acid torsion conventions OK No errors were detected in aspartic acid torsion angle conventions. # 34 # Note: Glutamic acid torsion conventions OK No errors were detected in glutamic acid torsion angle conventions. # 35 # Note: Phosphate group names OK in DNA/RNA No errors were detected in nucleic acid phosphate group naming conventions. # 36 # 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. # 37 # Warning: Unusual bond lengths The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given. Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length. 101 LEU ( 101-) A - N CA 1.38 -4.4 101 LEU ( 101-) A - CA CB 1.64 5.6 101 LEU ( 101-) A - CB CG 1.62 4.6 138 GLU ( 138-) A - CA C 1.61 4.2 138 GLU ( 138-) A - N -C 1.42 4.6 139 ARG ( 139-) A - N -C 1.42 4.5 140 THR ( 140-) A - N -C 1.41 4.0 141 LEU ( 141-) A - CA C 1.62 4.5 141 LEU ( 141-) A - N -C 1.42 4.4 152 ARG ( 152-) A - CA C 1.39 -6.6 152 ARG ( 152-) A - CA CB 1.62 4.5 153 GLU ( 153-) A - N CA 1.36 -5.3 187 LEU ( 187-) A - CA C 1.65 6.0 # 38 # 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: 1.107 RMS-deviation in bond distances: 0.023 # 39 # 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. 2 ASN ( 2-) A - CA CB CG 108.47 -4.1 9 ASN ( 9-) A - CA CB CG 108.27 -4.3 14 PHE ( 14-) A - CA CB CG 107.71 -6.1 31 TYR ( 31-) A - CA CB CG 105.53 -4.2 34 GLY ( 34-) A - -C N CA 127.75 4.2 35 TYR ( 35-) A - -C N CA 137.46 8.8 35 TYR ( 35-) A - N CA CB 119.24 5.1 35 TYR ( 35-) A - CA CB CG 104.61 -4.7 37 HIS ( 37-) A - NE2 CD2 CG 110.54 4.0 43 HIS ( 43-) A - NE2 CD2 CG 110.55 4.1 44 PRO ( 44-) A - N CA C 123.02 4.5 46 GLN ( 46-) A - -C N CA 112.11 -5.3 48 ILE ( 48-) A - N CA CB 118.81 4.9 48 ILE ( 48-) A - C CA CB 118.68 4.5 48 ILE ( 48-) A - CA CB CG2 102.75 -4.6 48 ILE ( 48-) A - CA CB CG1 121.79 6.7 49 SER ( 49-) A - N CA CB 118.94 5.0 51 GLU ( 51-) A - N CA CB 119.97 5.6 51 GLU ( 51-) A - C CA CB 94.50 -8.2 64 PHE ( 64-) A - CA CB CG 108.27 -5.5 75 ASP ( 75-) A - CA CB CG 108.40 -4.2 81 PHE ( 81-) A - CA CB CG 108.11 -5.7 87 PHE ( 87-) A - CA CB CG 107.57 -6.2 89 TYR ( 89-) A - CA CB CG 104.64 -4.7 90 ASN ( 90-) A - CA CB CG 107.63 -5.0 99 SER ( 99-) A - N CA CB 103.01 -4.4 99 SER ( 99-) A - C CA CB 120.12 5.3 100 THR ( 100-) A - -C N CA 139.14 9.7 100 THR ( 100-) A - C CA CB 101.83 -4.4 101 LEU ( 101-) A - -C N CA 86.70 -19.4 101 LEU ( 101-) A - N CA CB 81.50 -17.1 101 LEU ( 101-) A - C CA CB 140.93 16.2 101 LEU ( 101-) A - CA CB CG 145.47 8.3 102 LEU ( 102-) A - -C N CA 129.65 4.4 103 GLN ( 103-) A - C CA CB 98.21 -6.3 103 GLN ( 103-) A - CA CB CG 103.33 -5.4 103 GLN ( 103-) A - CB CG CD 101.60 -6.5 103 GLN ( 103-) A - NE2 CD OE1 126.98 4.4 105 LEU ( 105-) A - -C N CA 111.57 -5.6 106 ASN ( 106-) A - CA CB CG 107.90 -4.7 107 ALA ( 107-) A - C CA CB 104.19 -4.2 109 ASN ( 109-) A - CA CB CG 106.33 -6.3 110 PHE ( 110-) A - CA CB CG 108.32 -5.5 115 ASN ( 115-) A - CB CG ND2 93.48 -15.3 115 ASN ( 115-) A - CB CG OD1 44.43 -38.2 115 ASN ( 115-) A - ND2 CG OD1 137.91 15.3 117 PHE ( 117-) A - CA CB CG 107.87 -5.9 121 ASN ( 121-) A - CA CB CG 108.59 -4.0 122 LYS ( 122-) A - N CA CB 120.17 5.7 128 TYR ( 128-) A - CA CB CG 92.69 -11.0 129 ASN ( 129-) A - -C N CA 113.43 -4.6 135 ARG ( 135-) A - N CA CB 118.60 4.8 136 GLU ( 136-) A - -C N CA 130.70 5.0 137 GLN ( 137-) A - -C N CA 132.20 5.8 137 GLN ( 137-) A - N CA C 126.17 5.3 138 GLU ( 138-) A - -C N CA 134.14 6.9 138 GLU ( 138-) A - N CA CB 117.83 4.3 139 ARG ( 139-) A - -C N CA 130.21 4.7 140 THR ( 140-) A - -C N CA 130.00 4.6 140 THR ( 140-) A - N CA C 125.23 5.0 141 LEU ( 141-) A - -CA -C N 127.56 5.7 141 LEU ( 141-) A - -C N CA 132.82 6.2 142 PHE ( 142-) A - -C N CA 131.21 5.3 142 PHE ( 142-) A - N CA CB 118.76 4.9 142 PHE ( 142-) A - CA CB CG 97.48 -16.3 148 LYS ( 148-) A - -C N CA 132.44 6.0 149 ASN ( 149-) A - CA CB CG 102.71 -9.9 150 VAL ( 150-) A - -C N CA 129.23 4.2 152 ARG ( 152-) A - -C N CA 133.62 6.6 152 ARG ( 152-) A - N CA C 98.49 -4.5 152 ARG ( 152-) A - N CA CB 125.97 9.1 152 ARG ( 152-) A - C CA CB 87.04 -12.1 152 ARG ( 152-) A - CA CB CG 138.84 12.4 152 ARG ( 152-) A - CB CG CD 129.54 7.7 153 GLU ( 153-) A - -O -C N 130.86 4.9 153 GLU ( 153-) A - -CA -C N 104.17 -6.0 153 GLU ( 153-) A - N CA C 95.18 -5.7 153 GLU ( 153-) A - N CA CB 100.38 -6.0 153 GLU ( 153-) A - C CA CB 134.19 12.7 154 THR ( 154-) A - -O -C N 114.00 -5.6 154 THR ( 154-) A - -CA -C N 127.65 5.7 154 THR ( 154-) A - -C N CA 129.47 4.3 154 THR ( 154-) A - N CA CB 118.50 4.7 154 THR ( 154-) A - C CA CB 101.00 -4.8 155 SER ( 155-) A - -C N CA 111.77 -5.5 155 SER ( 155-) A - N CA C 98.11 -4.7 155 SER ( 155-) A - N CA CB 125.29 8.7 156 LYS ( 156-) A - -C N CA 104.26 -9.7 156 LYS ( 156-) A - N CA C 99.37 -4.2 156 LYS ( 156-) A - CA C O 128.30 4.4 156 LYS ( 156-) A - N CA CB 123.22 7.5 157 PRO ( 157-) A - -O -C N 131.44 6.7 157 PRO ( 157-) A - -CA -C N 99.93 -11.3 163 ASN ( 163-) A - CA CB CG 107.00 -5.6 165 HIS ( 165-) A - NE2 CD2 CG 110.61 4.1 187 LEU ( 187-) A - -C N CA 140.14 10.2 187 LEU ( 187-) A - N CA C 135.95 8.8 188 LEU ( 188-) A - -O -C N 116.34 -4.2 188 LEU ( 188-) A - -CA -C N 127.15 5.5 188 LEU ( 188-) A - -C N CA 130.64 5.0 188 LEU ( 188-) A - N CA C 126.79 5.6 188 LEU ( 188-) A - C CA CB 96.10 -7.4 189 GLU ( 189-) A - -C N CA 137.51 8.8 189 GLU ( 189-) A - N CA CB 123.33 7.5 190 LEU ( 190-) A - -C N CA 134.76 7.3 190 LEU ( 190-) A - C CA CB 98.87 -5.9 192 PRO ( 192-) A - -CA -C N 110.43 -4.3 194 ILE ( 194-) A - -C N CA 113.28 -4.7 196 ASN ( 196-) A - CA C O 111.56 -5.4 196 ASN ( 196-) A - C CA CB 119.79 5.1 196 ASN ( 196-) A - CA CB CG 102.02 -10.6 197 PRO ( 197-) A - -CA -C N 128.34 7.6 198 ASN ( 198-) A - C CA CB 97.12 -6.8 199 LYS ( 199-) A - -C N CA 98.55 -12.9 200 ILE ( 200-) A - N CA CB 121.02 6.2 201 TYR ( 201-) A - C CA CB 101.90 -4.3 202 VAL ( 202-) A - -C N CA 113.48 -4.6 202 VAL ( 202-) A - N CA C 94.36 -6.0 204 GLN ( 204-) A - CB CG CD 103.13 -5.6 206 ILE ( 206-) A - -C N CA 114.28 -4.1 207 ASN ( 207-) A - CA CB CG 107.89 -4.7 208 VAL ( 208-) A - -C N CA 114.07 -4.2 215 SER ( 215-) A - -C N CA 113.46 -4.6 219 TYR ( 219-) A - CA CB CG 104.78 -4.6 222 LYS ( 222-) A - -C N CA 136.20 8.1 223 ARG ( 223-) A - -C N CA 110.82 -6.0 223 ARG ( 223-) A - N CA CB 118.70 4.8 234 ASN ( 234-) A - CA CB CG 108.09 -4.5 245 ASN ( 245-) A - CA CB CG 108.00 -4.6 247 ASN ( 247-) A - CA CB CG 108.07 -4.5 250 ASN ( 250-) A - CA CB CG 107.96 -4.6 252 ASN ( 252-) A - CA CB CG 108.47 -4.1 253 ASN ( 253-) A - CA CB CG 108.16 -4.4 # 40 # 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: 1.717 RMS-deviation in bond angles: 3.301 # 41 # 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. # 42 # 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. 44 PRO ( 44-) A - N -7.5 -29.58 -2.68 44 PRO ( 44-) A - CA -6.9 28.68 38.19 48 ILE ( 48-) A - CA -9.4 19.02 33.21 137 GLN ( 137-) A - CA -11.8 11.42 33.94 142 PHE ( 142-) A - CA -8.9 19.64 33.98 187 LEU ( 187-) A - CA -6.7 24.19 34.22 189 GLU ( 189-) A - CA -10.3 17.04 33.95 The average deviation= 1.634 # 43 # 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 : 1.551 # 44 # 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. 187 LEU ( 187-) A - 11.71 188 LEU ( 188-) A - 7.69 197 PRO ( 197-) A - 7.48 140 THR ( 140-) A - 6.66 202 VAL ( 202-) A - 6.06 137 GLN ( 137-) A - 5.81 103 GLN ( 103-) A - 5.55 153 GLU ( 153-) A - 5.55 138 GLU ( 138-) A - 5.46 205 ARG ( 205-) A - 5.26 155 SER ( 155-) A - 5.15 49 SER ( 49-) A - 4.92 199 LYS ( 199-) A - 4.81 152 ARG ( 152-) A - 4.80 156 LYS ( 156-) A - 4.62 150 VAL ( 150-) A - 4.57 108 GLY ( 108-) A - 4.46 223 ARG ( 223-) A - 4.27 173 LEU ( 173-) A - 4.20 174 SER ( 174-) A - 4.17 50 GLU ( 50-) A - 4.16 222 LYS ( 222-) A - 4.11 184 THR ( 184-) A - 4.02 # 45 # 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 : 2.322 # 46 # Note: Side chain planarity OK All of the side chains of residues that have an intact planar group are planar within expected RMS deviations. # 47 # 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 : -1.989 # 48 # 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 : -1.989 # 49 # 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. 193 THR ( 193-) A - -3.4 44 PRO ( 44-) A - -3.0 100 THR ( 100-) A - -2.7 133 LYS ( 133-) A - -2.7 153 GLU ( 153-) A - -2.5 97 LYS ( 97-) A - -2.2 174 SER ( 174-) A - -2.1 126 LYS ( 126-) A - -2.1 99 SER ( 99-) A - -2.1 101 LEU ( 101-) A - -2.1 138 GLU ( 138-) A - -2.1 147 SER ( 147-) A - -2.1 186 THR ( 186-) A - -2.0 # 50 # 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. 7 GLY ( 7-) A - Poor phi/psi 16 GLY ( 16-) A - Poor phi/psi 25 VAL ( 25-) A - Omega to (next) Pro poor 34 GLY ( 34-) A - Poor phi/psi 35 TYR ( 35-) A - Poor phi/psi 43 HIS ( 43-) A - Omega to (next) Pro poor 44 PRO ( 44-) A - Poor phi/psi 45 CYS ( 45-) A - Poor phi/psi 52 LYS ( 52-) A - Poor phi/psi 53 ALA ( 53-) A - omega poor 55 LYS ( 55-) A - Poor phi/psi 67 GLY ( 67-) A - Poor phi/psi 90 ASN ( 90-) A - Poor phi/psi 92 GLY ( 92-) A - Poor phi/psi 95 ALA ( 95-) A - Poor phi/psi 98 SER ( 98-) A - omega poor 99 SER ( 99-) A - Poor phi/psi 100 THR ( 100-) A - omega poor 101 LEU ( 101-) A - Poor phi/psi 113 ALA ( 113-) A - Poor phi/psi 114 ALA ( 114-) A - Poor phi/psi 125 GLY ( 125-) A - Poor phi/psi 130 GLY ( 130-) A - Poor phi/psi 133 LYS ( 133-) A - Poor phi/psi 137 GLN ( 137-) A - Poor phi/psi 139 ARG ( 139-) A - Poor phi/psi 142 PHE ( 142-) A - omega poor 147 SER ( 147-) A - Poor phi/psi 151 SER ( 151-) A - omega poor 152 ARG ( 152-) A - Poor phi/psi 153 GLU ( 153-) A - Poor phi/psi 154 THR ( 154-) A - omega poor 155 SER ( 155-) A - omega poor 156 LYS ( 156-) A - Poor phi/psi, omega to (next) 160 SER ( 160-) A - Poor phi/psi 168 LYS ( 168-) A - omega poor 169 LYS ( 169-) A - Poor phi/psi 171 ASP ( 171-) A - Poor phi/psi 174 SER ( 174-) A - Poor phi/psi 186 THR ( 186-) A - omega poor 187 LEU ( 187-) A - omega poor 188 LEU ( 188-) A - omega poor 189 GLU ( 189-) A - Poor phi/psi 190 LEU ( 190-) A - omega poor 191 ASN ( 191-) A - Omega to (next) Pro poor 193 THR ( 193-) A - Poor phi/psi 196 ASN ( 196-) A - Omega to (next) Pro poor 198 ASN ( 198-) A - Poor phi/psi 201 TYR ( 201-) A - omega poor 203 GLY ( 203-) A - Poor phi/psi 210 GLY ( 210-) A - Poor phi/psi 211 SER ( 211-) A - Omega to (next) Pro poor 215 SER ( 215-) A - Poor phi/psi 216 THR ( 216-) A - Poor phi/psi 219 TYR ( 219-) A - Poor phi/psi 222 LYS ( 222-) A - Poor phi/psi 224 GLY ( 224-) A - Poor phi/psi 229 GLY ( 229-) A - Poor phi/psi 245 ASN ( 245-) A - Omega to (next) Pro poor 257 GLY ( 257-) A - Poor phi/psi chi-1/chi-2 correlation Z-score : -2.865 # 51 # 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 : -2.865 # 52 # 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. 104 TYR ( 104-) A - 0.38 # 53 # 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! 33 ILE ( 33-) A - 0 35 TYR ( 35-) A - 0 42 VAL ( 42-) A - S 0 43 HIS ( 43-) A - 0 46 GLN ( 46-) A - H 0 52 LYS ( 52-) A - S 0 53 ALA ( 53-) A - S 0 54 GLU ( 54-) A - S 0 55 LYS ( 55-) A - S 0 93 LEU ( 93-) A - 0 97 LYS ( 97-) A - 0 99 SER ( 99-) A - 0 100 THR ( 100-) A - S 0 101 LEU ( 101-) A - 0 131 LEU ( 131-) A - 0 136 GLU ( 136-) A - 0 138 GLU ( 138-) A - S 0 140 THR ( 140-) A - S 0 141 LEU ( 141-) A - S 0 148 LYS ( 148-) A - 0 152 ARG ( 152-) A - 0 153 GLU ( 153-) A - 0 154 THR ( 154-) A - S 0 155 SER ( 155-) A - 0 156 LYS ( 156-) A - S 0 157 PRO ( 157-) A - 0 173 LEU ( 173-) A - 0 174 SER ( 174-) A - 0 175 GLU ( 175-) A - 0 188 LEU ( 188-) A - S 0 189 GLU ( 189-) A - 0 190 LEU ( 190-) A - 0 193 THR ( 193-) A - 0 194 ILE ( 194-) A - 0 195 LYS ( 195-) A - 0 197 PRO ( 197-) A - H 0 198 ASN ( 198-) A - H 0 214 LYS ( 214-) A - S 0 216 THR ( 216-) A - S 0 219 TYR ( 219-) A - S 0 220 LYS ( 220-) A - S 0 222 LYS ( 222-) A - S 0 223 ARG ( 223-) A - S 0 225 GLU ( 225-) A - 0 262 LEU ( 262-) A - 0 91 VAL ( 91-) A - S 1 95 ALA ( 95-) A - 1 96 LEU ( 96-) A - 1 98 SER ( 98-) A - 1 102 LEU ( 102-) A - 1 129 ASN ( 129-) A - S 1 137 GLN ( 137-) A - 1 146 GLU ( 146-) A - 1 169 LYS ( 169-) A - 1 170 GLY ( 170-) A - S 1 187 LEU ( 187-) A - S 1 191 ASN ( 191-) A - 1 202 VAL ( 202-) A - 1 226 THR ( 226-) A - 1 38 TYR ( 38-) A - S 2 44 PRO ( 44-) A - 2 94 GLY ( 94-) A - 2 139 ARG ( 139-) A - 2 147 SER ( 147-) A - S 2 171 ASP ( 171-) A - S 2 199 LYS ( 199-) A - H 2 201 TYR ( 201-) A - 2 218 LYS ( 218-) A - S 2 221 ILE ( 221-) A - S 2 # 54 # Warning: Backbone conformation Z-score low A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is unusual. Backbone conformation Z-score : -2.404 # 55 # Warning: Omega angle restraints not strong enough 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 of this distribution is above 7.0, which indicates that the omega values have been under-restrained. Omega average and std. deviation= 180.700 7.261 # 56 # Note: PRO puckering amplitude OK Puckering amplitudes for all PRO residues are within normal ranges. # 57 # 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]. 26 PRO ( 26-) A - -117.5 half-chair C-delta/C-gamma (-126 degrees) 212 PRO ( 212-) A - 102.0 envelop C-beta (108 degrees) 246 PRO ( 246-) A - -118.4 half-chair C-delta/C-gamma (-126 degrees) # 58 # Note: Backbone oxygen evaluation OK All residues for which similar local backbone conformations could be found in the WHAT CHECK database have a backbone oxygen position that has been observed at least a few times in that database. # 59 # Warning: Possible peptide flips For the residues listed in the table below, the backbone formed by the residue mentioned and the one N-terminal of it show systematic deviations from normality that are consistent with a peptide flip. This can either be a 180 degree flip of the entire peptide plane or a trans to cis flip. (Cis to trans flips cannot be detected yet). The type can be TT+, TC-, or TC+: TT+ indicates a 180 degree flip of the entire peptide plane. TC- indicates a trans to cis conversion that requires a flip of the N atom. TC+ indicates a trans to cis conversion that requires a flip of the O atom. Note that the method will only work correctly for PDB files with full isotropic B-factors. 208 VAL ( 208-) A - TT+ Likely # 60 # 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). 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. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively. 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. 152 ARG ( 152-) A - CB <--> 153 GLU ( 153-) A - N 1.04 1.66 INTRA BF 101 LEU ( 101-) A - CB <--> 188 LEU ( 188-) A - N 0.56 2.54 INTRA BF 101 LEU ( 101-) A - CG <--> 187 LEU ( 187-) A - N 0.50 2.60 INTRA BF 99 SER ( 99-) A - C <--> 189 GLU ( 189-) A - CA 0.49 2.71 INTRA BL 100 THR ( 100-) A - C <--> 101 LEU ( 101-) A - CB 0.47 2.33 INTRA BF 141 LEU ( 141-) A - CA <--> 154 THR ( 154-) A - N 0.45 2.65 INTRA BL 100 THR ( 100-) A - C <--> 101 LEU ( 101-) A - CA 0.45 1.85 INTRA BL 155 SER ( 155-) A - C <--> 156 LYS ( 156-) A - C 0.45 2.35 INTRA BL 101 LEU ( 101-) A - C <--> 187 LEU ( 187-) A - C 0.45 2.75 INTRA BL 138 GLU ( 138-) A - C <--> 152 ARG ( 152-) A - N 0.43 2.67 INTRA BL 101 LEU ( 101-) A - CG <--> 186 THR ( 186-) A - C 0.42 2.78 INTRA BF 101 LEU ( 101-) A - CB <--> 187 LEU ( 187-) A - C 0.40 2.80 INTRA BF 45 CYS ( 45-) A - SG <--> 48 ILE ( 48-) A - CG1 0.38 3.02 INTRA BF 140 THR ( 140-) A - N <--> 153 GLU ( 153-) A - CA 0.38 2.72 INTRA BL 99 SER ( 99-) A - CB <--> 101 LEU ( 101-) A - CG 0.38 2.82 INTRA BF 138 GLU ( 138-) A - CA <--> 152 ARG ( 152-) A - CD 0.38 2.82 INTRA BF 45 CYS ( 45-) A - SG <--> 48 ILE ( 48-) A - N 0.37 2.93 INTRA BF 141 LEU ( 141-) A - N <--> 153 GLU ( 153-) A - CB 0.37 2.73 INTRA BF 34 GLY ( 34-) A - N <--> 223 ARG ( 223-) A - CB 0.35 2.75 INTRA BF 101 LEU ( 101-) A - CA <--> 187 LEU ( 187-) A - C 0.34 2.86 INTRA BL 101 LEU ( 101-) A - CD2 <--> 188 LEU ( 188-) A - N 0.34 2.76 INTRA BF 100 THR ( 100-) A - O <--> 101 LEU ( 101-) A - CA 0.34 2.06 INTRA BL 138 GLU ( 138-) A - CA <--> 152 ARG ( 152-) A - CG 0.34 2.86 INTRA BF 95 ALA ( 95-) A - N <--> 188 LEU ( 188-) A - CB 0.34 2.76 INTRA BF 140 THR ( 140-) A - C <--> 154 THR ( 154-) A - N 0.33 2.77 INTRA BL 139 ARG ( 139-) A - N <--> 152 ARG ( 152-) A - CD 0.33 2.77 INTRA BF 35 TYR ( 35-) A - C <--> 224 GLY ( 224-) A - N 0.33 2.77 INTRA BL 33 ILE ( 33-) A - C <--> 45 CYS ( 45-) A - SG 0.33 3.07 INTRA BF 100 THR ( 100-) A - N <--> 189 GLU ( 189-) A - CA 0.32 2.78 INTRA BL 137 GLN ( 137-) A - C <--> 152 ARG ( 152-) A - CG 0.32 2.88 INTRA BF 101 LEU ( 101-) A - CG <--> 186 THR ( 186-) A - CA 0.32 2.88 INTRA BF 100 THR ( 100-) A - N <--> 189 GLU ( 189-) A - CB 0.32 2.78 INTRA BF 35 TYR ( 35-) A - CD2 <--> 222 LYS ( 222-) A - N 0.31 2.79 INTRA BF 100 THR ( 100-) A - N <--> 101 LEU ( 101-) A - CB 0.31 2.59 INTRA BF 169 LYS ( 169-) A - CB <--> 174 SER ( 174-) A - CB 0.31 2.89 INTRA BF 141 LEU ( 141-) A - N <--> 153 GLU ( 153-) A - CG 0.31 2.79 INTRA BF 141 LEU ( 141-) A - N <--> 153 GLU ( 153-) A - CA 0.31 2.79 INTRA BL 101 LEU ( 101-) A - CB <--> 187 LEU ( 187-) A - N 0.31 2.79 INTRA BF 100 THR ( 100-) A - N <--> 101 LEU ( 101-) A - CD1 0.31 2.69 INTRA BF 104 TYR ( 104-) A - CB <--> 187 LEU ( 187-) A - CD2 0.31 2.89 INTRA BF 139 ARG ( 139-) A - N <--> 152 ARG ( 152-) A - CB 0.31 2.79 INTRA BF 34 GLY ( 34-) A - C <--> 45 CYS ( 45-) A - CB 0.31 2.89 INTRA BF 141 LEU ( 141-) A - C <--> 153 GLU ( 153-) A - CB 0.30 2.90 INTRA BF 138 GLU ( 138-) A - N <--> 152 ARG ( 152-) A - CA 0.30 2.80 INTRA BL 51 GLU ( 51-) A - CG <--> 187 LEU ( 187-) A - CD2 0.30 2.90 INTRA BF 152 ARG ( 152-) A - CG <--> 155 SER ( 155-) A - CB 0.30 2.90 INTRA BF 152 ARG ( 152-) A - CG <--> 155 SER ( 155-) A - N 0.30 2.80 INTRA BF 141 LEU ( 141-) A - C <--> 154 THR ( 154-) A - N 0.30 2.80 INTRA BL 98 SER ( 98-) A - CB <--> 190 LEU ( 190-) A - CB 0.30 2.90 INTRA BF 142 PHE ( 142-) A - N <--> 154 THR ( 154-) A - C 0.30 2.80 INTRA BL 137 GLN ( 137-) A - CB <--> 152 ARG ( 152-) A - CA 0.30 2.90 INTRA BF 96 LEU ( 96-) A - N <--> 188 LEU ( 188-) A - CB 0.30 2.80 INTRA BF 107 ALA ( 107-) A - CB <--> 201 TYR ( 201-) A - CG 0.30 2.90 INTRA BF 126 LYS ( 126-) A - CD <--> 128 TYR ( 128-) A - CE1 0.30 2.90 INTRA BF 139 ARG ( 139-) A - C <--> 153 GLU ( 153-) A - CA 0.30 2.90 INTRA BL 33 ILE ( 33-) A - CG1 <--> 45 CYS ( 45-) A - SG 0.30 3.10 INTRA BF 101 LEU ( 101-) A - N <--> 188 LEU ( 188-) A - C 0.30 2.80 INTRA BL 100 THR ( 100-) A - CA <--> 189 GLU ( 189-) A - CB 0.29 2.91 INTRA BF 103 GLN ( 103-) A - CG <--> 198 ASN ( 198-) A - N 0.29 2.81 INTRA BF 34 GLY ( 34-) A - CA <--> 46 GLN ( 46-) A - N 0.29 2.81 INTRA BL 95 ALA ( 95-) A - N <--> 188 LEU ( 188-) A - CA 0.29 2.81 INTRA BL 138 GLU ( 138-) A - N <--> 152 ARG ( 152-) A - N 0.29 2.56 INTRA BL 99 SER ( 99-) A - CB <--> 101 LEU ( 101-) A - CD2 0.29 2.91 INTRA BF 143 LEU ( 143-) A - CG <--> 182 THR ( 182-) A - CG2 0.29 2.91 INTRA BF 142 PHE ( 142-) A - CB <--> 155 SER ( 155-) A - N 0.29 2.81 INTRA BF 45 CYS ( 45-) A - N <--> 48 ILE ( 48-) A - CD1 0.29 2.81 INTRA BF 144 THR ( 144-) A - CG2 <--> 163 ASN ( 163-) A - N 0.29 2.81 INTRA BL 101 LEU ( 101-) A - CA <--> 187 LEU ( 187-) A - CA 0.29 2.91 INTRA BL 34 GLY ( 34-) A - N <--> 223 ARG ( 223-) A - CD 0.29 2.81 INTRA BF 103 GLN ( 103-) A - NE2 <--> 200 ILE ( 200-) A - CB 0.28 2.82 INTRA BF 191 ASN ( 191-) A - CB <--> 196 ASN ( 196-) A - CG 0.28 2.92 INTRA BF 53 ALA ( 53-) A - N <--> 92 GLY ( 92-) A - CA 0.28 2.82 INTRA BL 137 GLN ( 137-) A - CB <--> 151 SER ( 151-) A - C 0.28 2.92 INTRA BF 36 GLY ( 36-) A - N <--> 225 GLU ( 225-) A - C 0.28 2.82 INTRA BL 95 ALA ( 95-) A - CA <--> 188 LEU ( 188-) A - CD1 0.28 2.92 INTRA BF 189 GLU ( 189-) A - CG <--> 196 ASN ( 196-) A - CB 0.28 2.92 INTRA BF 104 TYR ( 104-) A - CE2 <--> 132 VAL ( 132-) A - CG1 0.28 2.92 INTRA BF 90 ASN ( 90-) A - N <--> 97 LYS ( 97-) A - CE 0.28 2.82 INTRA BF 103 GLN ( 103-) A - CB <--> 198 ASN ( 198-) A - CA 0.28 2.92 INTRA BF 156 LYS ( 156-) A - CA <--> 157 PRO ( 157-) A - CD 0.28 2.52 INTRA BL 116 GLU ( 116-) A - CG <--> 169 LYS ( 169-) A - CG 0.28 2.92 INTRA BF 43 HIS ( 43-) A - CB <--> 227 LEU ( 227-) A - CB 0.28 2.92 INTRA BF 216 THR ( 216-) A - N <--> 219 TYR ( 219-) A - CD2 0.28 2.82 INTRA BF 36 GLY ( 36-) A - N <--> 226 THR ( 226-) A - CA 0.28 2.82 INTRA BL 116 GLU ( 116-) A - CB <--> 169 LYS ( 169-) A - CB 0.28 2.92 INTRA BF 43 HIS ( 43-) A - NE2 <--> 56 LEU ( 56-) A - CD2 0.28 2.82 INTRA BF 29 LYS ( 29-) A - N <--> 116 GLU ( 116-) A - CG 0.28 2.82 INTRA BF 142 PHE ( 142-) A - CA <--> 155 SER ( 155-) A - N 0.28 2.82 INTRA BL 51 GLU ( 51-) A - CG <--> 187 LEU ( 187-) A - CD1 0.27 2.93 INTRA BF 99 SER ( 99-) A - CB <--> 101 LEU ( 101-) A - CD1 0.27 2.93 INTRA BF 100 THR ( 100-) A - CG2 <--> 200 ILE ( 200-) A - CG2 0.27 2.93 INTRA BF 102 LEU ( 102-) A - CD1 <--> 213 VAL ( 213-) A - CA 0.27 2.93 INTRA BF 170 GLY ( 170-) A - N <--> 174 SER ( 174-) A - CB 0.27 2.83 INTRA BF 193 THR ( 193-) A - CG2 <--> 195 LYS ( 195-) A - N 0.27 2.83 INTRA BF 104 TYR ( 104-) A - CD1 <--> 201 TYR ( 201-) A - CE1 0.27 2.93 INTRA BF 140 THR ( 140-) A - C <--> 153 GLU ( 153-) A - C 0.27 2.93 INTRA BL 99 SER ( 99-) A - CB <--> 189 GLU ( 189-) A - N 0.27 2.83 INTRA BF 99 SER ( 99-) A - CB <--> 188 LEU ( 188-) A - CB 0.27 2.93 INTRA BF 126 LYS ( 126-) A - CE <--> 137 GLN ( 137-) A - CD 0.27 2.93 INTRA BF 215 SER ( 215-) A - CB <--> 219 TYR ( 219-) A - CG 0.27 2.93 INTRA BF 129 ASN ( 129-) A - CB <--> 166 VAL ( 166-) A - CG1 0.27 2.93 INTRA BL 48 ILE ( 48-) A - CB <--> 51 GLU ( 51-) A - CG 0.27 2.93 INTRA BF 137 GLN ( 137-) A - C <--> 149 ASN ( 149-) A - CB 0.27 2.93 INTRA BL 35 TYR ( 35-) A - CB <--> 221 ILE ( 221-) A - CA 0.27 2.93 INTRA BF 35 TYR ( 35-) A - CD2 <--> 221 ILE ( 221-) A - CB 0.27 2.93 INTRA BF 45 CYS ( 45-) A - C <--> 225 GLU ( 225-) A - CB 0.27 2.93 INTRA BF 93 LEU ( 93-) A - CB <--> 101 LEU ( 101-) A - CD2 0.27 2.93 INTRA BF 142 PHE ( 142-) A - CD2 <--> 153 GLU ( 153-) A - CB 0.27 2.93 INTRA BF 126 LYS ( 126-) A - CB <--> 137 GLN ( 137-) A - CG 0.27 2.93 INTRA BF 50 GLU ( 50-) A - CB <--> 180 ILE ( 180-) A - CD1 0.26 2.94 INTRA BF 137 GLN ( 137-) A - C <--> 152 ARG ( 152-) A - CA 0.26 2.94 INTRA BL 189 GLU ( 189-) A - CB <--> 196 ASN ( 196-) A - C 0.26 2.94 INTRA BF 194 ILE ( 194-) A - CG2 <--> 199 LYS ( 199-) A - CG 0.26 2.94 INTRA BF 114 ALA ( 114-) A - CA <--> 131 LEU ( 131-) A - CD1 0.26 2.94 INTRA BL 101 LEU ( 101-) A - CD1 <--> 186 THR ( 186-) A - CA 0.26 2.94 INTRA BF 189 GLU ( 189-) A - CG <--> 196 ASN ( 196-) A - C 0.26 2.94 INTRA BF 100 THR ( 100-) A - C <--> 103 GLN ( 103-) A - NE2 0.26 2.84 INTRA BF 142 PHE ( 142-) A - CB <--> 155 SER ( 155-) A - CB 0.26 2.94 INTRA BF 107 ALA ( 107-) A - CB <--> 204 GLN ( 204-) A - CG 0.26 2.94 INTRA BF 101 LEU ( 101-) A - CB <--> 187 LEU ( 187-) A - CA 0.26 2.94 INTRA BF 48 ILE ( 48-) A - CA <--> 51 GLU ( 51-) A - CG 0.26 2.94 INTRA BF 114 ALA ( 114-) A - C <--> 131 LEU ( 131-) A - CD1 0.26 2.94 INTRA BL 112 LYS ( 112-) A - CD <--> 118 LEU ( 118-) A - CB 0.26 2.94 INTRA BF 198 ASN ( 198-) A - O <--> 199 LYS ( 199-) A - CA 0.26 2.14 INTRA BL 102 LEU ( 102-) A - CD2 <--> 213 VAL ( 213-) A - CB 0.26 2.94 INTRA BF 48 ILE ( 48-) A - CG2 <--> 105 LEU ( 105-) A - CB 0.26 2.94 INTRA BF 168 LYS ( 168-) A - CD <--> 175 GLU ( 175-) A - CB 0.26 2.94 INTRA BF 127 VAL ( 127-) A - CG2 <--> 136 GLU ( 136-) A - CD 0.26 2.94 INTRA BF 98 SER ( 98-) A - CB <--> 190 LEU ( 190-) A - CD1 0.26 2.94 INTRA BF 184 THR ( 184-) A - CA <--> 187 LEU ( 187-) A - CD1 0.26 2.94 INTRA BF 46 GLN ( 46-) A - CA <--> 225 GLU ( 225-) A - CG 0.26 2.94 INTRA BF 31 TYR ( 31-) A - CE1 <--> 170 GLY ( 170-) A - C 0.26 2.94 INTRA BL 112 LYS ( 112-) A - CG <--> 118 LEU ( 118-) A - CB 0.26 2.94 INTRA BF 107 ALA ( 107-) A - CA <--> 204 GLN ( 204-) A - CD 0.26 2.94 INTRA BF 112 LYS ( 112-) A - CE <--> 118 LEU ( 118-) A - CB 0.26 2.94 INTRA BF 98 SER ( 98-) A - CB <--> 190 LEU ( 190-) A - CG 0.26 2.94 INTRA BF 118 LEU ( 118-) A - CD2 <--> 133 LYS ( 133-) A - CE 0.26 2.94 INTRA BF 135 ARG ( 135-) A - CG <--> 142 PHE ( 142-) A - CZ 0.26 2.94 INTRA BF 48 ILE ( 48-) A - CG1 <--> 105 LEU ( 105-) A - CD2 0.26 2.94 INTRA BF 126 LYS ( 126-) A - CG <--> 136 GLU ( 136-) A - CG 0.26 2.94 INTRA BF 143 LEU ( 143-) A - CD1 <--> 182 THR ( 182-) A - CG2 0.26 2.94 INTRA BF 43 HIS ( 43-) A - CB <--> 227 LEU ( 227-) A - CD2 0.26 2.94 INTRA BF 134 ARG ( 134-) A - CZ <--> 166 VAL ( 166-) A - CG2 0.26 2.94 INTRA BF 165 HIS ( 165-) A - CB <--> 178 LYS ( 178-) A - CG 0.26 2.94 INTRA BL 132 VAL ( 132-) A - CB <--> 134 ARG ( 134-) A - CD 0.26 2.94 INTRA BF 53 ALA ( 53-) A - CB <--> 91 VAL ( 91-) A - CG2 0.26 2.94 INTRA BL 102 LEU ( 102-) A - CD2 <--> 213 VAL ( 213-) A - CG2 0.26 2.94 INTRA BF 94 GLY ( 94-) A - CA <--> 187 LEU ( 187-) A - C 0.26 2.94 INTRA BL 93 LEU ( 93-) A - CA <--> 96 LEU ( 96-) A - CB 0.26 2.94 INTRA BF 101 LEU ( 101-) A - CB <--> 186 THR ( 186-) A - C 0.26 2.94 INTRA BF 142 PHE ( 142-) A - CD2 <--> 152 ARG ( 152-) A - C 0.26 2.94 INTRA BF 52 LYS ( 52-) A - CB <--> 55 LYS ( 55-) A - C 0.26 2.94 INTRA BF 42 VAL ( 42-) A - CG2 <--> 229 GLY ( 229-) A - C 0.26 2.94 INTRA BL 51 GLU ( 51-) A - CA <--> 187 LEU ( 187-) A - CD1 0.26 2.94 INTRA BF 225 GLU ( 225-) A - C <--> 227 LEU ( 227-) A - CD1 0.25 2.95 INTRA BF 45 CYS ( 45-) A - SG <--> 46 GLN ( 46-) A - N 0.25 2.95 INTRA BF 106 ASN ( 106-) A - CB <--> 208 VAL ( 208-) A - CG2 0.25 2.95 INTRA BF 126 LYS ( 126-) A - CE <--> 137 GLN ( 137-) A - CG 0.25 2.95 INTRA BF 102 LEU ( 102-) A - N <--> 103 GLN ( 103-) A - N 0.25 2.35 INTRA BL 51 GLU ( 51-) A - CA <--> 184 THR ( 184-) A - CG2 0.25 2.95 INTRA BF 50 GLU ( 50-) A - C <--> 184 THR ( 184-) A - CG2 0.25 2.95 INTRA BF 134 ARG ( 134-) A - CZ <--> 182 THR ( 182-) A - CG2 0.25 2.95 INTRA BF 116 GLU ( 116-) A - CG <--> 169 LYS ( 169-) A - CB 0.25 2.95 INTRA BF 189 GLU ( 189-) A - CB <--> 197 PRO ( 197-) A - CA 0.25 2.95 INTRA BF 156 LYS ( 156-) A - N <--> 157 PRO ( 157-) A - N 0.25 2.35 INTRA BL 208 VAL ( 208-) A - CG1 <--> 219 TYR ( 219-) A - CE1 0.25 2.95 INTRA BF 111 GLN ( 111-) A - CG <--> 133 LYS ( 133-) A - CG 0.25 2.95 INTRA BF 106 ASN ( 106-) A - CB <--> 219 TYR ( 219-) A - CE1 0.25 2.95 INTRA BF 111 GLN ( 111-) A - CD <--> 133 LYS ( 133-) A - CB 0.25 2.95 INTRA BF 28 GLU ( 28-) A - C <--> 169 LYS ( 169-) A - CD 0.25 2.95 INTRA BF 152 ARG ( 152-) A - CZ <--> 156 LYS ( 156-) A - CB 0.25 2.95 INTRA BF 28 GLU ( 28-) A - CA <--> 169 LYS ( 169-) A - CD 0.25 2.95 INTRA BF 214 LYS ( 214-) A - CD <--> 220 LYS ( 220-) A - CE 0.25 2.95 INTRA BF 161 LYS ( 161-) A - CG <--> 178 LYS ( 178-) A - CE 0.25 2.95 INTRA BF 138 GLU ( 138-) A - CD <--> 152 ARG ( 152-) A - CZ 0.25 2.95 INTRA BF 135 ARG ( 135-) A - CG <--> 142 PHE ( 142-) A - CE1 0.25 2.95 INTRA BF 217 LEU ( 217-) A - CD2 <--> 222 LYS ( 222-) A - CD 0.25 2.95 INTRA BL 118 LEU ( 118-) A - CB <--> 133 LYS ( 133-) A - CE 0.25 2.95 INTRA BF 42 VAL ( 42-) A - CG2 <--> 229 GLY ( 229-) A - CA 0.25 2.95 INTRA BL 93 LEU ( 93-) A - CD1 <--> 96 LEU ( 96-) A - CD2 0.25 2.95 INTRA BF 132 VAL ( 132-) A - CG1 <--> 134 ARG ( 134-) A - CG 0.25 2.95 INTRA BF 10 LEU ( 10-) A - CD2 <--> 12 LYS ( 12-) A - CE 0.25 2.95 INTRA BF 50 GLU ( 50-) A - CG <--> 180 ILE ( 180-) A - CD1 0.25 2.95 INTRA BF 142 PHE ( 142-) A - N <--> 154 THR ( 154-) A - N 0.25 2.60 INTRA BL 107 ALA ( 107-) A - CB <--> 201 TYR ( 201-) A - CD2 0.25 2.95 INTRA BF 107 ALA ( 107-) A - CB <--> 201 TYR ( 201-) A - CD1 0.25 2.95 INTRA BF 126 LYS ( 126-) A - CE <--> 135 ARG ( 135-) A - NE 0.25 2.85 INTRA BF 43 HIS ( 43-) A - C <--> 227 LEU ( 227-) A - CB 0.25 2.95 INTRA BF 38 TYR ( 38-) A - CB <--> 226 THR ( 226-) A - CG2 0.25 2.95 INTRA BF 144 THR ( 144-) A - CG2 <--> 162 THR ( 162-) A - C 0.25 2.95 INTRA BL 107 ALA ( 107-) A - CA <--> 204 GLN ( 204-) A - NE2 0.25 2.85 INTRA BF 35 TYR ( 35-) A - CE1 <--> 228 THR ( 228-) A - CB 0.25 2.95 INTRA BF 120 TRP ( 120-) A - CD1 <--> 128 TYR ( 128-) A - CD2 0.25 2.95 INTRA BL 45 CYS ( 45-) A - CB <--> 48 ILE ( 48-) A - CG1 0.24 2.96 INTRA BF 152 ARG ( 152-) A - CG <--> 155 SER ( 155-) A - CA 0.24 2.96 INTRA BF 35 TYR ( 35-) A - CD2 <--> 221 ILE ( 221-) A - CA 0.24 2.96 INTRA BF 105 LEU ( 105-) A - CD2 <--> 219 TYR ( 219-) A - C 0.24 2.96 INTRA BF 136 GLU ( 136-) A - CG <--> 149 ASN ( 149-) A - ND2 0.24 2.86 INTRA BF 102 LEU ( 102-) A - CB <--> 213 VAL ( 213-) A - CG2 0.24 2.96 INTRA BF 191 ASN ( 191-) A - N <--> 196 ASN ( 196-) A - CB 0.24 2.86 INTRA BF 29 LYS ( 29-) A - CB <--> 174 SER ( 174-) A - CB 0.24 2.96 INTRA BF 101 LEU ( 101-) A - C <--> 187 LEU ( 187-) A - CA 0.24 2.96 INTRA BL 46 GLN ( 46-) A - CB <--> 223 ARG ( 223-) A - NH1 0.24 2.86 INTRA BF 109 ASN ( 109-) A - CG <--> 218 LYS ( 218-) A - CD 0.24 2.96 INTRA BL 53 ALA ( 53-) A - CB <--> 91 VAL ( 91-) A - CB 0.24 2.96 INTRA BL 102 LEU ( 102-) A - CD2 <--> 198 ASN ( 198-) A - ND2 0.24 2.86 INTRA BF 134 ARG ( 134-) A - NE <--> 166 VAL ( 166-) A - CG2 0.24 2.86 INTRA BF 98 SER ( 98-) A - C <--> 190 LEU ( 190-) A - CB 0.24 2.96 INTRA BF 168 LYS ( 168-) A - CG <--> 175 GLU ( 175-) A - CB 0.24 2.96 INTRA BF 30 TYR ( 30-) A - CE2 <--> 115 ASN ( 115-) A - CB 0.24 2.96 INTRA BF 116 GLU ( 116-) A - CD <--> 169 LYS ( 169-) A - CG 0.23 2.97 INTRA BF 105 LEU ( 105-) A - CD1 <--> 106 ASN ( 106-) A - ND2 0.23 2.87 INTRA BF 162 THR ( 162-) A - CG2 <--> 165 HIS ( 165-) A - ND1 0.23 2.87 INTRA BL 30 TYR ( 30-) A - CZ <--> 115 ASN ( 115-) A - ND2 0.23 2.87 INTRA BF 136 GLU ( 136-) A - CB <--> 163 ASN ( 163-) A - ND2 0.23 2.87 INTRA BF 119 LYS ( 119-) A - CD <--> 129 ASN ( 129-) A - ND2 0.23 2.87 INTRA BF 102 LEU ( 102-) A - CD1 <--> 198 ASN ( 198-) A - ND2 0.23 2.87 INTRA BF 10 LEU ( 10-) A - CD2 <--> 12 LYS ( 12-) A - CG 0.23 2.97 INTRA BF 126 LYS ( 126-) A - CE <--> 135 ARG ( 135-) A - NH2 0.23 2.87 INTRA BF 252 ASN ( 252-) A - ND2 <--> 254 ILE ( 254-) A - CG2 0.23 2.87 INTRA BF 126 LYS ( 126-) A - CE <--> 137 GLN ( 137-) A - NE2 0.23 2.87 INTRA BF 120 TRP ( 120-) A - CD1 <--> 128 TYR ( 128-) A - CE2 0.23 2.97 INTRA BL 91 VAL ( 91-) A - CA <--> 93 LEU ( 93-) A - CD2 0.23 2.97 INTRA BF 135 ARG ( 135-) A - CZ <--> 137 GLN ( 137-) A - NE2 0.23 2.87 INTRA BF 103 GLN ( 103-) A - CG <--> 198 ASN ( 198-) A - CA 0.23 2.97 INTRA BF 198 ASN ( 198-) A - C <--> 199 LYS ( 199-) A - CA 0.22 2.08 INTRA BL 137 GLN ( 137-) A - C <--> 152 ARG ( 152-) A - CB 0.22 2.98 INTRA BF 102 LEU ( 102-) A - CD1 <--> 213 VAL ( 213-) A - CG2 0.22 2.98 INTRA BF 33 ILE ( 33-) A - CG2 <--> 223 ARG ( 223-) A - CB 0.22 2.98 INTRA BF 29 LYS ( 29-) A - CB <--> 169 LYS ( 169-) A - CB 0.22 2.98 INTRA BF 102 LEU ( 102-) A - CG <--> 213 VAL ( 213-) A - CG2 0.22 2.98 INTRA BF 146 GLU ( 146-) A - CD <--> 148 LYS ( 148-) A - CB 0.22 2.98 INTRA BF 48 ILE ( 48-) A - CB <--> 51 GLU ( 51-) A - CD 0.22 2.98 INTRA BF 45 CYS ( 45-) A - SG <--> 47 VAL ( 47-) A - CG2 0.22 3.18 INTRA BF 152 ARG ( 152-) A - NH2 <--> 156 LYS ( 156-) A - CB 0.21 2.89 INTRA BF 103 GLN ( 103-) A - CD <--> 198 ASN ( 198-) A - N 0.21 2.89 INTRA BF 127 VAL ( 127-) A - N <--> 136 GLU ( 136-) A - CG 0.21 2.89 INTRA BF 41 ASP ( 41-) A - CG <--> 43 HIS ( 43-) A - ND1 0.21 2.89 INTRA BF 188 LEU ( 188-) A - CG <--> 189 GLU ( 189-) A - N 0.20 2.80 INTRA BF 189 GLU ( 189-) A - CG <--> 190 LEU ( 190-) A - N 0.20 2.80 INTRA BF 95 ALA ( 95-) A - C <--> 188 LEU ( 188-) A - CB 0.20 3.00 INTRA BF 44 PRO ( 44-) A - CB <--> 48 ILE ( 48-) A - CD1 0.20 3.00 INTRA BF 118 LEU ( 118-) A - CD2 <--> 119 LYS ( 119-) A - N 0.20 2.80 INTRA BL 146 GLU ( 146-) A - CG <--> 149 ASN ( 149-) A - ND2 0.20 2.90 INTRA BF 141 LEU ( 141-) A - N <--> 154 THR ( 154-) A - N 0.20 2.65 INTRA BL 126 LYS ( 126-) A - CE <--> 135 ARG ( 135-) A - CZ 0.20 3.00 INTRA BF 89 TYR ( 89-) A - CA <--> 97 LYS ( 97-) A - CE 0.20 3.00 INTRA BF 142 PHE ( 142-) A - CB <--> 152 ARG ( 152-) A - CB 0.20 3.00 INTRA BF 217 LEU ( 217-) A - CD2 <--> 222 LYS ( 222-) A - NZ 0.19 2.91 INTRA BL 116 GLU ( 116-) A - CD <--> 117 PHE ( 117-) A - N 0.19 2.81 INTRA BF 119 LYS ( 119-) A - NZ <--> 127 VAL ( 127-) A - CG2 0.19 2.91 INTRA BF 28 GLU ( 28-) A - C <--> 169 LYS ( 169-) A - NZ 0.19 2.91 INTRA BF 126 LYS ( 126-) A - CG <--> 137 GLN ( 137-) A - N 0.19 2.91 INTRA BF 26 PRO ( 26-) A - C <--> 169 LYS ( 169-) A - NZ 0.19 2.91 INTRA BF 94 GLY ( 94-) A - CA <--> 188 LEU ( 188-) A - N 0.19 2.91 INTRA BL 189 GLU ( 189-) A - CB <--> 197 PRO ( 197-) A - N 0.19 2.91 INTRA BF 144 THR ( 144-) A - CG2 <--> 145 GLY ( 145-) A - N 0.19 2.81 INTRA BL 35 TYR ( 35-) A - CG <--> 221 ILE ( 221-) A - CA 0.19 3.01 INTRA BF 35 TYR ( 35-) A - N <--> 225 GLU ( 225-) A - N 0.19 2.66 INTRA BL 33 ILE ( 33-) A - CG2 <--> 34 GLY ( 34-) A - N 0.18 2.82 INTRA BF 213 VAL ( 213-) A - CG1 <--> 214 LYS ( 214-) A - N 0.18 2.82 INTRA BF 182 THR ( 182-) A - CG2 <--> 183 SER ( 183-) A - N 0.18 2.82 INTRA BF 180 ILE ( 180-) A - CG2 <--> 181 LYS ( 181-) A - N 0.18 2.82 INTRA BF 44 PRO ( 44-) A - CB <--> 48 ILE ( 48-) A - C 0.18 3.02 INTRA BF 166 VAL ( 166-) A - CG1 <--> 167 VAL ( 167-) A - N 0.18 2.82 INTRA BL 44 PRO ( 44-) A - CG <--> 49 SER ( 49-) A - CA 0.18 3.02 INTRA BF 141 LEU ( 141-) A - CB <--> 158 LYS ( 158-) A - NZ 0.18 2.92 INTRA BF 23 LYS ( 23-) A - NZ <--> 172 THR ( 172-) A - CB 0.18 2.92 INTRA BF 101 LEU ( 101-) A - CD2 <--> 187 LEU ( 187-) A - N 0.18 2.92 INTRA BF 25 VAL ( 25-) A - CG1 <--> 26 PRO ( 26-) A - N 0.18 2.82 INTRA BL 105 LEU ( 105-) A - CD1 <--> 106 ASN ( 106-) A - N 0.18 2.82 INTRA BF 57 LEU ( 57-) A - CD2 <--> 58 ARG ( 58-) A - N 0.18 2.82 INTRA BF 102 LEU ( 102-) A - CD2 <--> 197 PRO ( 197-) A - CB 0.18 3.02 INTRA BF 77 THR ( 77-) A - CG2 <--> 78 GLN ( 78-) A - N 0.18 2.82 INTRA BL 1 MET ( 1-) A - CG <--> 2 ASN ( 2-) A - N 0.18 2.82 INTRA BL 139 ARG ( 139-) A - C <--> 153 GLU ( 153-) A - C 0.18 3.02 INTRA BL 193 THR ( 193-) A - CG2 <--> 194 ILE ( 194-) A - N 0.18 2.82 INTRA BF 159 THR ( 159-) A - CG2 <--> 160 SER ( 160-) A - N 0.18 2.82 INTRA BF 47 VAL ( 47-) A - CG2 <--> 48 ILE ( 48-) A - N 0.18 2.82 INTRA BF 99 SER ( 99-) A - CA <--> 189 GLU ( 189-) A - N 0.18 2.92 INTRA BL 191 ASN ( 191-) A - CB <--> 196 ASN ( 196-) A - CB 0.18 3.02 INTRA BF 29 LYS ( 29-) A - CG <--> 30 TYR ( 30-) A - N 0.18 2.82 INTRA BF 194 ILE ( 194-) A - CG2 <--> 195 LYS ( 195-) A - N 0.17 2.83 INTRA BF 74 VAL ( 74-) A - CG1 <--> 75 ASP ( 75-) A - N 0.17 2.83 INTRA BL 157 PRO ( 157-) A - CG <--> 160 SER ( 160-) A - CA 0.17 3.03 INTRA BL 11 ILE ( 11-) A - CD1 <--> 12 LYS ( 12-) A - N 0.17 2.83 INTRA BF 99 SER ( 99-) A - C <--> 189 GLU ( 189-) A - CB 0.17 3.03 INTRA BF 112 LYS ( 112-) A - CE <--> 118 LEU ( 118-) A - CD1 0.17 3.03 INTRA BF 248 ILE ( 248-) A - CD1 <--> 249 LYS ( 249-) A - N 0.17 2.83 INTRA BF 156 LYS ( 156-) A - CE <--> 157 PRO ( 157-) A - CD 0.17 3.03 INTRA BF 44 PRO ( 44-) A - CG <--> 52 LYS ( 52-) A - CG 0.17 3.03 INTRA BF 171 ASP ( 171-) A - CG <--> 172 THR ( 172-) A - N 0.17 2.83 INTRA BF 191 ASN ( 191-) A - CA <--> 196 ASN ( 196-) A - CB 0.17 3.03 INTRA BF 34 GLY ( 34-) A - CA <--> 223 ARG ( 223-) A - CB 0.17 3.03 INTRA BF 232 LYS ( 232-) A - CD <--> 233 LYS ( 233-) A - N 0.17 2.83 INTRA BF 30 TYR ( 30-) A - CE2 <--> 115 ASN ( 115-) A - ND2 0.17 2.93 INTRA BF 95 ALA ( 95-) A - CA <--> 188 LEU ( 188-) A - CB 0.17 3.03 INTRA BF 161 LYS ( 161-) A - CB <--> 178 LYS ( 178-) A - CE 0.17 3.03 INTRA BF 102 LEU ( 102-) A - CD1 <--> 198 ASN ( 198-) A - CG 0.17 3.03 INTRA BF 201 TYR ( 201-) A - CB <--> 204 GLN ( 204-) A - CG 0.17 3.03 INTRA BF 10 LEU ( 10-) A - CD2 <--> 11 ILE ( 11-) A - N 0.17 2.83 INTRA BF 26 PRO ( 26-) A - CD <--> 173 LEU ( 173-) A - CB 0.17 3.03 INTRA BF 206 ILE ( 206-) A - CG2 <--> 207 ASN ( 207-) A - N 0.17 2.83 INTRA BL 99 SER ( 99-) A - CA <--> 189 GLU ( 189-) A - CA 0.17 3.03 INTRA BL 161 LYS ( 161-) A - CG <--> 162 THR ( 162-) A - N 0.16 2.84 INTRA BF 98 SER ( 98-) A - CA <--> 190 LEU ( 190-) A - CB 0.16 3.04 INTRA BF 35 TYR ( 35-) A - N <--> 224 GLY ( 224-) A - N 0.16 2.69 INTRA BL 99 SER ( 99-) A - C <--> 101 LEU ( 101-) A - CD1 0.16 3.04 INTRA BF 52 LYS ( 52-) A - NZ <--> 57 LEU ( 57-) A - CD1 0.16 2.94 INTRA BF 101 LEU ( 101-) A - CA <--> 186 THR ( 186-) A - C 0.16 3.04 INTRA BL 103 GLN ( 103-) A - CD <--> 200 ILE ( 200-) A - CB 0.16 3.04 INTRA BF 154 THR ( 154-) A - C <--> 155 SER ( 155-) A - C 0.16 2.64 INTRA BL 199 LYS ( 199-) A - CE <--> 209 GLY ( 209-) A - CA 0.16 3.04 INTRA BF 155 SER ( 155-) A - C <--> 156 LYS ( 156-) A - CA 0.16 2.14 INTRA BL 176 ILE ( 176-) A - CG2 <--> 177 ALA ( 177-) A - N 0.16 2.84 INTRA BL 169 LYS ( 169-) A - C <--> 174 SER ( 174-) A - C 0.16 3.04 INTRA BL 96 LEU ( 96-) A - CG <--> 97 LYS ( 97-) A - N 0.16 2.84 INTRA BF 226 THR ( 226-) A - C <--> 227 LEU ( 227-) A - CD1 0.16 2.94 INTRA BF 141 LEU ( 141-) A - N <--> 153 GLU ( 153-) A - C 0.16 2.94 INTRA BL 206 ILE ( 206-) A - CG2 <--> 207 ASN ( 207-) A - ND2 0.16 2.94 INTRA BL 25 VAL ( 25-) A - CG2 <--> 168 LYS ( 168-) A - CE 0.16 3.04 INTRA BL 249 LYS ( 249-) A - CD <--> 250 ASN ( 250-) A - N 0.16 2.84 INTRA BF 45 CYS ( 45-) A - N <--> 49 SER ( 49-) A - N 0.16 2.69 INTRA BL 95 ALA ( 95-) A - C <--> 188 LEU ( 188-) A - CD2 0.16 3.04 INTRA BF 139 ARG ( 139-) A - CB <--> 152 ARG ( 152-) A - C 0.16 3.04 INTRA BF 144 THR ( 144-) A - CG2 <--> 163 ASN ( 163-) A - CG 0.16 3.04 INTRA BL 216 THR ( 216-) A - CB <--> 217 LEU ( 217-) A - N 0.15 2.55 INTRA BF 191 ASN ( 191-) A - CA <--> 192 PRO ( 192-) A - CD 0.15 2.65 INTRA BL 101 LEU ( 101-) A - N <--> 189 GLU ( 189-) A - N 0.15 2.70 INTRA BL 52 LYS ( 52-) A - C <--> 92 GLY ( 92-) A - CA 0.15 3.05 INTRA BL 196 ASN ( 196-) A - N <--> 197 PRO ( 197-) A - CD 0.15 2.85 INTRA BF 99 SER ( 99-) A - N <--> 189 GLU ( 189-) A - CA 0.15 2.95 INTRA BL 29 LYS ( 29-) A - N <--> 169 LYS ( 169-) A - CD 0.15 2.95 INTRA BF 218 LYS ( 218-) A - C <--> 219 TYR ( 219-) A - CD2 0.15 2.95 INTRA BF 218 LYS ( 218-) A - C <--> 219 TYR ( 219-) A - CG 0.15 2.95 INTRA BF 167 VAL ( 167-) A - CG2 <--> 168 LYS ( 168-) A - N 0.15 2.85 INTRA BL 83 ALA ( 83-) A - C <--> 84 LEU ( 84-) A - CD1 0.15 2.95 INTRA BF 143 LEU ( 143-) A - CD2 <--> 182 THR ( 182-) A - CG2 0.15 3.05 INTRA BF 34 GLY ( 34-) A - CA <--> 223 ARG ( 223-) A - CD 0.15 3.05 INTRA BF 101 LEU ( 101-) A - CD1 <--> 185 LYS ( 185-) A - O 0.15 2.65 INTRA BF 103 GLN ( 103-) A - N <--> 104 TYR ( 104-) A - N 0.15 2.45 INTRA BL 45 CYS ( 45-) A - O <--> 49 SER ( 49-) A - N 0.14 2.56 INTRA BL 119 LYS ( 119-) A - CD <--> 129 ASN ( 129-) A - CG 0.14 3.06 INTRA BF 215 SER ( 215-) A - C <--> 219 TYR ( 219-) A - CD2 0.14 3.06 INTRA BF 103 GLN ( 103-) A - CD <--> 198 ASN ( 198-) A - CA 0.14 3.06 INTRA BF 51 GLU ( 51-) A - CB <--> 187 LEU ( 187-) A - CB 0.14 3.06 INTRA BF 38 TYR ( 38-) A - CD2 <--> 39 GLY ( 39-) A - N 0.14 2.86 INTRA BF 152 ARG ( 152-) A - C <--> 153 GLU ( 153-) A - CB 0.14 2.66 INTRA BF 201 TYR ( 201-) A - C <--> 202 VAL ( 202-) A - C 0.14 2.66 INTRA BL 136 GLU ( 136-) A - CG <--> 149 ASN ( 149-) A - CG 0.14 3.06 INTRA BF 137 GLN ( 137-) A - O <--> 152 ARG ( 152-) A - CG 0.13 2.67 INTRA BF 140 THR ( 140-) A - C <--> 153 GLU ( 153-) A - CA 0.13 3.07 INTRA BL 152 ARG ( 152-) A - CD <--> 155 SER ( 155-) A - O 0.13 2.67 INTRA BF 176 ILE ( 176-) A - O <--> 180 ILE ( 180-) A - N 0.13 2.57 INTRA BL 215 SER ( 215-) A - N <--> 219 TYR ( 219-) A - CB 0.13 2.97 INTRA BF 194 ILE ( 194-) A - CG2 <--> 199 LYS ( 199-) A - NZ 0.13 2.97 INTRA BF 93 LEU ( 93-) A - O <--> 188 LEU ( 188-) A - N 0.13 2.57 INTRA BL 142 PHE ( 142-) A - CD1 <--> 143 LEU ( 143-) A - N 0.13 2.87 INTRA BF 26 PRO ( 26-) A - CG <--> 173 LEU ( 173-) A - CB 0.13 3.07 INTRA BF 101 LEU ( 101-) A - O <--> 104 TYR ( 104-) A - N 0.13 2.57 INTRA BL 103 GLN ( 103-) A - CD <--> 200 ILE ( 200-) A - N 0.13 2.97 INTRA BF 159 THR ( 159-) A - CG2 <--> 161 LYS ( 161-) A - N 0.13 2.97 INTRA BF 136 GLU ( 136-) A - CD <--> 146 GLU ( 146-) A - CG 0.13 3.07 INTRA BF 138 GLU ( 138-) A - C <--> 152 ARG ( 152-) A - CD 0.13 3.07 INTRA BF 152 ARG ( 152-) A - NE <--> 155 SER ( 155-) A - C 0.13 2.97 INTRA BF 193 THR ( 193-) A - CG2 <--> 195 LYS ( 195-) A - C 0.12 3.08 INTRA BF 35 TYR ( 35-) A - CE1 <--> 227 LEU ( 227-) A - C 0.12 3.08 INTRA BF 116 GLU ( 116-) A - CD <--> 169 LYS ( 169-) A - CD 0.12 3.08 INTRA BF 100 THR ( 100-) A - N <--> 189 GLU ( 189-) A - N 0.12 2.73 INTRA BL 48 ILE ( 48-) A - O <--> 51 GLU ( 51-) A - N 0.12 2.58 INTRA BL 138 GLU ( 138-) A - CG <--> 152 ARG ( 152-) A - NE 0.12 2.98 INTRA BF 52 LYS ( 52-) A - CA <--> 92 GLY ( 92-) A - CA 0.12 3.08 INTRA BL 99 SER ( 99-) A - C <--> 189 GLU ( 189-) A - N 0.12 2.98 INTRA BL 156 LYS ( 156-) A - N <--> 157 PRO ( 157-) A - CD 0.12 2.88 INTRA BL 107 ALA ( 107-) A - CB <--> 204 GLN ( 204-) A - CD 0.12 3.08 INTRA BF 126 LYS ( 126-) A - CB <--> 149 ASN ( 149-) A - ND2 0.12 2.98 INTRA BF 168 LYS ( 168-) A - CG <--> 175 GLU ( 175-) A - N 0.12 2.98 INTRA BL 103 GLN ( 103-) A - NE2 <--> 198 ASN ( 198-) A - N 0.12 2.73 INTRA BF 26 PRO ( 26-) A - CB <--> 169 LYS ( 169-) A - NZ 0.12 2.98 INTRA BF 89 TYR ( 89-) A - CA <--> 97 LYS ( 97-) A - NZ 0.12 2.98 INTRA BF 53 ALA ( 53-) A - CA <--> 92 GLY ( 92-) A - N 0.12 2.98 INTRA BL 136 GLU ( 136-) A - CD <--> 146 GLU ( 146-) A - CB 0.12 3.08 INTRA BF 93 LEU ( 93-) A - CB <--> 184 THR ( 184-) A - O 0.12 2.68 INTRA BF 107 ALA ( 107-) A - CB <--> 201 TYR ( 201-) A - CE1 0.12 3.08 INTRA BF 138 GLU ( 138-) A - CA <--> 152 ARG ( 152-) A - N 0.11 2.99 INTRA BL 38 TYR ( 38-) A - N <--> 226 THR ( 226-) A - CG2 0.11 2.99 INTRA BF 33 ILE ( 33-) A - O <--> 47 VAL ( 47-) A - N 0.11 2.59 INTRA BL 51 GLU ( 51-) A - CG <--> 187 LEU ( 187-) A - CG 0.11 3.09 INTRA BF 126 LYS ( 126-) A - CD <--> 135 ARG ( 135-) A - CB 0.11 3.09 INTRA BF 50 GLU ( 50-) A - CB <--> 180 ILE ( 180-) A - CG1 0.11 3.09 INTRA BF 155 SER ( 155-) A - C <--> 157 PRO ( 157-) A - N 0.11 2.79 INTRA BL 43 HIS ( 43-) A - CA <--> 44 PRO ( 44-) A - CD 0.11 2.69 INTRA BF 93 LEU ( 93-) A - O <--> 96 LEU ( 96-) A - N 0.11 2.59 INTRA BL 168 LYS ( 168-) A - CE <--> 175 GLU ( 175-) A - CB 0.11 3.09 INTRA BF 102 LEU ( 102-) A - CG <--> 103 GLN ( 103-) A - N 0.11 2.89 INTRA BF 136 GLU ( 136-) A - CD <--> 149 ASN ( 149-) A - ND2 0.11 2.99 INTRA BF 183 SER ( 183-) A - O <--> 187 LEU ( 187-) A - N 0.11 2.59 INTRA BL 104 TYR ( 104-) A - CD1 <--> 186 THR ( 186-) A - O 0.10 2.70 INTRA BF 102 LEU ( 102-) A - C <--> 104 TYR ( 104-) A - N 0.10 2.80 INTRA BL 193 THR ( 193-) A - C <--> 194 ILE ( 194-) A - C 0.10 2.70 INTRA BL 152 ARG ( 152-) A - CB <--> 153 GLU ( 153-) A - CA 0.10 2.90 INTRA BF 111 GLN ( 111-) A - CG <--> 133 LYS ( 133-) A - CB 0.10 3.10 INTRA BF 35 TYR ( 35-) A - O <--> 224 GLY ( 224-) A - N 0.10 2.60 INTRA BL 190 LEU ( 190-) A - CD2 <--> 191 ASN ( 191-) A - CA 0.10 3.00 INTRA BF 170 GLY ( 170-) A - C <--> 174 SER ( 174-) A - O 0.10 2.70 INTRA BL 126 LYS ( 126-) A - CD <--> 135 ARG ( 135-) A - NE 0.10 3.00 INTRA BF 219 TYR ( 219-) A - CB <--> 220 LYS ( 220-) A - N 0.10 2.60 INTRA BF 34 GLY ( 34-) A - C <--> 223 ARG ( 223-) A - CB 0.10 3.10 INTRA BF 103 GLN ( 103-) A - OE1 <--> 200 ILE ( 200-) A - N 0.10 2.60 INTRA BF 99 SER ( 99-) A - N <--> 190 LEU ( 190-) A - N 0.10 2.75 INTRA BL 116 GLU ( 116-) A - CB <--> 169 LYS ( 169-) A - CA 0.10 3.10 INTRA BF 198 ASN ( 198-) A - C <--> 200 ILE ( 200-) A - N 0.10 2.80 INTRA BL 38 TYR ( 38-) A - CG <--> 39 GLY ( 39-) A - N 0.10 2.90 INTRA BF 153 GLU ( 153-) A - C <--> 155 SER ( 155-) A - N 0.10 2.80 INTRA BL 107 ALA ( 107-) A - CB <--> 201 TYR ( 201-) A - CE2 0.10 3.10 INTRA BF 100 THR ( 100-) A - CA <--> 189 GLU ( 189-) A - OE1 0.10 2.70 INTRA BF 94 GLY ( 94-) A - C <--> 96 LEU ( 96-) A - N 0.10 2.80 INTRA BL 215 SER ( 215-) A - CB <--> 219 TYR ( 219-) A - CD2 0.10 3.10 INTRA BF 159 THR ( 159-) A - CA <--> 185 LYS ( 185-) A - CD 0.10 3.10 INTRA BF 134 ARG ( 134-) A - NH1 <--> 182 THR ( 182-) A - CG2 0.10 3.00 INTRA BF 36 GLY ( 36-) A - CA <--> 226 THR ( 226-) A - CA 0.10 3.10 INTRA BL 34 GLY ( 34-) A - O <--> 223 ARG ( 223-) A - N 0.10 2.60 INTRA BL 152 ARG ( 152-) A - CG <--> 155 SER ( 155-) A - C 0.10 3.10 INTRA BF 53 ALA ( 53-) A - N <--> 92 GLY ( 92-) A - N 0.10 2.75 INTRA BL 103 GLN ( 103-) A - OE1 <--> 201 TYR ( 201-) A - N 0.09 2.61 INTRA BF 89 TYR ( 89-) A - CE2 <--> 158 LYS ( 158-) A - CE 0.09 3.11 INTRA BF 98 SER ( 98-) A - C <--> 190 LEU ( 190-) A - N 0.09 3.01 INTRA BL 191 ASN ( 191-) A - O <--> 196 ASN ( 196-) A - N 0.09 2.61 INTRA BL 150 VAL ( 150-) A - CG2 <--> 151 SER ( 151-) A - N 0.09 2.91 INTRA BF 174 SER ( 174-) A - O <--> 176 ILE ( 176-) A - N 0.09 2.61 INTRA BL 49 SER ( 49-) A - N <--> 50 GLU ( 50-) A - N 0.09 2.51 INTRA BL 45 CYS ( 45-) A - O <--> 49 SER ( 49-) A - CB 0.09 2.71 INTRA BL 180 ILE ( 180-) A - O <--> 184 THR ( 184-) A - CG2 0.09 2.71 INTRA BF 48 ILE ( 48-) A - O <--> 51 GLU ( 51-) A - CG 0.09 2.71 INTRA BF 138 GLU ( 138-) A - CG <--> 149 ASN ( 149-) A - O 0.09 2.71 INTRA BF 102 LEU ( 102-) A - N <--> 187 LEU ( 187-) A - O 0.09 2.61 INTRA BL 179 LYS ( 179-) A - O <--> 183 SER ( 183-) A - N 0.09 2.61 INTRA BL 99 SER ( 99-) A - O <--> 189 GLU ( 189-) A - CD 0.09 2.71 INTRA BF 50 GLU ( 50-) A - O <--> 184 THR ( 184-) A - CG2 0.09 2.71 INTRA BF 189 GLU ( 189-) A - OE1 <--> 200 ILE ( 200-) A - CD1 0.09 2.71 INTRA BF 43 HIS ( 43-) A - CB <--> 44 PRO ( 44-) A - CD 0.09 3.01 INTRA BF 58 ARG ( 58-) A - CB <--> 91 VAL ( 91-) A - CG2 0.09 3.11 INTRA BF 210 GLY ( 210-) A - N <--> 211 SER ( 211-) A - N 0.09 2.51 INTRA BL 48 ILE ( 48-) A - CG2 <--> 51 GLU ( 51-) A - CG 0.09 3.11 INTRA BF 138 GLU ( 138-) A - N <--> 152 ARG ( 152-) A - CG 0.09 3.01 INTRA BF 184 THR ( 184-) A - O <--> 187 LEU ( 187-) A - N 0.09 2.61 INTRA BL 51 GLU ( 51-) A - CB <--> 187 LEU ( 187-) A - CD1 0.09 3.11 INTRA BF 224 GLY ( 224-) A - O <--> 226 THR ( 226-) A - N 0.08 2.62 INTRA BL 48 ILE ( 48-) A - O <--> 51 GLU ( 51-) A - CB 0.08 2.72 INTRA BF 204 GLN ( 204-) A - O <--> 208 VAL ( 208-) A - N 0.08 2.62 INTRA BL 137 GLN ( 137-) A - CB <--> 152 ARG ( 152-) A - N 0.08 3.02 INTRA BF 140 THR ( 140-) A - O <--> 154 THR ( 154-) A - CG2 0.08 2.72 INTRA BF 100 THR ( 100-) A - CB <--> 101 LEU ( 101-) A - CD1 0.08 3.02 INTRA BF 34 GLY ( 34-) A - C <--> 223 ARG ( 223-) A - CA 0.08 3.12 INTRA BL 134 ARG ( 134-) A - NH2 <--> 166 VAL ( 166-) A - CG2 0.08 3.02 INTRA BF 101 LEU ( 101-) A - CA <--> 186 THR ( 186-) A - O 0.08 2.72 INTRA BL 196 ASN ( 196-) A - C <--> 197 PRO ( 197-) A - C 0.08 2.72 INTRA BL 112 LYS ( 112-) A - CG <--> 133 LYS ( 133-) A - CE 0.08 3.12 INTRA BF 139 ARG ( 139-) A - C <--> 153 GLU ( 153-) A - O 0.08 2.72 INTRA BL 137 GLN ( 137-) A - CD <--> 151 SER ( 151-) A - O 0.08 2.72 INTRA BF 34 GLY ( 34-) A - C <--> 223 ARG ( 223-) A - N 0.08 3.02 INTRA BL 154 THR ( 154-) A - O <--> 158 LYS ( 158-) A - N 0.08 2.62 INTRA BL 169 LYS ( 169-) A - O <--> 175 GLU ( 175-) A - C 0.08 2.72 INTRA BL 199 LYS ( 199-) A - N <--> 200 ILE ( 200-) A - N 0.08 2.52 INTRA BL 107 ALA ( 107-) A - O <--> 111 GLN ( 111-) A - N 0.08 2.62 INTRA BL 103 GLN ( 103-) A - NE2 <--> 196 ASN ( 196-) A - O 0.08 2.62 INTRA BF 177 ALA ( 177-) A - O <--> 180 ILE ( 180-) A - CG2 0.08 2.72 INTRA BF 49 SER ( 49-) A - O <--> 55 LYS ( 55-) A - CA 0.08 2.72 INTRA BL 163 ASN ( 163-) A - O <--> 166 VAL ( 166-) A - CG1 0.08 2.72 INTRA BL 104 TYR ( 104-) A - CZ <--> 132 VAL ( 132-) A - CG1 0.08 3.12 INTRA BF 101 LEU ( 101-) A - C <--> 187 LEU ( 187-) A - O 0.08 2.72 INTRA BL 156 LYS ( 156-) A - CA <--> 157 PRO ( 157-) A - N 0.08 2.12 INTRA BL 101 LEU ( 101-) A - CD2 <--> 185 LYS ( 185-) A - O 0.08 2.72 INTRA BF 184 THR ( 184-) A - O <--> 187 LEU ( 187-) A - CB 0.08 2.72 INTRA BF 105 LEU ( 105-) A - CD2 <--> 220 LYS ( 220-) A - N 0.08 3.02 INTRA BF 209 GLY ( 209-) A - C <--> 211 SER ( 211-) A - N 0.08 2.82 INTRA BL 112 LYS ( 112-) A - CD <--> 115 ASN ( 115-) A - CB 0.08 3.12 INTRA BF 34 GLY ( 34-) A - C <--> 224 GLY ( 224-) A - N 0.08 3.02 INTRA BL 57 LEU ( 57-) A - CA <--> 92 GLY ( 92-) A - CA 0.08 3.12 INTRA BL 36 GLY ( 36-) A - N <--> 226 THR ( 226-) A - N 0.08 2.77 INTRA BL 107 ALA ( 107-) A - CB <--> 204 GLN ( 204-) A - NE2 0.07 3.03 INTRA BF 103 GLN ( 103-) A - CA <--> 106 ASN ( 106-) A - ND2 0.07 3.03 INTRA BF 103 GLN ( 103-) A - OE1 <--> 200 ILE ( 200-) A - CB 0.07 2.73 INTRA BF 35 TYR ( 35-) A - CE1 <--> 227 LEU ( 227-) A - O 0.07 2.73 INTRA BF 173 LEU ( 173-) A - C <--> 174 SER ( 174-) A - C 0.07 2.73 INTRA BL 50 GLU ( 50-) A - CD <--> 176 ILE ( 176-) A - CD1 0.07 3.13 INTRA BL 102 LEU ( 102-) A - C <--> 103 GLN ( 103-) A - C 0.07 2.73 INTRA BL 92 GLY ( 92-) A - O <--> 96 LEU ( 96-) A - CB 0.07 2.73 INTRA BF 102 LEU ( 102-) A - CG <--> 198 ASN ( 198-) A - CG 0.07 3.13 INTRA BF 170 GLY ( 170-) A - N <--> 174 SER ( 174-) A - O 0.07 2.63 INTRA BL 102 LEU ( 102-) A - O <--> 105 LEU ( 105-) A - CD1 0.07 2.73 INTRA BF 152 ARG ( 152-) A - CA <--> 153 GLU ( 153-) A - N 0.07 2.13 INTRA BL 142 PHE ( 142-) A - CB <--> 155 SER ( 155-) A - CA 0.07 3.13 INTRA BF 101 LEU ( 101-) A - O <--> 104 TYR ( 104-) A - CB 0.07 2.73 INTRA BF 33 ILE ( 33-) A - O <--> 46 GLN ( 46-) A - CB 0.07 2.73 INTRA BF 103 GLN ( 103-) A - CA <--> 198 ASN ( 198-) A - OD1 0.07 2.73 INTRA BF 47 VAL ( 47-) A - O <--> 50 GLU ( 50-) A - CB 0.07 2.73 INTRA BL 139 ARG ( 139-) A - N <--> 152 ARG ( 152-) A - CG 0.07 3.03 INTRA BF 45 CYS ( 45-) A - O <--> 225 GLU ( 225-) A - CB 0.07 2.73 INTRA BF 54 GLU ( 54-) A - N <--> 55 LYS ( 55-) A - N 0.07 2.53 INTRA BL 195 LYS ( 195-) A - O <--> 199 LYS ( 199-) A - CB 0.07 2.73 INTRA BF 138 GLU ( 138-) A - CB <--> 150 VAL ( 150-) A - O 0.07 2.73 INTRA BF 146 GLU ( 146-) A - CG <--> 147 SER ( 147-) A - N 0.07 2.93 INTRA BF 112 LYS ( 112-) A - CD <--> 115 ASN ( 115-) A - OD1 0.07 2.73 INTRA BF 134 ARG ( 134-) A - NH1 <--> 179 LYS ( 179-) A - CB 0.07 3.03 INTRA BF 190 LEU ( 190-) A - CB <--> 191 ASN ( 191-) A - N 0.07 2.63 INTRA BF 171 ASP ( 171-) A - C <--> 173 LEU ( 173-) A - O 0.07 2.73 INTRA BL 191 ASN ( 191-) A - C <--> 196 ASN ( 196-) A - CB 0.07 3.13 INTRA BF 102 LEU ( 102-) A - CD1 <--> 198 ASN ( 198-) A - OD1 0.07 2.73 INTRA BF 112 LYS ( 112-) A - CB <--> 131 LEU ( 131-) A - O 0.07 2.73 INTRA BF 136 GLU ( 136-) A - CB <--> 149 ASN ( 149-) A - OD1 0.07 2.73 INTRA BF 111 GLN ( 111-) A - OE1 <--> 201 TYR ( 201-) A - CE2 0.07 2.73 INTRA BF 103 GLN ( 103-) A - OE1 <--> 200 ILE ( 200-) A - CG2 0.07 2.73 INTRA BF 146 GLU ( 146-) A - CD <--> 148 LYS ( 148-) A - N 0.07 3.03 INTRA BF 130 GLY ( 130-) A - O <--> 133 LYS ( 133-) A - CE 0.07 2.73 INTRA BF 29 LYS ( 29-) A - CG <--> 170 GLY ( 170-) A - O 0.07 2.73 INTRA BF 101 LEU ( 101-) A - O <--> 187 LEU ( 187-) A - CD2 0.07 2.73 INTRA BF 35 TYR ( 35-) A - CD1 <--> 227 LEU ( 227-) A - O 0.06 2.74 INTRA BF 137 GLN ( 137-) A - O <--> 155 SER ( 155-) A - CB 0.06 2.74 INTRA BF 33 ILE ( 33-) A - O <--> 46 GLN ( 46-) A - N 0.06 2.64 INTRA BL 203 GLY ( 203-) A - O <--> 206 ILE ( 206-) A - CG2 0.06 2.74 INTRA BL 141 LEU ( 141-) A - O <--> 153 GLU ( 153-) A - CB 0.06 2.74 INTRA BF 204 GLN ( 204-) A - C <--> 205 ARG ( 205-) A - C 0.06 2.74 INTRA BL 60 ASP ( 60-) A - N <--> 90 ASN ( 90-) A - ND2 0.06 2.79 INTRA BF 138 GLU ( 138-) A - CB <--> 149 ASN ( 149-) A - O 0.06 2.74 INTRA BF 143 LEU ( 143-) A - O <--> 159 THR ( 159-) A - CG2 0.06 2.74 INTRA BF 32 THR ( 32-) A - CB <--> 223 ARG ( 223-) A - CD 0.06 3.14 INTRA BF 112 LYS ( 112-) A - CD <--> 115 ASN ( 115-) A - O 0.06 2.74 INTRA BF 104 TYR ( 104-) A - CE1 <--> 201 TYR ( 201-) A - CE1 0.06 3.14 INTRA BF 183 SER ( 183-) A - O <--> 186 THR ( 186-) A - C 0.06 2.74 INTRA BL 35 TYR ( 35-) A - CB <--> 220 LYS ( 220-) A - O 0.06 2.74 INTRA BF 96 LEU ( 96-) A - O <--> 188 LEU ( 188-) A - CD2 0.06 2.74 INTRA BF 100 THR ( 100-) A - CG2 <--> 200 ILE ( 200-) A - CB 0.06 3.14 INTRA BF 136 GLU ( 136-) A - OE1 <--> 146 GLU ( 146-) A - CB 0.06 2.74 INTRA BF 135 ARG ( 135-) A - O <--> 142 PHE ( 142-) A - CD1 0.06 2.74 INTRA BF 215 SER ( 215-) A - O <--> 221 ILE ( 221-) A - CG1 0.06 2.74 INTRA BL 135 ARG ( 135-) A - NH1 <--> 137 GLN ( 137-) A - NE2 0.06 2.79 INTRA BF 35 TYR ( 35-) A - CA <--> 225 GLU ( 225-) A - O 0.06 2.74 INTRA BL 46 GLN ( 46-) A - O <--> 50 GLU ( 50-) A - CG 0.06 2.74 INTRA BL 57 LEU ( 57-) A - CG <--> 92 GLY ( 92-) A - O 0.06 2.74 INTRA BF 41 ASP ( 41-) A - C <--> 228 THR ( 228-) A - O 0.06 2.74 INTRA BL 146 GLU ( 146-) A - OE1 <--> 148 LYS ( 148-) A - N 0.06 2.64 INTRA BF 122 LYS ( 122-) A - CB <--> 128 TYR ( 128-) A - OH 0.06 2.74 INTRA BL 26 PRO ( 26-) A - O <--> 169 LYS ( 169-) A - CE 0.06 2.74 INTRA BF 164 THR ( 164-) A - O <--> 167 VAL ( 167-) A - CG2 0.06 2.74 INTRA BL 28 GLU ( 28-) A - CB <--> 116 GLU ( 116-) A - OE2 0.06 2.74 INTRA BF 183 SER ( 183-) A - O <--> 187 LEU ( 187-) A - CG 0.06 2.74 INTRA BF 127 VAL ( 127-) A - CG2 <--> 129 ASN ( 129-) A - OD1 0.06 2.74 INTRA BL 195 LYS ( 195-) A - C <--> 197 PRO ( 197-) A - CD 0.06 3.14 INTRA BF 53 ALA ( 53-) A - CB <--> 56 LEU ( 56-) A - O 0.06 2.74 INTRA BL 191 ASN ( 191-) A - O <--> 196 ASN ( 196-) A - CB 0.06 2.74 INTRA BF 101 LEU ( 101-) A - CB <--> 189 GLU ( 189-) A - N 0.06 3.04 INTRA BF 189 GLU ( 189-) A - OE1 <--> 200 ILE ( 200-) A - CG1 0.06 2.74 INTRA BF 181 LYS ( 181-) A - O <--> 185 LYS ( 185-) A - CG 0.06 2.74 INTRA BF 144 THR ( 144-) A - CG2 <--> 163 ASN ( 163-) A - CA 0.06 3.14 INTRA BL 93 LEU ( 93-) A - O <--> 101 LEU ( 101-) A - CD2 0.06 2.74 INTRA BF 109 ASN ( 109-) A - OD1 <--> 218 LYS ( 218-) A - CB 0.06 2.74 INTRA BL 111 GLN ( 111-) A - OE1 <--> 133 LYS ( 133-) A - CB 0.06 2.74 INTRA BF 42 VAL ( 42-) A - CG1 <--> 229 GLY ( 229-) A - O 0.06 2.74 INTRA BL 110 PHE ( 110-) A - CD1 <--> 207 ASN ( 207-) A - OD1 0.06 2.74 INTRA BL 139 ARG ( 139-) A - CD <--> 153 GLU ( 153-) A - OE2 0.06 2.74 INTRA BF 35 TYR ( 35-) A - O <--> 222 LYS ( 222-) A - C 0.06 2.74 INTRA BL 195 LYS ( 195-) A - O <--> 199 LYS ( 199-) A - CG 0.06 2.74 INTRA BF 50 GLU ( 50-) A - OE2 <--> 176 ILE ( 176-) A - CD1 0.06 2.74 INTRA BL 29 LYS ( 29-) A - O <--> 116 GLU ( 116-) A - CG 0.06 2.74 INTRA BF 28 GLU ( 28-) A - CA <--> 116 GLU ( 116-) A - OE2 0.06 2.74 INTRA BF 48 ILE ( 48-) A - CG2 <--> 51 GLU ( 51-) A - OE2 0.05 2.75 INTRA BF 119 LYS ( 119-) A - CD <--> 129 ASN ( 129-) A - OD1 0.05 2.75 INTRA BF 116 GLU ( 116-) A - OE1 <--> 169 LYS ( 169-) A - CG 0.05 2.75 INTRA BF 204 GLN ( 204-) A - O <--> 209 GLY ( 209-) A - N 0.05 2.65 INTRA BL 55 LYS ( 55-) A - N <--> 56 LEU ( 56-) A - N 0.05 2.55 INTRA BL 169 LYS ( 169-) A - CB <--> 174 SER ( 174-) A - CA 0.05 3.15 INTRA BF 28 GLU ( 28-) A - OE1 <--> 30 TYR ( 30-) A - CE1 0.05 2.75 INTRA BF 31 TYR ( 31-) A - CE1 <--> 170 GLY ( 170-) A - O 0.05 2.75 INTRA BL 36 GLY ( 36-) A - N <--> 224 GLY ( 224-) A - C 0.05 3.05 INTRA BL 53 ALA ( 53-) A - N <--> 56 LEU ( 56-) A - O 0.05 2.65 INTRA BL 51 GLU ( 51-) A - O <--> 184 THR ( 184-) A - CB 0.05 2.75 INTRA BF 103 GLN ( 103-) A - OE1 <--> 200 ILE ( 200-) A - CA 0.05 2.75 INTRA BF 91 VAL ( 91-) A - O <--> 96 LEU ( 96-) A - CD2 0.05 2.75 INTRA BF 169 LYS ( 169-) A - O <--> 176 ILE ( 176-) A - CA 0.05 2.75 INTRA BL 194 ILE ( 194-) A - CD1 <--> 199 LYS ( 199-) A - NZ 0.05 3.05 INTRA BF 98 SER ( 98-) A - N <--> 188 LEU ( 188-) A - CD2 0.05 3.05 INTRA BF 105 LEU ( 105-) A - CD1 <--> 219 TYR ( 219-) A - CA 0.05 3.15 INTRA BF 106 ASN ( 106-) A - ND2 <--> 198 ASN ( 198-) A - OD1 0.05 2.65 INTRA BF 157 PRO ( 157-) A - CB <--> 160 SER ( 160-) A - N 0.05 3.05 INTRA BL 1 MET ( 1-) A - CB <--> 2 ASN ( 2-) A - N 0.05 2.65 INTRA BL 169 LYS ( 169-) A - O <--> 179 LYS ( 179-) A - CE 0.05 2.75 INTRA BF 142 PHE ( 142-) A - CB <--> 155 SER ( 155-) A - OG 0.05 2.75 INTRA BF 103 GLN ( 103-) A - O <--> 107 ALA ( 107-) A - N 0.05 2.65 INTRA BL 138 GLU ( 138-) A - N <--> 152 ARG ( 152-) A - CB 0.05 3.05 INTRA BF 120 TRP ( 120-) A - NE1 <--> 122 LYS ( 122-) A - CG 0.05 3.05 INTRA BL 238 VAL ( 238-) A - CG1 <--> 239 SER ( 239-) A - N 0.05 2.95 INTRA BL 101 LEU ( 101-) A - C <--> 103 GLN ( 103-) A - N 0.05 2.85 INTRA BL 216 THR ( 216-) A - C <--> 219 TYR ( 219-) A - CD2 0.05 3.15 INTRA BF 101 LEU ( 101-) A - C <--> 103 GLN ( 103-) A - CG 0.05 3.15 INTRA BF 128 TYR ( 128-) A - CE1 <--> 135 ARG ( 135-) A - CB 0.05 3.15 INTRA BF 263 LYS ( 263-) A - CG <--> 265 LYS ( 263-) A - O'' 0.05 2.75 INTRA BL 108 GLY ( 108-) A - N <--> 109 ASN ( 109-) A - N 0.04 2.56 INTRA BL 136 GLU ( 136-) A - OE1 <--> 163 ASN ( 163-) A - CG 0.04 2.76 INTRA BF 182 THR ( 182-) A - O <--> 185 LYS ( 185-) A - N 0.04 2.66 INTRA BL 136 GLU ( 136-) A - O <--> 155 SER ( 155-) A - CB 0.04 2.76 INTRA BF 127 VAL ( 127-) A - CG2 <--> 136 GLU ( 136-) A - OE1 0.04 2.76 INTRA BF 169 LYS ( 169-) A - CE <--> 174 SER ( 174-) A - CA 0.04 3.16 INTRA BF 139 ARG ( 139-) A - NH1 <--> 153 GLU ( 153-) A - OE2 0.04 2.66 INTRA BF 120 TRP ( 120-) A - CB <--> 128 TYR ( 128-) A - CD2 0.04 3.16 INTRA BL 52 LYS ( 52-) A - CB <--> 55 LYS ( 55-) A - O 0.04 2.76 INTRA BF 137 GLN ( 137-) A - CA <--> 149 ASN ( 149-) A - CB 0.04 3.16 INTRA BL 152 ARG ( 152-) A - NE <--> 155 SER ( 155-) A - O 0.04 2.66 INTRA BF 103 GLN ( 103-) A - O <--> 106 ASN ( 106-) A - ND2 0.04 2.66 INTRA BF 101 LEU ( 101-) A - CA <--> 187 LEU ( 187-) A - N 0.04 3.06 INTRA BL 77 THR ( 77-) A - C <--> 78 GLN ( 78-) A - CG 0.04 3.06 INTRA BF 137 GLN ( 137-) A - NE2 <--> 151 SER ( 151-) A - O 0.04 2.66 INTRA BF 29 LYS ( 29-) A - O <--> 115 ASN ( 115-) A - ND2 0.04 2.66 INTRA BF 200 ILE ( 200-) A - CG2 <--> 201 TYR ( 201-) A - N 0.04 2.96 INTRA BF 140 THR ( 140-) A - OG1 <--> 153 GLU ( 153-) A - CG 0.04 2.76 INTRA BF 170 GLY ( 170-) A - O <--> 174 SER ( 174-) A - CB 0.04 2.76 INTRA BF 104 TYR ( 104-) A - CE2 <--> 186 THR ( 186-) A - OG1 0.04 2.76 INTRA BF 100 THR ( 100-) A - CA <--> 101 LEU ( 101-) A - CB 0.04 2.96 INTRA BF 93 LEU ( 93-) A - C <--> 96 LEU ( 96-) A - CB 0.04 3.16 INTRA BF 152 ARG ( 152-) A - CB <--> 153 GLU ( 153-) A - C 0.04 2.96 INTRA BF 95 ALA ( 95-) A - N <--> 96 LEU ( 96-) A - N 0.04 2.56 INTRA BL 191 ASN ( 191-) A - CB <--> 196 ASN ( 196-) A - OD1 0.04 2.76 INTRA BF 199 LYS ( 199-) A - O <--> 205 ARG ( 205-) A - NH1 0.04 2.66 INTRA BL 204 GLN ( 204-) A - N <--> 205 ARG ( 205-) A - N 0.04 2.56 INTRA BL 36 GLY ( 36-) A - O <--> 226 THR ( 226-) A - CA 0.04 2.76 INTRA BL 92 GLY ( 92-) A - N <--> 93 LEU ( 93-) A - N 0.04 2.56 INTRA BL 101 LEU ( 101-) A - CB <--> 188 LEU ( 188-) A - CA 0.04 3.16 INTRA BF 136 GLU ( 136-) A - OE2 <--> 146 GLU ( 146-) A - CG 0.04 2.76 INTRA BF 25 VAL ( 25-) A - CA <--> 26 PRO ( 26-) A - CD 0.04 2.76 INTRA BL 201 TYR ( 201-) A - O <--> 205 ARG ( 205-) A - NH1 0.04 2.66 INTRA BL 136 GLU ( 136-) A - OE2 <--> 149 ASN ( 149-) A - ND2 0.04 2.66 INTRA BF 125 GLY ( 125-) A - N <--> 126 LYS ( 126-) A - N 0.04 2.56 INTRA BL 46 GLN ( 46-) A - CD <--> 223 ARG ( 223-) A - NH1 0.04 3.06 INTRA BF 76 VAL ( 76-) A - CG2 <--> 77 THR ( 77-) A - N 0.04 2.96 INTRA BL 138 GLU ( 138-) A - OE2 <--> 152 ARG ( 152-) A - NH2 0.04 2.66 INTRA BF 48 ILE ( 48-) A - C <--> 50 GLU ( 50-) A - N 0.04 2.86 INTRA BL 45 CYS ( 45-) A - C <--> 49 SER ( 49-) A - N 0.04 3.06 INTRA BL 29 LYS ( 29-) A - CE <--> 170 GLY ( 170-) A - O 0.04 2.76 INTRA BF 89 TYR ( 89-) A - OH <--> 154 THR ( 154-) A - CG2 0.04 2.76 INTRA BF 137 GLN ( 137-) A - OE1 <--> 150 VAL ( 150-) A - CG2 0.04 2.76 INTRA BF 90 ASN ( 90-) A - CB <--> 91 VAL ( 91-) A - N 0.03 2.67 INTRA BF 15 GLU ( 15-) A - CG <--> 16 GLY ( 16-) A - N 0.03 2.97 INTRA BF 42 VAL ( 42-) A - CG1 <--> 229 GLY ( 229-) A - C 0.03 3.17 INTRA BL 177 ALA ( 177-) A - CA <--> 180 ILE ( 180-) A - CG2 0.03 3.17 INTRA BF 127 VAL ( 127-) A - N <--> 136 GLU ( 136-) A - CD 0.03 3.07 INTRA BF 99 SER ( 99-) A - O <--> 189 GLU ( 189-) A - CG 0.03 2.77 INTRA BF 103 GLN ( 103-) A - C <--> 106 ASN ( 106-) A - ND2 0.03 3.07 INTRA BF 169 LYS ( 169-) A - C <--> 174 SER ( 174-) A - O 0.03 2.77 INTRA BL 107 ALA ( 107-) A - CB <--> 201 TYR ( 201-) A - CZ 0.03 3.17 INTRA BF 126 LYS ( 126-) A - CA <--> 149 ASN ( 149-) A - ND2 0.03 3.07 INTRA BL 33 ILE ( 33-) A - O <--> 45 CYS ( 45-) A - SG 0.03 2.82 INTRA BF 161 LYS ( 161-) A - CG <--> 165 HIS ( 165-) A - ND1 0.03 3.07 INTRA BF 129 ASN ( 129-) A - O <--> 134 ARG ( 134-) A - CD 0.03 2.77 INTRA BF 102 LEU ( 102-) A - N <--> 187 LEU ( 187-) A - C 0.03 3.07 INTRA BL 136 GLU ( 136-) A - OE1 <--> 163 ASN ( 163-) A - ND2 0.03 2.67 INTRA BF 179 LYS ( 179-) A - CG <--> 180 ILE ( 180-) A - N 0.03 2.97 INTRA BF 132 VAL ( 132-) A - CB <--> 134 ARG ( 134-) A - CG 0.03 3.17 INTRA BF 122 LYS ( 122-) A - CG <--> 128 TYR ( 128-) A - CE2 0.03 3.17 INTRA BL 35 TYR ( 35-) A - CZ <--> 228 THR ( 228-) A - CB 0.03 3.17 INTRA BF 142 PHE ( 142-) A - N <--> 155 SER ( 155-) A - N 0.03 2.82 INTRA BL 141 LEU ( 141-) A - CG <--> 158 LYS ( 158-) A - NZ 0.03 3.07 INTRA BF 158 LYS ( 158-) A - N <--> 159 THR ( 159-) A - N 0.03 2.57 INTRA BL 44 PRO ( 44-) A - CB <--> 48 ILE ( 48-) A - O 0.03 2.77 INTRA BF 143 LEU ( 143-) A - CD1 <--> 144 THR ( 144-) A - OG1 0.03 2.77 INTRA BF 203 GLY ( 203-) A - C <--> 204 GLN ( 204-) A - NE2 0.03 2.97 INTRA BF 193 THR ( 193-) A - CG2 <--> 196 ASN ( 196-) A - N 0.03 3.07 INTRA BF 189 GLU ( 189-) A - CB <--> 196 ASN ( 196-) A - O 0.02 2.78 INTRA BF 119 LYS ( 119-) A - NZ <--> 129 ASN ( 129-) A - ND2 0.02 2.83 INTRA BF 144 THR ( 144-) A - CG2 <--> 161 LYS ( 161-) A - O 0.02 2.78 INTRA BL 36 GLY ( 36-) A - O <--> 226 THR ( 226-) A - CG2 0.02 2.78 INTRA BF 211 SER ( 211-) A - CA <--> 212 PRO ( 212-) A - CD 0.02 2.78 INTRA BF 99 SER ( 99-) A - OG <--> 101 LEU ( 101-) A - CD2 0.02 2.78 INTRA BF 70 LYS ( 70-) A - NZ <--> 72 LEU ( 72-) A - CD1 0.02 3.08 INTRA BF 183 SER ( 183-) A - C <--> 184 THR ( 184-) A - C 0.02 2.78 INTRA BL 137 GLN ( 137-) A - O <--> 149 ASN ( 149-) A - CB 0.02 2.78 INTRA BL 116 GLU ( 116-) A - CB <--> 169 LYS ( 169-) A - CG 0.02 3.18 INTRA BF 139 ARG ( 139-) A - CB <--> 152 ARG ( 152-) A - O 0.02 2.78 INTRA BF 169 LYS ( 169-) A - CE <--> 174 SER ( 174-) A - OG 0.02 2.78 INTRA BF 138 GLU ( 138-) A - CB <--> 150 VAL ( 150-) A - C 0.02 3.18 INTRA BF 60 ASP ( 60-) A - O <--> 90 ASN ( 90-) A - ND2 0.02 2.68 INTRA BF 126 LYS ( 126-) A - CE <--> 128 TYR ( 128-) A - OH 0.02 2.78 INTRA BF 157 PRO ( 157-) A - C <--> 158 LYS ( 158-) A - C 0.02 2.78 INTRA BL 107 ALA ( 107-) A - C <--> 108 GLY ( 108-) A - C 0.02 2.78 INTRA BL 101 LEU ( 101-) A - CB <--> 188 LEU ( 188-) A - C 0.02 3.18 INTRA BF 146 GLU ( 146-) A - N <--> 163 ASN ( 163-) A - OD1 0.02 2.68 INTRA BL 167 VAL ( 167-) A - C <--> 168 LYS ( 168-) A - C 0.02 2.78 INTRA BL 159 THR ( 159-) A - CA <--> 185 LYS ( 185-) A - CE 0.02 3.18 INTRA BF 96 LEU ( 96-) A - O <--> 99 SER ( 99-) A - CB 0.02 2.78 INTRA BF 35 TYR ( 35-) A - OH <--> 228 THR ( 228-) A - CB 0.02 2.78 INTRA BF 146 GLU ( 146-) A - CG <--> 149 ASN ( 149-) A - CG 0.02 3.18 INTRA BF 169 LYS ( 169-) A - N <--> 174 SER ( 174-) A - C 0.02 3.08 INTRA BL 31 TYR ( 31-) A - OH <--> 171 ASP ( 171-) A - CB 0.02 2.78 INTRA BF 132 VAL ( 132-) A - CG1 <--> 201 TYR ( 201-) A - OH 0.02 2.78 INTRA BF 48 ILE ( 48-) A - C <--> 49 SER ( 49-) A - C 0.02 2.78 INTRA BL 10 LEU ( 10-) A - CD2 <--> 12 LYS ( 12-) A - CD 0.02 3.18 INTRA BF 29 LYS ( 29-) A - CB <--> 174 SER ( 174-) A - OG 0.02 2.78 INTRA BF 132 VAL ( 132-) A - CG2 <--> 183 SER ( 183-) A - OG 0.02 2.78 INTRA BF 30 TYR ( 30-) A - CE1 <--> 115 ASN ( 115-) A - ND2 0.02 3.08 INTRA BF 44 PRO ( 44-) A - O <--> 227 LEU ( 227-) A - CB 0.02 2.78 INTRA BF 144 THR ( 144-) A - CB <--> 163 ASN ( 163-) A - ND2 0.02 3.08 INTRA BL 152 ARG ( 152-) A - CD <--> 153 GLU ( 153-) A - O 0.01 2.69 INTRA BF 45 CYS ( 45-) A - O <--> 225 GLU ( 225-) A - CG 0.01 2.79 INTRA BF 36 GLY ( 36-) A - CA <--> 226 THR ( 226-) A - OG1 0.01 2.79 INTRA BF 60 ASP ( 60-) A - CB <--> 90 ASN ( 90-) A - OD1 0.01 2.79 INTRA BF 170 GLY ( 170-) A - CA <--> 176 ILE ( 176-) A - CB 0.01 3.19 INTRA BL 172 THR ( 172-) A - OG1 <--> 173 LEU ( 173-) A - CD2 0.01 2.79 INTRA BF 184 THR ( 184-) A - N <--> 185 LYS ( 185-) A - N 0.01 2.59 INTRA BL 106 ASN ( 106-) A - CB <--> 219 TYR ( 219-) A - CD1 0.01 3.19 INTRA BF 167 VAL ( 167-) A - N <--> 168 LYS ( 168-) A - N 0.01 2.59 INTRA BL 201 TYR ( 201-) A - C <--> 205 ARG ( 205-) A - NH1 0.01 3.09 INTRA BL 93 LEU ( 93-) A - C <--> 94 GLY ( 94-) A - C 0.01 2.79 INTRA BL 204 GLN ( 204-) A - OE1 <--> 208 VAL ( 208-) A - CG2 0.01 2.79 INTRA BF 244 LEU ( 244-) A - CD2 <--> 245 ASN ( 245-) A - N 0.01 2.99 INTRA BF 137 GLN ( 137-) A - CA <--> 152 ARG ( 152-) A - CA 0.01 3.19 INTRA BL 107 ALA ( 107-) A - C <--> 109 ASN ( 109-) A - N 0.01 2.89 INTRA BL 142 PHE ( 142-) A - CD2 <--> 152 ARG ( 152-) A - CA 0.01 3.19 INTRA BF 104 TYR ( 104-) A - C <--> 105 LEU ( 105-) A - CA 0.01 2.29 INTRA BL 152 ARG ( 152-) A - CG <--> 153 GLU ( 153-) A - O 0.01 2.69 INTRA BF 86 SER ( 86-) A - C <--> 87 PHE ( 87-) A - CG 0.01 3.09 INTRA BF 43 HIS ( 43-) A - C <--> 44 PRO ( 44-) A - CD 0.01 2.29 INTRA BF 128 TYR ( 128-) A - OH <--> 135 ARG ( 135-) A - NH2 0.01 2.69 INTRA BF 189 GLU ( 189-) A - CD <--> 196 ASN ( 196-) A - CB 0.01 3.19 INTRA BF 49 SER ( 49-) A - OG <--> 227 LEU ( 227-) A - CD2 0.01 2.79 INTRA BF 161 LYS ( 161-) A - CD <--> 165 HIS ( 165-) A - ND1 0.01 3.09 INTRA BF 48 ILE ( 48-) A - C <--> 51 GLU ( 51-) A - N 0.01 3.09 INTRA BL 20 LYS ( 20-) A - CG <--> 21 ALA ( 21-) A - N 0.01 2.99 INTRA BF 190 LEU ( 190-) A - CD2 <--> 192 PRO ( 192-) A - CD 0.01 3.19 INTRA BF 104 TYR ( 104-) A - CE1 <--> 186 THR ( 186-) A - O 0.01 2.79 INTRA BF 141 LEU ( 141-) A - CD2 <--> 158 LYS ( 158-) A - CE 0.01 3.19 INTRA BF 154 THR ( 154-) A - C <--> 155 SER ( 155-) A - CA 0.01 2.29 INTRA BL 195 LYS ( 195-) A - O <--> 199 LYS ( 199-) A - N 0.01 2.69 INTRA BL # 61 # 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: 109.529 Total bump value per residue: 2.769 Total number of bumps: 731 Total squared bump value: 25.210 Total number of bumps in the mildest bin: 559 Total number of bumps in the second bin: 169 Total number of bumps in the middle bin: 2 Total number of bumps in the fourth bin: 0 Total number of bumps in the worst bin: 1 # 62 # 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 : 1.368 # 63 # 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. 255 TYR ( 255-) A - -8.46 14 PHE ( 14-) A - -7.39 5 GLN ( 5-) A - -7.37 18 ARG ( 18-) A - -7.21 262 LEU ( 262-) A - -6.97 87 PHE ( 87-) A - -6.90 244 LEU ( 244-) A - -6.86 22 TYR ( 22-) A - -6.80 89 TYR ( 89-) A - -6.50 38 TYR ( 38-) A - -6.29 37 HIS ( 37-) A - -6.27 73 LYS ( 73-) A - -6.12 84 LEU ( 84-) A - -6.10 242 MET ( 242-) A - -5.88 20 LYS ( 20-) A - -5.74 71 LEU ( 71-) A - -5.66 12 LYS ( 12-) A - -5.58 78 GLN ( 78-) A - -5.57 15 GLU ( 15-) A - -5.39 207 ASN ( 207-) A - -5.34 117 PHE ( 117-) A - -5.31 223 ARG ( 223-) A - -5.29 241 LEU ( 241-) A - -5.26 261 ARG ( 261-) A - -5.26 233 LYS ( 233-) A - -5.22 235 LYS ( 235-) A - -5.19 156 LYS ( 156-) A - -5.16 194 ILE ( 194-) A - -5.14 # 64 # 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. 1 MET ( 1-) A - 3 --- ILE 3- (A ) - -4.62 37 HIS ( 37-) A - 39 --- GLY 39- (A ) - -5.55 61 VAL ( 61-) A - 63 --- GLU 63- (A ) - -4.64 240 GLN ( 240-) A - 244 --- LEU 244- (A ) - -5.26 253 ASN ( 253-) A - 256 --- ALA 256- (A ) - -5.30 260 ILE ( 260-) A - 262 --- LEU 262- (A ) - -5.51 # 65 # 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 - 264 : -2.715 # 66 # 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. 166 VAL ( 166-) A - -2.78 # 67 # 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. # 68 # 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. 43 HIS ( 43-) A - 109 ASN ( 109-) A - 111 GLN ( 111-) A - 191 ASN ( 191-) A - 204 GLN ( 204-) A - # 69 # 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. 37 HIS ( 37-) A - HIS-D 0.35 HIS-E 1.45 43 HIS ( 43-) A - HIS-D 0.35 165 HIS ( 165-) A - HIS-D 0.36 # 70 # 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. 2 ASN ( 2-) A - N 29 LYS ( 29-) A - N 34 GLY ( 34-) A - N 35 TYR ( 35-) A - N 36 GLY ( 36-) A - N 43 HIS ( 43-) A - N 45 CYS ( 45-) A - N 49 SER ( 49-) A - N 55 LYS ( 55-) A - N 57 LEU ( 57-) A - N 60 ASP ( 60-) A - N 78 GLN ( 78-) A - N 83 ALA ( 83-) A - N 92 GLY ( 92-) A - N 99 SER ( 99-) A - N 100 THR ( 100-) A - N 101 LEU ( 101-) A - N 103 GLN ( 103-) A - N 103 GLN ( 103-) A - NE2 109 ASN ( 109-) A - ND2 115 ASN ( 115-) A - ND2 117 PHE ( 117-) A - N 118 LEU ( 118-) A - N 126 LYS ( 126-) A - N 126 LYS ( 126-) A - NZ 127 VAL ( 127-) A - N 128 TYR ( 128-) A - OH 131 LEU ( 131-) A - N 132 VAL ( 132-) A - N 133 LYS ( 133-) A - NZ 134 ARG ( 134-) A - NH1 134 ARG ( 134-) A - NH2 137 GLN ( 137-) A - N 138 GLU ( 138-) A - N 144 THR ( 144-) A - N 148 LYS ( 148-) A - N 149 ASN ( 149-) A - N 149 ASN ( 149-) A - ND2 150 VAL ( 150-) A - N 152 ARG ( 152-) A - N 153 GLU ( 153-) A - N 154 THR ( 154-) A - OG1 155 SER ( 155-) A - N 158 LYS ( 158-) A - NZ 160 SER ( 160-) A - N 161 LYS ( 161-) A - N 169 LYS ( 169-) A - N 171 ASP ( 171-) A - N 174 SER ( 174-) A - N 174 SER ( 174-) A - OG 175 GLU ( 175-) A - N 177 ALA ( 177-) A - N 178 LYS ( 178-) A - NZ 179 LYS ( 179-) A - NZ 183 SER ( 183-) A - OG 189 GLU ( 189-) A - N 190 LEU ( 190-) A - N 195 LYS ( 195-) A - N 198 ASN ( 198-) A - N 198 ASN ( 198-) A - ND2 204 GLN ( 204-) A - N 204 GLN ( 204-) A - NE2 205 ARG ( 205-) A - NH1 210 GLY ( 210-) A - N 214 LYS ( 214-) A - N 215 SER ( 215-) A - N 218 LYS ( 218-) A - N 220 LYS ( 220-) A - N 221 ILE ( 221-) A - N 224 GLY ( 224-) A - N 225 GLU ( 225-) A - N # 71 # 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. 116 GLU ( 116-) A - OE2 204 GLN ( 204-) A - OE1 # 72 # 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: 405 of which buried: 156 Total number of acceptors: 395 of which buried: 117 Total number of donor+acceptors: 51 (e.g. the Ser Ogamma that can donate and accept) of which buried: 10 Buried donors: 156 without H-bond: 59 essentially without H-bond: 1 with only a very poor H-bond: 2 with a poor H-bond: 7 with a H-bond: 87 Buried acceptors: 117 without H-bond: 47 essentially without H-bond: 0 with only a very poor H-bond: 3 with a poor H-bond: 3 with a H-bond: 64 # 73 # 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. # 74 # 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. # 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) 263 ( 263) A Protein checkset 2 264 ( 264) 264 ( 264) A Sugar checkset 3 265 ( 263) 265 ( 263) A K O2 <- 263 checkset # 76 # 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 : -1.000 1st generation packing quality : -5.536 (poor) 2nd generation packing quality : -5.851 (bad) Ramachandran plot appearance : -1.989 chi-1/chi-2 rotamer normality : -2.865 Backbone conformation : -2.404 Inside/Outside distribution : 1.368 (unusual) RMS Z-scores, should be close to 1.0: Bond lengths : 1.107 Bond angles : 1.717 Omega angle restraints : 1.320 (loose) Side chain planarity : 0.539 (tight) Improper dihedral distribution : 1.551 (loose) # 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.