************************************************************************ ********** REPORT OF PROTEIN ANALYSIS by the WHAT IF program ********** ************************************************************************ Date : 2005-03-09 This report was created by WHAT IF version 20050215-1726 INTRODUCTION ------------ This document contains a report of findings by the WHAT IF program during the analysis of one or more proteins. It contains a separate section for each of the proteins that have been analysed. Each reported fact has an assigned severity, one of: * error: severe errors encountered during the analyses. 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 by all checks. Legend ------ Some notations need a little explanation: RESIDUE: Residues in tables are normally given in 3-5 parts: - A number. This is the internal sequence number of the residue used by WHAT IF. - The residue name. Normally this is a three letter amino acid name. - 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 invisible. - A model number (only for NMR structures). Z-VALUE: 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. ======================================================================== ==== Compound code /home/whatif/httpd/htdocs/servers/tmp//@18328.1//====1.fil ======================================================================== # 1 # Note: No strange inter-chain connections detected No covalent bonds have been detected between molecules with non-identical chain identifiers # 2 # Note: No duplicate atom names All atom names seem adequately unique # 3 # Error: Non-triclinic spacegroup-symbol is missing The CRYST1 card present in the PDB file gives a valid non-triclinic cell, but the space group symbol is not given. The CRYST1 cell dimensions A =1000.000 B =1000.000 C =1000.000 Alpha= 90.000 Beta= 90.000 Gamma= 90.000 # 4 # Error: Missing unit cell information No SCALE matrix is given in the PDB file. # 5 # Error: Missing symmetry information Problem: No CRYST1 card is given in the PDB file. # 6 # Note: Proposal for corrected SCALE matrix A corrected SCALE matrix has been derived. Proposed scale matrix 0.001000 0.000000 0.000000 0.000000 0.001000 0.000000 0.000000 0.000000 0.001000 # 7 # Note: No rounded coordinates detected No significant rounding of atom coordinates has been detected. # 8 # Note: Valine nomenclature OK No errors were detected in valine nomenclature. # 9 # Note: Threonine nomenclature OK No errors were detected in threonine nomenclature. # 10 # Note: Isoleucine nomenclature OK No errors were detected in isoleucine nomenclature. # 11 # Note: Leucine nomenclature OK No errors were detected in leucine nomenclature. # 12 # Note: Arginine nomenclature OK No errors were detected in arginine nomenclature. # 13 # Warning: Tyrosine convention problem The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0 66 TYR ( 66 ) 1 119 TYR ( 52 ) 2 186 TYR ( 52 ) 3 200 TYR ( 66 ) 3 253 TYR ( 52 ) 4 334 TYR ( 66 ) 5 387 TYR ( 52 ) 6 401 TYR ( 66 ) 6 426 TYR ( 24 ) 7 493 TYR ( 24 ) 8 535 TYR ( 66 ) 8 588 TYR ( 52 ) 9 669 TYR ( 66 ) 10 694 TYR ( 24 ) 11 722 TYR ( 52 ) 11 803 TYR ( 66 ) 12 870 TYR ( 66 ) 13 895 TYR ( 24 ) 14 1004 TYR ( 66 ) 15 1029 TYR ( 24 ) 16 1057 TYR ( 52 ) 16 1096 TYR ( 24 ) 17 1138 TYR ( 66 ) 17 1163 TYR ( 24 ) 18 1258 TYR ( 52 ) 19 1325 TYR ( 52 ) 20 # 14 # Warning: Phenylalanine convention problem The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0. 6 PHE ( 6 ) 1 102 PHE ( 35 ) 2 140 PHE ( 6 ) 3 159 PHE ( 25 ) 3 226 PHE ( 25 ) 4 274 PHE ( 6 ) 5 293 PHE ( 25 ) 5 341 PHE ( 6 ) 6 370 PHE ( 35 ) 6 408 PHE ( 6 ) 7 427 PHE ( 25 ) 7 494 PHE ( 25 ) 8 504 PHE ( 35 ) 8 561 PHE ( 25 ) 9 571 PHE ( 35 ) 9 628 PHE ( 25 ) 10 676 PHE ( 6 ) 11 705 PHE ( 35 ) 11 762 PHE ( 25 ) 12 829 PHE ( 25 ) 13 839 PHE ( 35 ) 13 877 PHE ( 6 ) 14 906 PHE ( 35 ) 14 973 PHE ( 35 ) 15 1011 PHE ( 6 ) 16 1040 PHE ( 35 ) 16 1078 PHE ( 6 ) 17 1097 PHE ( 25 ) 17 1107 PHE ( 35 ) 17 1145 PHE ( 6 ) 18 1212 PHE ( 6 ) 19 1231 PHE ( 25 ) 19 1279 PHE ( 6 ) 20 1298 PHE ( 25 ) 20 1308 PHE ( 35 ) 20 # 15 # Warning: Aspartic acid convention problem The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2. 27 ASP ( 27 ) 1 74 ASP ( 7 ) 2 76 ASP ( 9 ) 2 94 ASP ( 27 ) 2 135 ASP ( 1 ) 3 161 ASP ( 27 ) 3 173 ASP ( 39 ) 3 210 ASP ( 9 ) 4 240 ASP ( 39 ) 4 269 ASP ( 1 ) 5 277 ASP ( 9 ) 5 307 ASP ( 39 ) 5 336 ASP ( 1 ) 6 344 ASP ( 9 ) 6 362 ASP ( 27 ) 6 374 ASP ( 39 ) 6 429 ASP ( 27 ) 7 543 ASP ( 7 ) 9 563 ASP ( 27 ) 9 610 ASP ( 7 ) 10 612 ASP ( 9 ) 10 630 ASP ( 27 ) 10 671 ASP ( 1 ) 11 677 ASP ( 7 ) 11 679 ASP ( 9 ) 11 697 ASP ( 27 ) 11 776 ASP ( 39 ) 12 811 ASP ( 7 ) 13 813 ASP ( 9 ) 13 872 ASP ( 1 ) 14 939 ASP ( 1 ) 15 947 ASP ( 9 ) 15 1012 ASP ( 7 ) 16 1079 ASP ( 7 ) 17 1099 ASP ( 27 ) 17 1140 ASP ( 1 ) 18 1146 ASP ( 7 ) 18 1166 ASP ( 27 ) 18 1213 ASP ( 7 ) 19 1233 ASP ( 27 ) 19 1274 ASP ( 1 ) 20 1300 ASP ( 27 ) 20 # 16 # Warning: Glutamic acid convention problem The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2. 55 GLU ( 55 ) 1 56 GLU ( 56 ) 1 117 GLU ( 50 ) 2 184 GLU ( 50 ) 3 206 GLU ( 5 ) 4 251 GLU ( 50 ) 4 259 GLU ( 58 ) 4 323 GLU ( 55 ) 5 324 GLU ( 56 ) 5 340 GLU ( 5 ) 6 385 GLU ( 50 ) 6 390 GLU ( 55 ) 6 391 GLU ( 56 ) 6 407 GLU ( 5 ) 7 586 GLU ( 50 ) 9 594 GLU ( 58 ) 9 653 GLU ( 50 ) 10 658 GLU ( 55 ) 10 659 GLU ( 56 ) 10 661 GLU ( 58 ) 10 720 GLU ( 50 ) 11 726 GLU ( 56 ) 11 728 GLU ( 58 ) 11 792 GLU ( 55 ) 12 793 GLU ( 56 ) 12 795 GLU ( 58 ) 12 854 GLU ( 50 ) 13 860 GLU ( 56 ) 13 876 GLU ( 5 ) 14 921 GLU ( 50 ) 14 926 GLU ( 55 ) 14 927 GLU ( 56 ) 14 929 GLU ( 58 ) 14 993 GLU ( 55 ) 15 994 GLU ( 56 ) 15 996 GLU ( 58 ) 15 1060 GLU ( 55 ) 16 1063 GLU ( 58 ) 16 1077 GLU ( 5 ) 17 1127 GLU ( 55 ) 17 1128 GLU ( 56 ) 17 1130 GLU ( 58 ) 17 1144 GLU ( 5 ) 18 1197 GLU ( 58 ) 18 1261 GLU ( 55 ) 19 1262 GLU ( 56 ) 19 1264 GLU ( 58 ) 19 1278 GLU ( 5 ) 20 1323 GLU ( 50 ) 20 1329 GLU ( 56 ) 20 1331 GLU ( 58 ) 20 # 17 # Warning: Heavy atom naming problem The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometomes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Swapped OP1 and OP2 on nucleic acid phosphors also are reported elsewhere). 67 VAL ( 67 ) 1 O <--> OT1 134 VAL ( 67 ) 2 O <--> OT1 201 VAL ( 67 ) 3 O <--> O2 268 VAL ( 67 ) 4 O <--> O2 335 VAL ( 67 ) 5 O <--> OT1 402 VAL ( 67 ) 6 O <--> OT1 469 VAL ( 67 ) 7 O <--> OT1 536 VAL ( 67 ) 8 O <--> OT1 603 VAL ( 67 ) 9 O <--> OT1 670 VAL ( 67 ) 10 O <--> OT1 737 VAL ( 67 ) 11 O <--> O2 804 VAL ( 67 ) 12 O <--> O2 871 VAL ( 67 ) 13 O <--> OT1 938 VAL ( 67 ) 14 O <--> O2 1005 VAL ( 67 ) 15 O <--> OT1 1072 VAL ( 67 ) 16 O <--> OT1 1139 VAL ( 67 ) 17 O <--> OT1 1206 VAL ( 67 ) 18 O <--> OT1 1273 VAL ( 67 ) 19 O <--> OT1 1340 VAL ( 67 ) 20 O <--> O2 1346 VAL ( OXT ) 3 O2 <--> OT1 1348 VAL ( OXT ) 4 O2 <--> OT1 1362 VAL ( OXT ) 11 O2 <--> OT1 1364 VAL ( OXT ) 12 O2 <--> OT1 1368 VAL ( OXT ) 14 O2 <--> OT1 1380 VAL ( OXT ) 20 O2 <--> OT1 # 18 # 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 don't 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. 505 ARG ( 36 ) 8 CA -6.0 24.5 34.0 # 19 # 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 : 1.508 # 20 # Note: Per-model averages for chirality check The table below gives the per-model improper dihedral RMS Z-scores. Model 1 : 1.538 Model 2 : 1.497 Model 3 : 1.390 Model 4 : 1.474 Model 5 : 1.823 Model 6 : 1.483 Model 7 : 1.493 Model 8 : 1.489 Model 9 : 1.344 Model 10 : 1.460 Model 11 : 1.599 Model 12 : 1.330 Model 13 : 1.495 Model 14 : 1.527 Model 15 : 1.302 Model 16 : 1.569 Model 17 : 1.527 Model 18 : 1.605 Model 19 : 1.494 Model 20 : 1.638 # 21 # Note: No missing atoms detected All expected atoms are present. # 22 # Note: OXT check OK All required C-terminal oxygen atoms are present. # 23 # Note: No extra C-terminal groups found No C-terminal groups are present for non C-terminal residues # 24 # 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 sigma 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 "--SS", the disulphide bridge has a deviating length. 40 HIS ( 40 ) 1 CG CD2 1.296 -5.5 107 HIS ( 40 ) 2 CG CD2 1.286 -6.4 174 HIS ( 40 ) 3 CG CD2 1.289 -6.1 308 HIS ( 40 ) 5 CG CD2 1.279 -7.0 375 HIS ( 40 ) 6 CG CD2 1.266 -8.2 442 HIS ( 40 ) 7 CB CG 1.431 -4.7 442 HIS ( 40 ) 7 CG CD2 1.292 -5.8 442 HIS ( 40 ) 7 ND1 CE1 1.263 -4.3 509 HIS ( 40 ) 8 CG CD2 1.295 -5.5 576 HIS ( 40 ) 9 CG CD2 1.305 -4.6 643 HIS ( 40 ) 10 CG CD2 1.294 -5.6 710 HIS ( 40 ) 11 CG CD2 1.290 -6.0 777 HIS ( 40 ) 12 CG CD2 1.279 -7.0 844 HIS ( 40 ) 13 CG CD2 1.291 -5.9 911 HIS ( 40 ) 14 CG CD2 1.296 -5.5 978 HIS ( 40 ) 15 CG CD2 1.288 -6.2 1045 HIS ( 40 ) 16 CG CD2 1.278 -7.1 1112 HIS ( 40 ) 17 CG CD2 1.289 -6.1 1179 HIS ( 40 ) 18 CG CD2 1.292 -5.8 1189 GLU ( 50 ) 18 N -C 1.234 -4.8 1246 HIS ( 40 ) 19 CG CD2 1.282 -6.7 1313 HIS ( 40 ) 20 CG CD2 1.252 -9.4 # 25 # 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: 0.831 RMS-deviation in bond distances: 0.016 # 26 # Note: Per-model averages for bond-length check The table below gives the per-model bond-length RMS Z-scores. Model 1 : 0.827 Model 2 : 0.828 Model 3 : 0.787 Model 4 : 0.794 Model 5 : 0.867 Model 6 : 0.859 Model 7 : 0.906 Model 8 : 0.795 Model 9 : 0.818 Model 10 : 0.768 Model 11 : 0.857 Model 12 : 0.823 Model 13 : 0.780 Model 14 : 0.833 Model 15 : 0.801 Model 16 : 0.833 Model 17 : 0.837 Model 18 : 0.870 Model 19 : 0.832 Model 20 : 0.899 # 27 # 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. 16 HIS ( 16 ) 1 CG ND1 CE1 109.733 4.1 97 ASN ( 30 ) 2 CA CB CG 117.638 5.0 236 PHE ( 35 ) 4 CA CB CG 118.211 4.4 351 HIS ( 16 ) 6 CG ND1 CE1 109.750 4.2 365 ASN ( 30 ) 6 CA CB CG 117.961 5.4 552 HIS ( 16 ) 9 CG ND1 CE1 109.604 4.0 777 HIS ( 40 ) 12 CA CB CG 117.838 4.0 820 HIS ( 16 ) 13 CG ND1 CE1 109.818 4.2 1088 HIS ( 16 ) 17 CG ND1 CE1 109.630 4.0 1222 HIS ( 16 ) 19 CG ND1 CE1 109.741 4.1 1241 PHE ( 35 ) 19 CA CB CG 118.909 5.1 # 28 # 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 around 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. More common values are around 1.55. RMS Z-score for bond angles: 0.768 RMS-deviation in bond angles: 1.385 # 29 # Note: Per-model averages for bond-angle check The table below gives the per-model bond-angle RMS Z-scores. Model 1 : 0.768 Model 2 : 0.781 Model 3 : 0.744 Model 4 : 0.734 Model 5 : 0.729 Model 6 : 0.803 Model 7 : 0.820 Model 8 : 0.785 Model 9 : 0.747 Model 10 : 0.750 Model 11 : 0.757 Model 12 : 0.727 Model 13 : 0.739 Model 14 : 0.788 Model 15 : 0.718 Model 16 : 0.853 Model 17 : 0.783 Model 18 : 0.757 Model 19 : 0.765 Model 20 : 0.795 # 30 # Note: Side chain planarity OK All of the side chains of residues that have a planar group are planar within expected RMS deviations. # 31 # Error: Connections to aromatic rings out of plane The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane. For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures. 1313 HIS ( 40 ) 20 CB 11.324 375 HIS ( 40 ) 6 CB 10.790 1045 HIS ( 40 ) 16 CB 10.590 777 HIS ( 40 ) 12 CB 10.245 1179 HIS ( 40 ) 18 CB 10.212 643 HIS ( 40 ) 10 CB 10.094 174 HIS ( 40 ) 3 CB 10.071 1246 HIS ( 40 ) 19 CB 9.710 1112 HIS ( 40 ) 17 CB 9.669 844 HIS ( 40 ) 13 CB 9.596 911 HIS ( 40 ) 14 CB 9.587 710 HIS ( 40 ) 11 CB 9.565 40 HIS ( 40 ) 1 CB 9.480 509 HIS ( 40 ) 8 CB 9.374 978 HIS ( 40 ) 15 CB 9.262 576 HIS ( 40 ) 9 CB 9.120 107 HIS ( 40 ) 2 CB 9.083 308 HIS ( 40 ) 5 CB 8.975 442 HIS ( 40 ) 7 CB 8.620 241 HIS ( 40 ) 4 CB 6.715 # 32 # Note: PRO puckering amplitude OK Puckering amplitudes for all PRO residues are within normal ranges. # 33 # 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. 2 PRO ( 2 ) 1 -135.6 envelop C-delta (-144 degrees) 8 PRO ( 8 ) 1 -42.8 envelop C-alpha (-36 degrees) 252 PRO ( 51 ) 4 34.3 envelop C-delta (36 degrees) 337 PRO ( 2 ) 6 27.9 envelop C-delta (36 degrees) 453 PRO ( 51 ) 7 -23.4 half-chair C-alpha/N (-18 degrees) 544 PRO ( 8 ) 9 -64.4 envelop C-beta (-72 degrees) 605 PRO ( 2 ) 10 3.2 envelop N (0 degrees) 654 PRO ( 51 ) 10 -58.1 half-chair C-beta/C-alpha (-54 degrees) 678 PRO ( 8 ) 11 -52.6 half-chair C-beta/C-alpha (-54 degrees) 721 PRO ( 51 ) 11 -54.4 half-chair C-beta/C-alpha (-54 degrees) 739 PRO ( 2 ) 12 -114.6 envelop C-gamma (-108 degrees) 879 PRO ( 8 ) 14 -60.0 half-chair C-beta/C-alpha (-54 degrees) 922 PRO ( 51 ) 14 51.8 half-chair C-delta/C-gamma (54 degrees) 1056 PRO ( 51 ) 16 -51.4 half-chair C-beta/C-alpha (-54 degrees) 1123 PRO ( 51 ) 17 15.6 half-chair N/C-delta (18 degrees) 1190 PRO ( 51 ) 18 4.5 envelop N (0 degrees) 1257 PRO ( 51 ) 19 29.4 envelop C-delta (36 degrees) 1275 PRO ( 2 ) 20 -121.1 half-chair C-delta/C-gamma (-126 degrees) 1324 PRO ( 51 ) 20 114.3 envelop C-beta (108 degrees) # 34 # 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 IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position. 1190 PRO ( 51 ) 18 -2.9579 605 PRO ( 2 ) 10 -2.9371 453 PRO ( 51 ) 7 -2.8652 1324 PRO ( 51 ) 20 -2.8341 1056 PRO ( 51 ) 16 -2.8265 1123 PRO ( 51 ) 17 -2.6590 879 PRO ( 8 ) 14 -2.6454 678 PRO ( 8 ) 11 -2.6164 8 PRO ( 8 ) 1 -2.3400 795 GLU ( 58 ) 12 -2.3198 1257 PRO ( 51 ) 19 -2.2856 652 VAL ( 49 ) 10 -2.2481 721 PRO ( 51 ) 11 -2.1920 193 ARG ( 59 ) 3 -2.1912 654 PRO ( 51 ) 10 -2.1807 256 GLU ( 55 ) 4 -2.1719 458 GLU ( 56 ) 7 -2.1709 1255 VAL ( 49 ) 19 -2.1622 337 PRO ( 2 ) 6 -2.1475 332 GLY ( 64 ) 5 -2.1428 5 GLU ( 5 ) 1 -2.1427 198 GLY ( 64 ) 3 -2.1013 466 GLY ( 64 ) 7 -2.0676 467 SER ( 65 ) 7 -2.0673 343 PRO ( 8 ) 6 -2.0643 1077 GLU ( 5 ) 17 -2.0637 182 SER ( 48 ) 3 -2.0634 1271 SER ( 65 ) 19 -2.0623 252 PRO ( 51 ) 4 -2.0583 1069 GLY ( 64 ) 16 -2.0571 1323 GLU ( 50 ) 20 -2.0247 544 PRO ( 8 ) 9 -2.0111 1174 PHE ( 35 ) 18 -2.0050 333 SER ( 65 ) 5 -2.0020 131 GLY ( 64 ) 2 -2.0015 204 ASN ( 3 ) 4 -2.0007 # 35 # Warning: Backbone torsion angle evaluation shows 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. 8 PRO ( 8 ) 1 Poor PRO-phi 22 ALA ( 22 ) 1 Poor phi/psi 55 GLU ( 55 ) 1 Poor phi/psi 61 ALA ( 61 ) 1 Poor phi/psi 81 GLY ( 14 ) 2 Poor phi/psi 83 HIS ( 16 ) 2 Poor phi/psi 84 ARG ( 17 ) 2 Poor phi/psi 89 ALA ( 22 ) 2 Poor phi/psi 115 SER ( 48 ) 2 Poor phi/psi 117 GLU ( 50 ) 2 Poor phi/psi 122 GLU ( 55 ) 2 Poor phi/psi 123 GLU ( 56 ) 2 Poor phi/psi 136 PRO ( 2 ) 3 Poor phi/psi 138 ALA ( 4 ) 3 Poor phi/psi 150 HIS ( 16 ) 3 Poor phi/psi 151 ARG ( 17 ) 3 Poor phi/psi 156 ALA ( 22 ) 3 Poor phi/psi 182 SER ( 48 ) 3 Poor phi/psi 185 PRO ( 51 ) 3 Poor PRO-phi 186 TYR ( 52 ) 3 Poor phi/psi 192 GLU ( 58 ) 3 Poor phi/psi 195 ALA ( 61 ) 3 Poor phi/psi 204 ASN ( 3 ) 4 Poor phi/psi 217 HIS ( 16 ) 4 Poor phi/psi 218 ARG ( 17 ) 4 Poor phi/psi 223 ALA ( 22 ) 4 Poor phi/psi 252 PRO ( 51 ) 4 Poor PRO-phi 255 GLN ( 54 ) 4 Poor phi/psi 257 GLU ( 56 ) 4 Poor phi/psi 261 ALA ( 60 ) 4 Poor phi/psi 272 ALA ( 4 ) 5 Poor phi/psi 290 ALA ( 22 ) 5 Poor phi/psi 316 SER ( 48 ) 5 Poor phi/psi 322 GLN ( 54 ) 5 Poor phi/psi 323 GLU ( 55 ) 5 Poor phi/psi 324 GLU ( 56 ) 5 Poor phi/psi 325 ALA ( 57 ) 5 Poor phi/psi 329 ALA ( 61 ) 5 Poor phi/psi 333 SER ( 65 ) 5 Poor phi/psi 337 PRO ( 2 ) 6 Poor PRO-phi 338 ASN ( 3 ) 6 Poor phi/psi 339 ALA ( 4 ) 6 Poor phi/psi 343 PRO ( 8 ) 6 Poor PRO-phi 357 ALA ( 22 ) 6 Poor phi/psi 383 SER ( 48 ) 6 Poor phi/psi 385 GLU ( 50 ) 6 Poor phi/psi 390 GLU ( 55 ) 6 Poor phi/psi 394 ARG ( 59 ) 6 Poor phi/psi 400 SER ( 65 ) 6 Poor phi/psi 405 ASN ( 3 ) 7 Poor phi/psi 418 HIS ( 16 ) 7 Poor phi/psi 419 ARG ( 17 ) 7 Poor phi/psi 424 ALA ( 22 ) 7 Poor phi/psi 451 VAL ( 49 ) 7 Poor phi/psi 453 PRO ( 51 ) 7 Poor PRO-phi 457 GLU ( 55 ) 7 Poor phi/psi 458 GLU ( 56 ) 7 Poor phi/psi 461 ARG ( 59 ) 7 Poor phi/psi 462 ALA ( 60 ) 7 Poor phi/psi 467 SER ( 65 ) 7 Poor phi/psi 473 ALA ( 4 ) 8 Poor phi/psi 491 ALA ( 22 ) 8 Poor phi/psi 517 SER ( 48 ) 8 Poor phi/psi 519 GLU ( 50 ) 8 Poor phi/psi 527 GLU ( 58 ) 8 Poor phi/psi 530 ALA ( 61 ) 8 Poor phi/psi 539 ASN ( 3 ) 9 Poor phi/psi 540 ALA ( 4 ) 9 Poor phi/psi 541 GLU ( 5 ) 9 Poor phi/psi 544 PRO ( 8 ) 9 Poor PRO-phi 547 PRO ( 11 ) 9 Poor phi/psi 558 ALA ( 22 ) 9 Poor phi/psi 588 TYR ( 52 ) 9 Poor phi/psi 591 GLU ( 55 ) 9 Poor phi/psi 594 GLU ( 58 ) 9 Poor phi/psi 605 PRO ( 2 ) 10 Poor phi/psi 606 ASN ( 3 ) 10 Poor phi/psi 608 GLU ( 5 ) 10 Poor phi/psi 619 HIS ( 16 ) 10 Poor phi/psi 620 ARG ( 17 ) 10 Poor phi/psi 625 ALA ( 22 ) 10 Poor phi/psi 653 GLU ( 50 ) 10 Poor phi/psi 654 PRO ( 51 ) 10 Poor PRO-phi 655 TYR ( 52 ) 10 Poor phi/psi 657 GLN ( 54 ) 10 Poor phi/psi 658 GLU ( 55 ) 10 Poor phi/psi 659 GLU ( 56 ) 10 Poor phi/psi 662 ARG ( 59 ) 10 Poor phi/psi 664 ALA ( 61 ) 10 Poor phi/psi 666 MET ( 63 ) 10 Poor phi/psi 673 ASN ( 3 ) 11 Poor phi/psi 678 PRO ( 8 ) 11 Poor PRO-phi 692 ALA ( 22 ) 11 Poor phi/psi 721 PRO ( 51 ) 11 Poor PRO-phi 722 TYR ( 52 ) 11 Poor phi/psi 725 GLU ( 55 ) 11 Poor phi/psi 726 GLU ( 56 ) 11 Poor phi/psi 741 ALA ( 4 ) 12 Poor phi/psi 745 PRO ( 8 ) 12 Poor PRO-phi 759 ALA ( 22 ) 12 Poor phi/psi 785 SER ( 48 ) 12 Poor phi/psi 791 GLN ( 54 ) 12 Poor phi/psi 792 GLU ( 55 ) 12 Poor phi/psi 802 SER ( 65 ) 12 Poor phi/psi 807 ASN ( 3 ) 13 Poor phi/psi 820 HIS ( 16 ) 13 Poor phi/psi 821 ARG ( 17 ) 13 Poor phi/psi 826 ALA ( 22 ) 13 Poor phi/psi 862 GLU ( 58 ) 13 Poor phi/psi 863 ARG ( 59 ) 13 Poor phi/psi 869 SER ( 65 ) 13 Poor phi/psi 874 ASN ( 3 ) 14 Poor phi/psi 879 PRO ( 8 ) 14 Poor PRO-phi 893 ALA ( 22 ) 14 Poor phi/psi 926 GLU ( 55 ) 14 Poor phi/psi 930 ARG ( 59 ) 14 Poor phi/psi 931 ALA ( 60 ) 14 Poor phi/psi 934 MET ( 63 ) 14 Poor phi/psi 937 TYR ( 66 ) 14 Poor phi/psi 942 ALA ( 4 ) 15 Poor phi/psi 960 ALA ( 22 ) 15 Poor phi/psi 986 SER ( 48 ) 15 Poor phi/psi 987 VAL ( 49 ) 15 Poor phi/psi 991 SER ( 53 ) 15 Poor phi/psi 994 GLU ( 56 ) 15 Poor phi/psi 995 ALA ( 57 ) 15 Poor phi/psi 997 ARG ( 59 ) 15 Poor phi/psi 1009 ALA ( 4 ) 16 Poor phi/psi 1013 PRO ( 8 ) 16 Poor PRO-phi 1021 HIS ( 16 ) 16 Poor phi/psi 1022 ARG ( 17 ) 16 Poor phi/psi 1027 ALA ( 22 ) 16 Poor phi/psi 1053 SER ( 48 ) 16 Poor phi/psi 1056 PRO ( 51 ) 16 Poor PRO-phi 1057 TYR ( 52 ) 16 Poor phi/psi 1059 GLN ( 54 ) 16 Poor phi/psi 1060 GLU ( 55 ) 16 Poor phi/psi 1061 GLU ( 56 ) 16 Poor phi/psi 1065 ALA ( 60 ) 16 Poor phi/psi 1071 TYR ( 66 ) 16 Poor phi/psi 1075 ASN ( 3 ) 17 Poor phi/psi 1094 ALA ( 22 ) 17 Poor phi/psi 1123 PRO ( 51 ) 17 Poor PRO-phi 1125 SER ( 53 ) 17 Poor phi/psi 1127 GLU ( 55 ) 17 Poor phi/psi 1129 ALA ( 57 ) 17 Poor phi/psi 1142 ASN ( 3 ) 18 Poor phi/psi 1161 ALA ( 22 ) 18 Poor phi/psi 1190 PRO ( 51 ) 18 Poor PRO-phi 1194 GLU ( 55 ) 18 Poor phi/psi 1197 GLU ( 58 ) 18 Poor phi/psi 1220 GLY ( 14 ) 19 Poor phi/psi 1222 HIS ( 16 ) 19 Poor phi/psi 1223 ARG ( 17 ) 19 Poor phi/psi 1228 ALA ( 22 ) 19 Poor phi/psi 1255 VAL ( 49 ) 19 Poor phi/psi 1257 PRO ( 51 ) 19 Poor PRO-phi 1260 GLN ( 54 ) 19 Poor phi/psi 1261 GLU ( 55 ) 19 Poor phi/psi 1264 GLU ( 58 ) 19 Poor phi/psi 1277 ALA ( 4 ) 20 Poor phi/psi 1281 PRO ( 8 ) 20 Poor PRO-phi 1287 GLY ( 14 ) 20 Poor phi/psi 1289 HIS ( 16 ) 20 Poor phi/psi 1290 ARG ( 17 ) 20 Poor phi/psi 1295 ALA ( 22 ) 20 Poor phi/psi 1322 VAL ( 49 ) 20 Poor phi/psi 1323 GLU ( 50 ) 20 Poor phi/psi 1324 PRO ( 51 ) 20 Poor PRO-phi 1325 TYR ( 52 ) 20 Poor phi/psi 1327 GLN ( 54 ) 20 Poor phi/psi 1332 ARG ( 59 ) 20 Poor phi/psi 1333 ALA ( 60 ) 20 Poor phi/psi 1337 GLY ( 64 ) 20 Poor phi/psi # 36 # Error: Ramachandran Z-score very low The score expressing how well the backbone conformations of all residues are corresponding to the known allowed areas in the Ramachandran plot is very low. Ramachandran Z-score : -4.849 # 37 # Note: Per-model averages for Ramachandran check The table below gives the per-model Ramachandran Z-scores. Model 1 : -5.302 Model 2 : -4.617 Model 3 : -5.378 Model 4 : -4.835 Model 5 : -4.233 Model 6 : -5.027 Model 7 : -4.132 Model 8 : -5.392 Model 9 : -4.465 Model 10 : -5.246 Model 11 : -3.673 Model 12 : -4.563 Model 13 : -4.919 Model 14 : -4.665 Model 15 : -5.434 Model 16 : -5.357 Model 17 : -4.898 Model 18 : -4.501 Model 19 : -5.650 Model 20 : -4.700 # 38 # Warning: Omega angles too tightly restrained The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly constrained. This seems to be the case with the current structure, as the observed standard deviation is below 4.0 degrees. Standard deviation of omega values : 3.771 # 39 # Note: Per-model averages for omega angle check The table below gives the per-model omega angle standard deviations. Model 1 : 3.610 Model 2 : 3.423 Model 3 : 3.499 Model 4 : 3.878 Model 5 : 3.571 Model 6 : 3.690 Model 7 : 3.968 Model 8 : 4.105 Model 9 : 3.717 Model 10 : 3.835 Model 11 : 3.400 Model 12 : 3.435 Model 13 : 3.734 Model 14 : 3.564 Model 15 : 3.627 Model 16 : 4.385 Model 17 : 3.870 Model 18 : 4.261 Model 19 : 3.754 Model 20 : 4.106 # 40 # Note: chi-1/chi-2 angle correlation Z-score OK The score expressing how well the chi-1/chi-2 angles of all residues are corresponding to the populated areas in the database is within expected ranges for well-refined structures. chi-1/chi-2 correlation Z-score : -1.327 # 41 # Note: Per-model averages for chi-1/chi-2 angle check The table below gives the per-model chi-1/chi-2 correlation Z-scores. Model 1 : -1.806 Model 2 : -0.300 Model 3 : -1.774 Model 4 : -0.926 Model 5 : -0.885 Model 6 : -0.845 Model 7 : -1.136 Model 8 : -1.726 Model 9 : -1.676 Model 10 : -0.482 Model 11 : -2.057 Model 12 : -1.542 Model 13 : -1.532 Model 14 : -1.141 Model 15 : -0.628 Model 16 : -2.068 Model 17 : -3.009 Model 18 : -1.845 Model 19 : -0.274 Model 20 : -0.891 # 42 # Note: Ramachandran plot In this Ramachandran plot X-signs represent glycines, squares represent prolines and small plus-signs represent the other residues. If too many plus-signs fall outside the contoured areas then the molecule is poorly refined (or worse). In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. "Allowed" regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. In the TeX file, a plot has been inserted here Model number 1 # 43 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 2 # 44 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 3 # 45 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 4 # 46 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 5 # 47 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 6 # 48 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 7 # 49 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 8 # 50 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 9 # 51 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 10 # 52 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 11 # 53 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 12 # 54 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 13 # 55 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 14 # 56 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 15 # 57 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 16 # 58 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 17 # 59 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 18 # 60 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 19 # 61 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 20 # 62 # Note: Inside/Outside residue distribution normal The distribution of residue types over the inside and the outside of the protein is normal. inside/outside RMS Z-score : 1.135 # 63 # Note: Per-model averages for inside/outside residue distribution check The table below gives the per-model inside/outside residue distribution RMS Z-scores. Model 1 : 1.160 Model 2 : 1.143 Model 3 : 1.179 Model 4 : 1.084 Model 5 : 1.129 Model 6 : 1.141 Model 7 : 1.173 Model 8 : 1.049 Model 9 : 1.111 Model 10 : 1.102 Model 11 : 1.182 Model 12 : 1.159 Model 13 : 1.114 Model 14 : 1.082 Model 15 : 1.053 Model 16 : 1.227 Model 17 : 1.114 Model 18 : 1.128 Model 19 : 1.095 Model 20 : 1.255 # 64 # Note: Inside/Outside RMS Z-score plot The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns. In the TeX file, a plot has been inserted here Model number 1 # 65 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 2 # 66 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 3 # 67 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 4 # 68 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 5 # 69 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 6 # 70 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 7 # 71 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 8 # 72 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 9 # 73 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 10 # 74 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 11 # 75 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 12 # 76 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 13 # 77 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 14 # 78 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 15 # 79 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 16 # 80 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 17 # 81 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 18 # 82 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 19 # 83 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 20 # 84 # Note: Secondary structure This is the secondary structure according to DSSP. Only helix (H), strand (S), turn (T) and coil (blank) are shown. [REF] Secondary structure assignment 10 20 30 40 50 60 | | | | | | 1 - 60 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 1 - 60 T TTT3333TTSSTTTTSS TTHHHHHHHTT HHHHHHHHHHT TTTT 61 - 67 AGMGSYV 61 - 67 T 70 80 90 100 110 120 | | | | | | 68 - 127 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 68 - 127 TTTTTTTTT TTTT TTHHHHHHHTT HHHHHHHHHHTT 333T 130 | 128 - 134 AGMGSYV 128 - 134 140 150 160 170 180 190 | | | | | | 135 - 194 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 135 - 194 T TT TTT3333TT TTTT TTHHHHHHHTT HHHHHHHHHHTTT TTT T 200 | 195 - 201 AGMGSYV 195 - 201 T 210 220 230 240 250 260 | | | | | | 202 - 261 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 202 - 261 TT TTT3333TT 333T TTHHHHHHHTT HHHHHHHHHH TT TTTT T 262 - 268 AGMGSYV 262 - 268 TT 270 280 290 300 310 320 | | | | | | 269 - 328 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 269 - 328 TTT3333TTSS333TSS TTHHHHHHHTTTHHHHHHHHHHT T TTTT 330 | 329 - 335 AGMGSYV 329 - 335 T 340 350 360 370 380 390 | | | | | | 336 - 395 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 336 - 395 T TT TTTTTTTTT TTTT TTHHHHHHHTT HHHHHHHHHHTT TTTT 400 | 396 - 402 AGMGSYV 396 - 402 410 420 430 440 450 460 | | | | | | 403 - 462 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 403 - 462 TT TTTTTTTTT TTTT TTHHHHHHHTT HHHHHHHHHHHTT T333T 463 - 469 AGMGSYV 463 - 469 470 480 490 500 510 520 | | | | | | 470 - 529 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 470 - 529 TTT3333T SSTTTTSS TTHHHHHHHHT HHHHHHHHHH TTTT 530 | 530 - 536 AGMGSYV 530 - 536 TTTT 540 550 560 570 580 590 | | | | | | 537 - 596 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 537 - 596 TT TTTTTTTTTSSTTTTSS TTHHHHHHHTT HHHHHHHHHHTTTTT TTTTT T 600 | 597 - 603 AGMGSYV 597 - 603 TT T 610 620 630 640 650 660 | | | | | | 604 - 663 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 604 - 663 T TTT3333TT TTTT TTHHHHHHHTT HHHHHHHHHHTT TTTT T 670 | 664 - 670 AGMGSYV 664 - 670 T 680 690 700 710 720 730 | | | | | | 671 - 730 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 671 - 730 TT TT TTTTT TTTSSTTTTSS T HHHHHHHT HHHHHHHHHHHT TTT 731 - 737 AGMGSYV 731 - 737 T 740 750 760 770 780 790 | | | | | | 738 - 797 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 738 - 797 TTTT333 SSTTTTSS TTHHHHHHHTT HHHHHHHHHH TT TTTT 800 | 798 - 804 AGMGSYV 798 - 804 T 810 820 830 840 850 860 | | | | | | 805 - 864 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 805 - 864 TTTT333TT TTTT TTHHHHHHHTT HHHHHHHHHHTTTT TTTTT T 870 | 865 - 871 AGMGSYV 865 - 871 T 880 890 900 910 920 930 | | | | | | 872 - 931 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 872 - 931 TT TTTT333TTSSTTTTSS TTHHHHHHHT HHHHHHHHHHHHT TTTTT T 932 - 938 AGMGSYV 932 - 938 T 940 950 960 970 980 990 | | | | | | 939 - 998 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 939 - 998 TTT3333 TSSTTTTSS TTHHHHHHHTT HHHHHHHHHH T T T3333 1000 | 999 -1005 AGMGSYV 999 -1005 1010 1020 1030 1040 1050 1060 | | | | | | 1006 -1065 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 1006 -1065 TT TT TTTTTTTT TTTT TTHHHHHHHTT HHHHHHHHHHTT TTTTT T 1070 | 1066 -1072 AGMGSYV 1066 -1072 T 1080 1090 1100 1110 1120 1130 | | | | | | 1073 -1132 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 1073 -1132 TTT TTT3333TTSSTTTTSS TTHHHHHHHTT HHHHHHHHHHTTTT TTTT T 1133 -1139 AGMGSYV 1133 -1139 T 1140 1150 1160 1170 1180 1190 | | | | | | 1140 -1199 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 1140 -1199 T TTTT333TTSSTTTTSS TTHHHHHHHT HHHHHHHHHHHT TT T T 1200 | 1200 -1206 AGMGSYV 1200 -1206 T 1210 1220 1230 1240 1250 1260 | | | | | | 1207 -1266 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 1207 -1266 T TTT3333TTT TTTT TTHHHHHHHH HHHHHHHHHHTT TTTTTT T 1270 | 1267 -1273 AGMGSYV 1267 -1273 T 1280 1290 1300 1310 1320 1330 | | | | | | 1274 -1333 DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVEPYSQEEAERA 1274 -1333 T TTTTTTTTT TTTT TTHHHHHHHHT HHHHHHHHHTT TTTTTTT T 1340 | 1334 -1340 AGMGSYV 1334 -1340 T # 85 # Error: Abnormally short interatomic distances The pairs of atoms listed in the table below have an unusually short distance. 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 centers of the two atoms. The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterium 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 aren't there anyway. Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. 94 ASP ( 27 ) 2 CG -- 95 SER ( 28 ) 2 N 0.251 2.849 INTRA 27 ASP ( 27 ) 1 CG -- 28 SER ( 28 ) 1 N 0.231 2.869 INTRA 1032 ASP ( 27 ) 16 CG -- 1033 SER ( 28 ) 16 N 0.201 2.899 INTRA 1157 CYS ( 18 ) 18 SG -- 1174 PHE ( 35 ) 18 CE1 0.197 3.203 INTRA 1233 ASP ( 27 ) 19 CG -- 1234 SER ( 28 ) 19 N 0.196 2.904 INTRA 688 CYS ( 18 ) 11 SG -- 705 PHE ( 35 ) 11 CE1 0.191 3.209 INTRA 795 GLU ( 58 ) 12 CD -- 796 ARG ( 59 ) 12 N 0.177 2.923 INTRA 621 CYS ( 18 ) 10 SG -- 638 PHE ( 35 ) 10 CE1 0.173 3.227 INTRA 429 ASP ( 27 ) 7 CG -- 430 SER ( 28 ) 7 N 0.172 2.928 INTRA 1224 CYS ( 18 ) 19 SG -- 1241 PHE ( 35 ) 19 CE1 0.165 3.235 INTRA 487 CYS ( 18 ) 8 SG -- 504 PHE ( 35 ) 8 CE1 0.155 3.245 INTRA 831 ASP ( 27 ) 13 CG -- 832 SER ( 28 ) 13 N 0.153 2.947 INTRA 1090 CYS ( 18 ) 17 SG -- 1107 PHE ( 35 ) 17 CE1 0.152 3.248 INTRA 1099 ASP ( 27 ) 17 CG -- 1100 SER ( 28 ) 17 N 0.145 2.955 INTRA 228 ASP ( 27 ) 4 CG -- 229 SER ( 28 ) 4 N 0.145 2.955 INTRA 496 ASP ( 27 ) 8 CG -- 497 SER ( 28 ) 8 N 0.137 2.963 INTRA 362 ASP ( 27 ) 6 CG -- 363 SER ( 28 ) 6 N 0.135 2.965 INTRA 764 ASP ( 27 ) 12 CG -- 765 SER ( 28 ) 12 N 0.126 2.974 INTRA 728 GLU ( 58 ) 11 N -- 729 ARG ( 59 ) 11 N 0.119 2.481 INTRA B3 264 MET ( 63 ) 4 SD -- 265 GLY ( 64 ) 4 N 0.116 3.184 INTRA 607 ALA ( 4 ) 10 N -- 608 GLU ( 5 ) 10 N 0.116 2.484 INTRA B3 885 GLY ( 14 ) 14 CA -- 888 ARG ( 17 ) 14 NH2 0.115 2.985 INTRA 485 HIS ( 16 ) 8 CE1 -- 497 SER ( 28 ) 8 OG 0.108 2.692 INTRA 563 ASP ( 27 ) 9 CG -- 564 SER ( 28 ) 9 N 0.106 2.994 INTRA 889 CYS ( 18 ) 14 SG -- 906 PHE ( 35 ) 14 CE1 0.103 3.297 INTRA 85 CYS ( 18 ) 2 SG -- 102 PHE ( 35 ) 2 CE1 0.102 3.298 INTRA 295 ASP ( 27 ) 5 CG -- 296 SER ( 28 ) 5 N 0.100 3.000 INTRA 652 VAL ( 49 ) 10 CG1 -- 653 GLU ( 50 ) 10 N 0.094 3.006 INTRA 898 ASP ( 27 ) 14 CG -- 899 SER ( 28 ) 14 N 0.093 3.007 INTRA 155 CYS ( 21 ) 3 SG -- 174 HIS ( 40 ) 3 CE1 0.091 3.309 INTRA 219 CYS ( 18 ) 4 SG -- 236 PHE ( 35 ) 4 CE1 0.089 3.311 INTRA 72 GLU ( 5 ) 2 N -- 73 PHE ( 6 ) 2 N 0.086 2.514 INTRA B3 902 LEU ( 31 ) 14 CD1 -- 906 PHE ( 35 ) 14 CE2 0.083 3.117 INTRA 1300 ASP ( 27 ) 20 CG -- 1301 SER ( 28 ) 20 N 0.080 3.020 INTRA 500 LEU ( 31 ) 8 CD1 -- 504 PHE ( 35 ) 8 CE2 0.078 3.122 INTRA 590 GLN ( 54 ) 9 CG -- 591 GLU ( 55 ) 9 N 0.078 3.022 INTRA 1211 GLU ( 5 ) 19 N -- 1212 PHE ( 6 ) 19 N 0.076 2.524 INTRA B3 1170 LEU ( 31 ) 18 CD1 -- 1174 PHE ( 35 ) 18 CE2 0.075 3.125 INTRA 474 GLU ( 5 ) 8 N -- 475 PHE ( 6 ) 8 N 0.075 2.525 INTRA B3 299 LEU ( 31 ) 5 CD1 -- 303 PHE ( 35 ) 5 CE2 0.075 3.125 INTRA 423 CYS ( 21 ) 7 SG -- 442 HIS ( 40 ) 7 CE1 0.074 3.326 INTRA 161 ASP ( 27 ) 3 CG -- 162 SER ( 28 ) 3 N 0.073 3.027 INTRA 433 LEU ( 31 ) 7 CD1 -- 437 PHE ( 35 ) 7 CE2 0.072 3.128 INTRA 317 VAL ( 49 ) 5 CG1 -- 318 GLU ( 50 ) 5 N 0.072 3.028 INTRA 1278 GLU ( 5 ) 20 N -- 1279 PHE ( 6 ) 20 N 0.072 2.528 INTRA B3 1291 CYS ( 18 ) 20 SG -- 1308 PHE ( 35 ) 20 CE1 0.072 3.328 INTRA 289 CYS ( 21 ) 5 SG -- 308 HIS ( 40 ) 5 CE1 0.070 3.330 INTRA 98 LEU ( 31 ) 2 CD1 -- 102 PHE ( 35 ) 2 CE2 0.067 3.133 INTRA 232 LEU ( 31 ) 4 CD1 -- 236 PHE ( 35 ) 4 CE2 0.065 3.135 INTRA 791 GLN ( 54 ) 12 CG -- 792 GLU ( 55 ) 12 N 0.065 3.035 INTRA 1255 VAL ( 49 ) 19 N -- 1256 GLU ( 50 ) 19 N 0.064 2.536 INTRA B3 1166 ASP ( 27 ) 18 CG -- 1167 SER ( 28 ) 18 N 0.064 3.036 INTRA 642 ASP ( 39 ) 10 CG -- 643 HIS ( 40 ) 10 N 0.063 3.037 INTRA 594 GLU ( 58 ) 9 CB -- 595 ARG ( 59 ) 9 N 0.061 2.639 INTRA B3 822 CYS ( 18 ) 13 SG -- 839 PHE ( 35 ) 13 CE1 0.060 3.340 INTRA 222 CYS ( 21 ) 4 SG -- 241 HIS ( 40 ) 4 CE1 0.057 3.343 INTRA 120 SER ( 53 ) 2 C -- 121 GLN ( 54 ) 2 CD 0.055 3.145 INTRA 835 LEU ( 31 ) 13 CD1 -- 839 PHE ( 35 ) 13 CE2 0.053 3.147 INTRA 768 LEU ( 31 ) 12 CD1 -- 772 PHE ( 35 ) 12 CE2 0.052 3.148 INTRA 1237 LEU ( 31 ) 19 CD1 -- 1241 PHE ( 35 ) 19 CE2 0.049 3.151 INTRA 1063 GLU ( 58 ) 16 N -- 1064 ARG ( 59 ) 16 N 0.047 2.553 INTRA B3 853 VAL ( 49 ) 13 CG1 -- 854 GLU ( 50 ) 13 N 0.047 3.053 INTRA 458 GLU ( 56 ) 7 N -- 459 ALA ( 57 ) 7 N 0.046 2.554 INTRA B3 1285 GLY ( 12 ) 20 N -- 1286 GLY ( 13 ) 20 N 0.046 2.554 INTRA B3 524 GLU ( 55 ) 8 N -- 525 GLU ( 56 ) 8 N 0.045 2.555 INTRA B3 55 GLU ( 55 ) 1 N -- 56 GLU ( 56 ) 1 N 0.045 2.555 INTRA B3 887 HIS ( 16 ) 14 ND1 -- 899 SER ( 28 ) 14 CB 0.041 3.059 INTRA 755 CYS ( 18 ) 12 SG -- 772 PHE ( 35 ) 12 CE1 0.040 3.360 INTRA 362 ASP ( 27 ) 6 OD1 -- 363 SER ( 28 ) 6 N 0.040 2.660 INTRA 935 GLY ( 64 ) 14 N -- 936 SER ( 65 ) 14 N 0.039 2.561 INTRA B3 1086 GLY ( 14 ) 17 N -- 1087 LEU ( 15 ) 17 N 0.038 2.562 INTRA B3 1195 GLU ( 56 ) 18 N -- 1196 ALA ( 57 ) 18 N 0.038 2.562 INTRA B3 340 GLU ( 5 ) 6 N -- 341 PHE ( 6 ) 6 N 0.036 2.564 INTRA B3 88 CYS ( 21 ) 2 SG -- 107 HIS ( 40 ) 2 CE1 0.035 3.365 INTRA 1323 GLU ( 50 ) 20 O -- 1324 PRO ( 51 ) 20 C 0.034 2.766 INTRA 701 LEU ( 31 ) 11 CD1 -- 705 PHE ( 35 ) 11 CE2 0.034 3.166 INTRA 567 LEU ( 31 ) 9 CD1 -- 571 PHE ( 35 ) 9 CE2 0.031 3.169 INTRA 1068 MET ( 63 ) 16 SD -- 1069 GLY ( 64 ) 16 N 0.031 3.269 INTRA 1103 LEU ( 31 ) 17 CD1 -- 1107 PHE ( 35 ) 17 CE2 0.031 3.169 INTRA 1304 LEU ( 31 ) 20 CD1 -- 1308 PHE ( 35 ) 20 CE2 0.031 3.169 INTRA 79 GLY ( 12 ) 2 N -- 80 GLY ( 13 ) 2 N 0.030 2.570 INTRA B3 1227 CYS ( 21 ) 19 SG -- 1246 HIS ( 40 ) 19 CE1 0.030 3.370 INTRA 371 ARG ( 36 ) 6 N -- 372 SER ( 37 ) 6 N 0.029 2.571 INTRA B3 1052 LEU ( 47 ) 16 N -- 1053 SER ( 48 ) 16 N 0.029 2.571 INTRA B3 892 CYS ( 21 ) 14 N -- 893 ALA ( 22 ) 14 N 0.028 2.572 INTRA B3 407 GLU ( 5 ) 7 N -- 408 PHE ( 6 ) 7 N 0.027 2.573 INTRA B3 732 GLY ( 62 ) 11 N -- 733 MET ( 63 ) 11 N 0.026 2.574 INTRA B3 194 ALA ( 60 ) 3 N -- 195 ALA ( 61 ) 3 N 0.025 2.575 INTRA B3 60 ALA ( 60 ) 1 N -- 61 ALA ( 61 ) 1 N 0.024 2.576 INTRA B3 1093 CYS ( 21 ) 17 SG -- 1112 HIS ( 40 ) 17 CE1 0.024 3.376 INTRA 21 CYS ( 21 ) 1 SG -- 40 HIS ( 40 ) 1 CE1 0.023 3.377 INTRA 1227 CYS ( 21 ) 19 N -- 1228 ALA ( 22 ) 19 N 0.023 2.577 INTRA B3 490 CYS ( 21 ) 8 SG -- 509 HIS ( 40 ) 8 CE1 0.022 3.378 INTRA 36 ARG ( 36 ) 1 N -- 37 SER ( 37 ) 1 N 0.022 2.578 INTRA B3 262 ALA ( 61 ) 4 N -- 263 GLY ( 62 ) 4 N 0.022 2.578 INTRA B3 165 LEU ( 31 ) 3 CD1 -- 169 PHE ( 35 ) 3 CE2 0.020 3.180 INTRA 624 CYS ( 21 ) 10 SG -- 643 HIS ( 40 ) 10 CE1 0.020 3.380 INTRA 892 CYS ( 21 ) 14 SG -- 911 HIS ( 40 ) 14 CE1 0.019 3.381 INTRA 1218 GLY ( 12 ) 19 N -- 1219 GLY ( 13 ) 19 N 0.018 2.582 INTRA B3 366 LEU ( 31 ) 6 CD1 -- 370 PHE ( 35 ) 6 CE2 0.018 3.182 INTRA 1036 LEU ( 31 ) 16 CD1 -- 1040 PHE ( 35 ) 16 CE2 0.018 3.182 INTRA 414 GLY ( 12 ) 7 N -- 415 GLY ( 13 ) 7 N 0.018 2.582 INTRA B3 420 CYS ( 18 ) 7 SG -- 437 PHE ( 35 ) 7 CE1 0.018 3.382 INTRA 139 GLU ( 5 ) 3 N -- 140 PHE ( 6 ) 3 N 0.018 2.582 INTRA B3 557 CYS ( 21 ) 9 SG -- 576 HIS ( 40 ) 9 CE1 0.017 3.383 INTRA 615 GLY ( 12 ) 10 N -- 616 GLY ( 13 ) 10 N 0.017 2.583 INTRA B3 860 GLU ( 56 ) 13 N -- 861 ALA ( 57 ) 13 N 0.017 2.583 INTRA B3 907 ARG ( 36 ) 14 N -- 908 SER ( 37 ) 14 N 0.017 2.583 INTRA B3 1255 VAL ( 49 ) 19 CG1 -- 1256 GLU ( 50 ) 19 N 0.017 3.083 INTRA 1026 CYS ( 21 ) 16 SG -- 1045 HIS ( 40 ) 16 CE1 0.016 3.384 INTRA 49 VAL ( 49 ) 1 CG2 -- 50 GLU ( 50 ) 1 N 0.016 3.084 INTRA 1263 ALA ( 57 ) 19 N -- 1264 GLU ( 58 ) 19 N 0.015 2.585 INTRA B3 250 VAL ( 49 ) 4 N -- 251 GLU ( 50 ) 4 N 0.015 2.585 INTRA B3 390 GLU ( 55 ) 6 N -- 391 GLU ( 56 ) 6 N 0.013 2.587 INTRA B3 594 GLU ( 58 ) 9 C -- 595 ARG ( 59 ) 9 CD 0.013 3.187 INTRA 1091 LEU ( 19 ) 17 CG -- 1092 ALA ( 20 ) 17 N 0.013 3.087 INTRA 286 CYS ( 18 ) 5 SG -- 303 PHE ( 35 ) 5 CE1 0.011 3.389 INTRA 883 GLY ( 12 ) 14 N -- 884 GLY ( 13 ) 14 N 0.010 2.590 INTRA B3 554 CYS ( 18 ) 9 SG -- 571 PHE ( 35 ) 9 CE1 0.009 3.391 INTRA 925 GLN ( 54 ) 14 CG -- 926 GLU ( 55 ) 14 N 0.009 3.091 INTRA 600 GLY ( 64 ) 9 N -- 601 SER ( 65 ) 9 N 0.007 2.593 INTRA B3 1175 ARG ( 36 ) 18 N -- 1176 SER ( 37 ) 18 N 0.006 2.594 INTRA B3 353 CYS ( 18 ) 6 SG -- 370 PHE ( 35 ) 6 CE1 0.006 3.394 INTRA 122 GLU ( 55 ) 2 N -- 123 GLU ( 56 ) 2 N 0.004 2.596 INTRA B3 485 HIS ( 16 ) 8 CE1 -- 497 SER ( 28 ) 8 N 0.003 3.097 INTRA 214 GLY ( 13 ) 4 C -- 216 LEU ( 15 ) 4 N 0.003 2.897 INTRA 881 LEU ( 10 ) 14 CB -- 888 ARG ( 17 ) 14 NH2 0.003 3.097 INTRA 985 LEU ( 47 ) 15 N -- 986 SER ( 48 ) 15 N 0.002 2.598 INTRA B3 213 GLY ( 12 ) 4 N -- 214 GLY ( 13 ) 4 N 0.002 2.598 INTRA B3 616 GLY ( 13 ) 10 C -- 618 LEU ( 15 ) 10 N 0.001 2.899 INTRA 952 GLY ( 14 ) 15 N -- 953 LEU ( 15 ) 15 N 0.001 2.599 INTRA B3 94 ASP ( 27 ) 2 OD2 -- 95 SER ( 28 ) 2 N 0.001 2.699 INTRA 354 LEU ( 19 ) 6 N -- 355 ALA ( 20 ) 6 N 0.001 2.599 INTRA B3 751 GLY ( 14 ) 12 N -- 752 LEU ( 15 ) 12 N 0.000 2.600 INTRA B3 # 86 # 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. 602 TYR ( 66 ) 9 -9.00 66 TYR ( 66 ) 1 -8.84 1004 TYR ( 66 ) 15 -8.81 736 TYR ( 66 ) 11 -8.76 401 TYR ( 66 ) 6 -8.76 1138 TYR ( 66 ) 17 -8.71 1205 TYR ( 66 ) 18 -8.50 1339 TYR ( 66 ) 20 -8.44 803 TYR ( 66 ) 12 -8.42 722 TYR ( 52 ) 11 -8.41 1272 TYR ( 66 ) 19 -8.40 133 TYR ( 66 ) 2 -8.34 669 TYR ( 66 ) 10 -8.31 334 TYR ( 66 ) 5 -8.26 535 TYR ( 66 ) 8 -8.25 200 TYR ( 66 ) 3 -8.22 465 MET ( 63 ) 7 -8.20 870 TYR ( 66 ) 13 -8.20 267 TYR ( 66 ) 4 -8.19 468 TYR ( 66 ) 7 -8.18 1071 TYR ( 66 ) 16 -8.17 1068 MET ( 63 ) 16 -8.15 331 MET ( 63 ) 5 -8.12 937 TYR ( 66 ) 14 -7.97 1131 ARG ( 59 ) 17 -7.94 1332 ARG ( 59 ) 20 -7.74 800 MET ( 63 ) 12 -7.74 532 MET ( 63 ) 8 -7.66 186 TYR ( 52 ) 3 -7.65 197 MET ( 63 ) 3 -7.62 796 ARG ( 59 ) 12 -7.44 930 ARG ( 59 ) 14 -7.41 1258 TYR ( 52 ) 19 -7.41 461 ARG ( 59 ) 7 -7.40 1336 MET ( 63 ) 20 -7.36 193 ARG ( 59 ) 3 -7.31 52 TYR ( 52 ) 1 -7.31 990 TYR ( 52 ) 15 -7.31 130 MET ( 63 ) 2 -7.21 1198 ARG ( 59 ) 18 -7.04 1202 MET ( 63 ) 18 -7.03 588 TYR ( 52 ) 9 -6.97 1064 ARG ( 59 ) 16 -6.88 1269 MET ( 63 ) 19 -6.80 59 ARG ( 59 ) 1 -6.64 327 ARG ( 59 ) 5 -6.63 944 PHE ( 6 ) 15 -6.49 724 GLN ( 54 ) 11 -6.42 676 PHE ( 6 ) 11 -6.40 6 PHE ( 6 ) 1 -6.39 867 MET ( 63 ) 13 -6.38 341 PHE ( 6 ) 6 -6.35 662 ARG ( 59 ) 10 -6.29 264 MET ( 63 ) 4 -6.28 1191 TYR ( 52 ) 18 -6.22 609 PHE ( 6 ) 10 -6.13 1011 PHE ( 6 ) 16 -6.13 599 MET ( 63 ) 9 -6.11 743 PHE ( 6 ) 12 -6.06 1265 ARG ( 59 ) 19 -6.05 253 TYR ( 52 ) 4 -6.05 260 ARG ( 59 ) 4 -6.05 274 PHE ( 6 ) 5 -6.03 126 ARG ( 59 ) 2 -6.01 398 MET ( 63 ) 6 -5.99 789 TYR ( 52 ) 12 -5.94 729 ARG ( 59 ) 11 -5.92 934 MET ( 63 ) 14 -5.90 877 PHE ( 6 ) 14 -5.86 1145 PHE ( 6 ) 18 -5.80 666 MET ( 63 ) 10 -5.77 140 PHE ( 6 ) 3 -5.77 144 LEU ( 10 ) 3 -5.77 149 LEU ( 15 ) 3 -5.74 1078 PHE ( 6 ) 17 -5.74 521 TYR ( 52 ) 8 -5.74 63 MET ( 63 ) 1 -5.69 91 TYR ( 24 ) 2 -5.68 394 ARG ( 59 ) 6 -5.67 1230 TYR ( 24 ) 19 -5.62 1325 TYR ( 52 ) 20 -5.60 595 ARG ( 59 ) 9 -5.60 923 TYR ( 52 ) 14 -5.58 1020 LEU ( 15 ) 16 -5.49 408 PHE ( 6 ) 7 -5.49 1008 ASN ( 3 ) 16 -5.48 655 TYR ( 52 ) 10 -5.48 121 GLN ( 54 ) 2 -5.42 627 TYR ( 24 ) 10 -5.42 856 TYR ( 52 ) 13 -5.41 207 PHE ( 6 ) 4 -5.41 54 GLN ( 54 ) 1 -5.39 158 TYR ( 24 ) 3 -5.39 475 PHE ( 6 ) 8 -5.39 830 ILE ( 26 ) 13 -5.37 810 PHE ( 6 ) 13 -5.37 629 ILE ( 26 ) 10 -5.37 10 LEU ( 10 ) 1 -5.32 326 GLU ( 58 ) 5 -5.31 160 ILE ( 26 ) 3 -5.29 996 GLU ( 58 ) 15 -5.28 680 LEU ( 10 ) 11 -5.28 428 ILE ( 26 ) 7 -5.27 250 VAL ( 49 ) 4 -5.27 1031 ILE ( 26 ) 16 -5.27 897 ILE ( 26 ) 14 -5.26 964 ILE ( 26 ) 15 -5.25 456 GLN ( 54 ) 7 -5.24 227 ILE ( 26 ) 4 -5.24 661 GLU ( 58 ) 10 -5.23 83 HIS ( 16 ) 2 -5.23 212 PRO ( 11 ) 4 -5.23 49 VAL ( 49 ) 1 -5.23 137 ASN ( 3 ) 3 -5.22 1212 PHE ( 6 ) 19 -5.22 145 PRO ( 11 ) 3 -5.21 886 LEU ( 15 ) 14 -5.19 1217 PRO ( 11 ) 19 -5.19 820 HIS ( 16 ) 13 -5.18 389 GLN ( 54 ) 6 -5.18 1082 LEU ( 10 ) 17 -5.17 614 PRO ( 11 ) 10 -5.15 518 VAL ( 49 ) 8 -5.14 338 ASN ( 3 ) 6 -5.14 11 PRO ( 11 ) 1 -5.14 652 VAL ( 49 ) 10 -5.13 480 PRO ( 11 ) 8 -5.11 93 ILE ( 26 ) 2 -5.11 763 ILE ( 26 ) 12 -5.10 1288 LEU ( 15 ) 20 -5.09 320 TYR ( 52 ) 5 -5.09 1299 ILE ( 26 ) 20 -5.09 1015 LEU ( 10 ) 16 -5.07 1232 ILE ( 26 ) 19 -5.07 992 GLN ( 54 ) 15 -5.06 116 VAL ( 49 ) 2 -5.06 925 GLN ( 54 ) 14 -5.04 606 ASN ( 3 ) 10 -5.04 359 TYR ( 24 ) 6 -5.02 # 87 # 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, but might also be an indication of misthreading. The table below lists the first and last residue in each stretch found, as well as the average residue score of the series. 9 ASP ( 9 ) 1 --- 12 GLY ( 12 ) 1 -4.70 58 GLU ( 58 ) 1 --- 60 ALA ( 60 ) 1 -5.11 143 ASP ( 9 ) 3 --- 147 GLY ( 13 ) 3 -4.68 210 ASP ( 9 ) 4 --- 213 GLY ( 12 ) 4 -4.45 277 ASP ( 9 ) 5 --- 280 GLY ( 12 ) 5 -4.30 326 GLU ( 58 ) 5 --- 328 ALA ( 60 ) 5 -5.38 393 GLU ( 58 ) 6 --- 398 MET ( 63 ) 6 -4.82 456 GLN ( 54 ) 7 --- 458 GLU ( 56 ) 7 -4.86 463 ALA ( 61 ) 7 --- 468 TYR ( 66 ) 7 -5.60 478 ASP ( 9 ) 8 --- 481 GLY ( 12 ) 8 -4.59 594 GLU ( 58 ) 9 --- 596 ALA ( 60 ) 9 -4.54 612 ASP ( 9 ) 10 --- 616 GLY ( 13 ) 10 -4.50 661 GLU ( 58 ) 10 --- 663 ALA ( 60 ) 10 -5.20 789 TYR ( 52 ) 12 --- 791 GLN ( 54 ) 12 -4.98 947 ASP ( 9 ) 15 --- 951 GLY ( 13 ) 15 -4.36 992 GLN ( 54 ) 15 --- 994 GLU ( 56 ) 15 -4.87 996 GLU ( 58 ) 15 --- 998 ALA ( 60 ) 15 -4.76 1066 ALA ( 61 ) 16 --- 1068 MET ( 63 ) 16 -5.57 1081 ASP ( 9 ) 17 --- 1084 GLY ( 12 ) 17 -4.61 1197 GLU ( 58 ) 18 --- 1199 ALA ( 60 ) 18 -5.15 1215 ASP ( 9 ) 19 --- 1218 GLY ( 12 ) 19 -4.48 # 88 # Error: Abnormal average packing environment The average quality control value for the structure is very low. A molecule is certain to be incorrect if the average quality 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 quality of 200 highly refined Xray structures was -0.5+/-0.4 [REF]. Average for range 1 -1340 : -2.215 # 89 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 1 # 90 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 2 # 91 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 3 # 92 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 4 # 93 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 5 # 94 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 6 # 95 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 7 # 96 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 8 # 97 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 9 # 98 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 10 # 99 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 11 # 100 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 12 # 101 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 13 # 102 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 14 # 103 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 15 # 104 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 16 # 105 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 17 # 106 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 18 # 107 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 19 # 108 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 20 # 109 # 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 quality 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. 63 MET ( 63 ) 1 -3.05 197 MET ( 63 ) 3 -3.05 331 MET ( 63 ) 5 -3.05 465 MET ( 63 ) 7 -3.05 666 MET ( 63 ) 10 -3.05 1001 MET ( 63 ) 15 -3.05 1068 MET ( 63 ) 16 -3.05 1202 MET ( 63 ) 18 -3.05 1336 MET ( 63 ) 20 -3.05 398 MET ( 63 ) 6 -3.05 130 MET ( 63 ) 2 -3.04 733 MET ( 63 ) 11 -3.04 1135 MET ( 63 ) 17 -3.03 264 MET ( 63 ) 4 -3.03 867 MET ( 63 ) 13 -3.00 66 TYR ( 66 ) 1 -2.95 870 TYR ( 66 ) 13 -2.95 1205 TYR ( 66 ) 18 -2.95 334 TYR ( 66 ) 5 -2.95 1071 TYR ( 66 ) 16 -2.94 133 TYR ( 66 ) 2 -2.94 669 TYR ( 66 ) 10 -2.94 1272 TYR ( 66 ) 19 -2.94 602 TYR ( 66 ) 9 -2.94 736 TYR ( 66 ) 11 -2.94 401 TYR ( 66 ) 6 -2.94 803 TYR ( 66 ) 12 -2.94 468 TYR ( 66 ) 7 -2.94 200 TYR ( 66 ) 3 -2.94 1004 TYR ( 66 ) 15 -2.94 1339 TYR ( 66 ) 20 -2.94 267 TYR ( 66 ) 4 -2.93 1138 TYR ( 66 ) 17 -2.92 532 MET ( 63 ) 8 -2.90 138 ALA ( 4 ) 3 -2.86 318 GLU ( 50 ) 5 -2.76 1269 MET ( 63 ) 19 -2.76 653 GLU ( 50 ) 10 -2.74 535 TYR ( 66 ) 8 -2.72 52 TYR ( 52 ) 1 -2.71 1325 TYR ( 52 ) 20 -2.64 224 ARG ( 23 ) 4 -2.62 157 ARG ( 23 ) 3 -2.60 827 ARG ( 23 ) 13 -2.59 1154 LEU ( 15 ) 18 -2.56 358 ARG ( 23 ) 6 -2.56 484 LEU ( 15 ) 8 -2.53 1229 ARG ( 23 ) 19 -2.53 652 VAL ( 49 ) 10 -2.51 23 ARG ( 23 ) 1 -2.50 425 ARG ( 23 ) 7 -2.50 # 110 # Warning: Abnormal packing Z-score for sequential residues A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading. The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series. 58 GLU ( 58 ) 1 --- 61 ALA ( 61 ) 1 -1.75 125 GLU ( 58 ) 2 --- 128 ALA ( 61 ) 2 -1.92 192 GLU ( 58 ) 3 --- 195 ALA ( 61 ) 3 -1.84 324 GLU ( 56 ) 5 --- 329 ALA ( 61 ) 5 -1.92 393 GLU ( 58 ) 6 --- 396 ALA ( 61 ) 6 -2.09 399 GLY ( 64 ) 6 --- 402 VAL ( 67 ) 6 -2.16 556 ALA ( 20 ) 9 --- 559 ARG ( 23 ) 9 -1.81 651 SER ( 48 ) 10 --- 655 TYR ( 52 ) 10 -2.04 661 GLU ( 58 ) 10 --- 666 MET ( 63 ) 10 -1.81 667 GLY ( 64 ) 10 --- 670 VAL ( 67 ) 10 -2.07 728 GLU ( 58 ) 11 --- 731 ALA ( 61 ) 11 -1.82 734 GLY ( 64 ) 11 --- 737 VAL ( 67 ) 11 -2.16 868 GLY ( 64 ) 13 --- 871 VAL ( 67 ) 13 -2.31 935 GLY ( 64 ) 14 --- 938 VAL ( 67 ) 14 -1.81 996 GLU ( 58 ) 15 --- 999 ALA ( 61 ) 15 -1.88 1136 GLY ( 64 ) 17 --- 1139 VAL ( 67 ) 17 -2.15 1331 GLU ( 58 ) 20 --- 1334 ALA ( 61 ) 20 -1.73 # 111 # Error: Abnormal structural average packing Z-score The quality control Z-score for the structure is very low. A molecule is certain to be incorrect if the Z-score is below -5.0. Poorly refined molecules, very well energy minimized misthreaded molecules and low homology models give values between -2.0 and -5.0. The average quality of properly refined Xray structures is 0.0+/-1.0. All contacts : Average = -0.668 Z-score = -4.42 BB-BB contacts : Average = 0.041 Z-score = 0.13 BB-SC contacts : Average = -0.866 Z-score = -5.71 SC-BB contacts : Average = -0.123 Z-score = -0.77 SC-SC contacts : Average = -0.753 Z-score = -4.42 # 112 # Note: Per-model averages for NQA The table below gives the per-model NQA averages and Z-scores. These are the numbers for all contacts. Model 1 : -0.746; -4.934 Model 2 : -0.768; -5.082 Model 3 : -0.820; -5.423 Model 4 : -0.702; -4.648 Model 5 : -0.658; -4.358 Model 6 : -0.749; -4.955 Model 7 : -0.534; -3.543 Model 8 : -0.599; -3.973 Model 9 : -0.630; -4.176 Model 10 : -0.678; -4.494 Model 11 : -0.628; -4.166 Model 12 : -0.679; -4.499 Model 13 : -0.710; -4.702 Model 14 : -0.564; -3.745 Model 15 : -0.599; -3.975 Model 16 : -0.591; -3.919 Model 17 : -0.557; -3.694 Model 18 : -0.600; -3.982 Model 19 : -0.758; -5.016 Model 20 : -0.783; -5.178 # 113 # Note: Second generation quality Z-score plot The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate "unusual" packing. In the TeX file, a plot has been inserted here Model number 1 # 114 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 2 # 115 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 3 # 116 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 4 # 117 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 5 # 118 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 6 # 119 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 7 # 120 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 8 # 121 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 9 # 122 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 10 # 123 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 11 # 124 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 12 # 125 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 13 # 126 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 14 # 127 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 15 # 128 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 16 # 129 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 17 # 130 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 18 # 131 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 19 # 132 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 20 # 133 # Warning: Backbone oxygen evaluation The residues listed in the table below have an unusual backbone oxygen position. For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some constraints on the neighboring backbone oxygens. In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking! 64 GLY ( 64 ) 1 2.14 11 799 GLY ( 62 ) 12 2.10 16 198 GLY ( 64 ) 3 1.83 25 1203 GLY ( 64 ) 18 1.60 24 593 ALA ( 57 ) 9 1.57 28 # 134 # 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. 302 HIS ( 34 ) 5 0.35 1110 LYS ( 38 ) 17 0.36 858 GLN ( 54 ) 13 0.36 919 SER ( 48 ) 14 0.38 584 SER ( 48 ) 9 0.39 # 135 # Warning: Unusual backbone conformations For the residues listed in the table below, the backbone formed by itself and two neighboring 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 center. 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! 5 GLU ( 5 ) 1 0 36 ARG ( 36 ) 1 0 50 GLU ( 50 ) 1 0 54 GLN ( 54 ) 1 0 55 GLU ( 55 ) 1 0 58 GLU ( 58 ) 1 0 60 ALA ( 60 ) 1 0 61 ALA ( 61 ) 1 0 70 ASN ( 3 ) 2 0 83 HIS ( 16 ) 2 0 84 ARG ( 17 ) 2 0 93 ILE ( 26 ) 2 0 121 GLN ( 54 ) 2 0 122 GLU ( 55 ) 2 0 123 GLU ( 56 ) 2 0 137 ASN ( 3 ) 3 0 138 ALA ( 4 ) 3 0 150 HIS ( 16 ) 3 0 151 ARG ( 17 ) 3 0 185 PRO ( 51 ) 3 0 188 GLN ( 54 ) 3 0 189 GLU ( 55 ) 3 0 191 ALA ( 57 ) 3 0 192 GLU ( 58 ) 3 0 195 ALA ( 61 ) 3 0 197 MET ( 63 ) 3 0 206 GLU ( 5 ) 4 0 217 HIS ( 16 ) 4 0 218 ARG ( 17 ) 4 0 254 SER ( 53 ) 4 0 256 GLU ( 55 ) 4 0 257 GLU ( 56 ) 4 0 264 MET ( 63 ) 4 0 271 ASN ( 3 ) 5 0 272 ALA ( 4 ) 5 0 321 SER ( 53 ) 5 0 323 GLU ( 55 ) 5 0 324 GLU ( 56 ) 5 0 325 ALA ( 57 ) 5 0 328 ALA ( 60 ) 5 0 329 ALA ( 61 ) 5 0 333 SER ( 65 ) 5 0 339 ALA ( 4 ) 6 0 356 CYS ( 21 ) 6 0 383 SER ( 48 ) 6 0 384 VAL ( 49 ) 6 0 385 GLU ( 50 ) 6 0 389 GLN ( 54 ) 6 0 390 GLU ( 55 ) 6 0 393 GLU ( 58 ) 6 0 394 ARG ( 59 ) 6 0 395 ALA ( 60 ) 6 0 396 ALA ( 61 ) 6 0 400 SER ( 65 ) 6 0 418 HIS ( 16 ) 7 0 419 ARG ( 17 ) 7 0 451 VAL ( 49 ) 7 0 456 GLN ( 54 ) 7 0 457 GLU ( 55 ) 7 0 458 GLU ( 56 ) 7 0 459 ALA ( 57 ) 7 0 460 GLU ( 58 ) 7 0 462 ALA ( 60 ) 7 0 467 SER ( 65 ) 7 0 472 ASN ( 3 ) 8 0 473 ALA ( 4 ) 8 0 517 SER ( 48 ) 8 0 519 GLU ( 50 ) 8 0 523 GLN ( 54 ) 8 0 524 GLU ( 55 ) 8 0 526 ALA ( 57 ) 8 0 532 MET ( 63 ) 8 0 539 ASN ( 3 ) 9 0 540 ALA ( 4 ) 9 0 541 GLU ( 5 ) 9 0 548 GLY ( 12 ) 9 0 572 ARG ( 36 ) 9 0 587 PRO ( 51 ) 9 0 588 TYR ( 52 ) 9 0 591 GLU ( 55 ) 9 0 594 GLU ( 58 ) 9 0 599 MET ( 63 ) 9 0 606 ASN ( 3 ) 10 0 607 ALA ( 4 ) 10 0 619 HIS ( 16 ) 10 0 620 ARG ( 17 ) 10 0 655 TYR ( 52 ) 10 0 658 GLU ( 55 ) 10 0 659 GLU ( 56 ) 10 0 660 ALA ( 57 ) 10 0 662 ARG ( 59 ) 10 0 664 ALA ( 61 ) 10 0 666 MET ( 63 ) 10 0 674 ALA ( 4 ) 11 0 719 VAL ( 49 ) 11 0 722 TYR ( 52 ) 11 0 723 SER ( 53 ) 11 0 724 GLN ( 54 ) 11 0 725 GLU ( 55 ) 11 0 726 GLU ( 56 ) 11 0 740 ASN ( 3 ) 12 0 741 ALA ( 4 ) 12 0 791 GLN ( 54 ) 12 0 792 GLU ( 55 ) 12 0 794 ALA ( 57 ) 12 0 795 GLU ( 58 ) 12 0 796 ARG ( 59 ) 12 0 797 ALA ( 60 ) 12 0 798 ALA ( 61 ) 12 0 802 SER ( 65 ) 12 0 820 HIS ( 16 ) 13 0 821 ARG ( 17 ) 13 0 854 GLU ( 50 ) 13 0 861 ALA ( 57 ) 13 0 862 GLU ( 58 ) 13 0 863 ARG ( 59 ) 13 0 864 ALA ( 60 ) 13 0 865 ALA ( 61 ) 13 0 869 SER ( 65 ) 13 0 876 GLU ( 5 ) 14 0 885 GLY ( 14 ) 14 0 888 ARG ( 17 ) 14 0 907 ARG ( 36 ) 14 0 926 GLU ( 55 ) 14 0 928 ALA ( 57 ) 14 0 929 GLU ( 58 ) 14 0 930 ARG ( 59 ) 14 0 931 ALA ( 60 ) 14 0 936 SER ( 65 ) 14 0 941 ASN ( 3 ) 15 0 986 SER ( 48 ) 15 0 987 VAL ( 49 ) 15 0 991 SER ( 53 ) 15 0 992 GLN ( 54 ) 15 0 996 GLU ( 58 ) 15 0 999 ALA ( 61 ) 15 0 1015 LEU ( 10 ) 16 0 1021 HIS ( 16 ) 16 0 1022 ARG ( 17 ) 16 0 1056 PRO ( 51 ) 16 0 1057 TYR ( 52 ) 16 0 1059 GLN ( 54 ) 16 0 1060 GLU ( 55 ) 16 0 1061 GLU ( 56 ) 16 0 1062 ALA ( 57 ) 16 0 1063 GLU ( 58 ) 16 0 1064 ARG ( 59 ) 16 0 1070 SER ( 65 ) 16 0 1076 ALA ( 4 ) 17 0 1093 CYS ( 21 ) 17 0 1123 PRO ( 51 ) 17 0 1124 TYR ( 52 ) 17 0 1125 SER ( 53 ) 17 0 1126 GLN ( 54 ) 17 0 1128 GLU ( 56 ) 17 0 1130 GLU ( 58 ) 17 0 1131 ARG ( 59 ) 17 0 1132 ALA ( 60 ) 17 0 1143 ALA ( 4 ) 18 0 1191 TYR ( 52 ) 18 0 1194 GLU ( 55 ) 18 0 1196 ALA ( 57 ) 18 0 1197 GLU ( 58 ) 18 0 1198 ARG ( 59 ) 18 0 1199 ALA ( 60 ) 18 0 1200 ALA ( 61 ) 18 0 1210 ALA ( 4 ) 19 0 1211 GLU ( 5 ) 19 0 1222 HIS ( 16 ) 19 0 1223 ARG ( 17 ) 19 0 1254 SER ( 48 ) 19 0 1255 VAL ( 49 ) 19 0 1259 SER ( 53 ) 19 0 1260 GLN ( 54 ) 19 0 1261 GLU ( 55 ) 19 0 1266 ALA ( 60 ) 19 0 1267 ALA ( 61 ) 19 0 1269 MET ( 63 ) 19 0 1271 SER ( 65 ) 19 0 1277 ALA ( 4 ) 20 0 1278 GLU ( 5 ) 20 0 1289 HIS ( 16 ) 20 0 1290 ARG ( 17 ) 20 0 1322 VAL ( 49 ) 20 0 1323 GLU ( 50 ) 20 0 1326 SER ( 53 ) 20 0 1327 GLN ( 54 ) 20 0 1331 GLU ( 58 ) 20 0 1333 ALA ( 60 ) 20 0 1336 MET ( 63 ) 20 0 4 ALA ( 4 ) 1 1 6 PHE ( 6 ) 1 1 37 SER ( 37 ) 1 1 71 ALA ( 4 ) 2 1 80 GLY ( 13 ) 2 1 88 CYS ( 21 ) 2 1 117 GLU ( 50 ) 2 1 125 GLU ( 58 ) 2 1 130 MET ( 63 ) 2 1 170 ARG ( 36 ) 3 1 186 TYR ( 52 ) 3 1 193 ARG ( 59 ) 3 1 194 ALA ( 60 ) 3 1 205 ALA ( 4 ) 4 1 255 GLN ( 54 ) 4 1 260 ARG ( 59 ) 4 1 261 ALA ( 60 ) 4 1 262 ALA ( 61 ) 4 1 318 GLU ( 50 ) 5 1 331 MET ( 63 ) 5 1 332 GLY ( 64 ) 5 1 340 GLU ( 5 ) 6 1 382 LEU ( 47 ) 6 1 392 ALA ( 57 ) 6 1 405 ASN ( 3 ) 7 1 406 ALA ( 4 ) 7 1 407 GLU ( 5 ) 7 1 455 SER ( 53 ) 7 1 461 ARG ( 59 ) 7 1 466 GLY ( 64 ) 7 1 518 VAL ( 49 ) 8 1 527 GLU ( 58 ) 8 1 530 ALA ( 61 ) 8 1 595 ARG ( 59 ) 9 1 596 ALA ( 60 ) 9 1 597 ALA ( 61 ) 9 1 608 GLU ( 5 ) 10 1 624 CYS ( 21 ) 10 1 652 VAL ( 49 ) 10 1 653 GLU ( 50 ) 10 1 656 SER ( 53 ) 10 1 661 GLU ( 58 ) 10 1 691 CYS ( 21 ) 11 1 718 SER ( 48 ) 11 1 720 GLU ( 50 ) 11 1 727 ALA ( 57 ) 11 1 728 GLU ( 58 ) 11 1 729 ARG ( 59 ) 11 1 731 ALA ( 61 ) 11 1 742 GLU ( 5 ) 12 1 752 LEU ( 15 ) 12 1 758 CYS ( 21 ) 12 1 785 SER ( 48 ) 12 1 853 VAL ( 49 ) 13 1 855 PRO ( 51 ) 13 1 860 GLU ( 56 ) 13 1 875 ALA ( 4 ) 14 1 886 LEU ( 15 ) 14 1 887 HIS ( 16 ) 14 1 892 CYS ( 21 ) 14 1 925 GLN ( 54 ) 14 1 934 MET ( 63 ) 14 1 974 ARG ( 36 ) 15 1 993 GLU ( 55 ) 15 1 994 GLU ( 56 ) 15 1 997 ARG ( 59 ) 15 1 1026 CYS ( 21 ) 16 1 1065 ALA ( 60 ) 16 1 1077 GLU ( 5 ) 17 1 1127 GLU ( 55 ) 17 1 1129 ALA ( 57 ) 17 1 1142 ASN ( 3 ) 18 1 1144 GLU ( 5 ) 18 1 1212 PHE ( 6 ) 19 1 1227 CYS ( 21 ) 19 1 1279 PHE ( 6 ) 20 1 1294 CYS ( 21 ) 20 1 1330 ALA ( 57 ) 20 1 13 GLY ( 13 ) 1 2 26 ILE ( 26 ) 1 2 49 VAL ( 49 ) 1 2 59 ARG ( 59 ) 1 2 72 GLU ( 5 ) 2 2 115 SER ( 48 ) 2 2 116 VAL ( 49 ) 2 2 119 TYR ( 52 ) 2 2 120 SER ( 53 ) 2 2 144 LEU ( 10 ) 3 2 147 GLY ( 13 ) 3 2 190 GLU ( 56 ) 3 2 214 GLY ( 13 ) 4 2 216 LEU ( 15 ) 4 2 251 GLU ( 50 ) 4 2 322 GLN ( 54 ) 5 2 326 GLU ( 58 ) 5 2 338 ASN ( 3 ) 6 2 348 GLY ( 13 ) 6 2 415 GLY ( 13 ) 7 2 452 GLU ( 50 ) 7 2 474 GLU ( 5 ) 8 2 475 PHE ( 6 ) 8 2 481 GLY ( 12 ) 8 2 482 GLY ( 13 ) 8 2 505 ARG ( 36 ) 8 2 534 SER ( 65 ) 8 2 550 GLY ( 14 ) 9 2 586 GLU ( 50 ) 9 2 590 GLN ( 54 ) 9 2 616 GLY ( 13 ) 10 2 618 LEU ( 15 ) 10 2 625 ALA ( 22 ) 10 2 657 GLN ( 54 ) 10 2 663 ALA ( 60 ) 10 2 683 GLY ( 13 ) 11 2 730 ALA ( 60 ) 11 2 790 SER ( 53 ) 12 2 800 MET ( 63 ) 12 2 817 GLY ( 13 ) 13 2 867 MET ( 63 ) 13 2 942 ALA ( 4 ) 15 2 952 GLY ( 14 ) 15 2 953 LEU ( 15 ) 15 2 988 GLU ( 50 ) 15 2 998 ALA ( 60 ) 15 2 1001 MET ( 63 ) 15 2 1009 ALA ( 4 ) 16 2 1017 GLY ( 12 ) 16 2 1018 GLY ( 13 ) 16 2 1019 GLY ( 14 ) 16 2 1053 SER ( 48 ) 16 2 1058 SER ( 53 ) 16 2 1066 ALA ( 61 ) 16 2 1075 ASN ( 3 ) 17 2 1085 GLY ( 13 ) 17 2 1108 ARG ( 36 ) 17 2 1133 ALA ( 61 ) 17 2 1152 GLY ( 13 ) 18 2 1187 SER ( 48 ) 18 2 1219 GLY ( 13 ) 19 2 1258 TYR ( 52 ) 19 2 1262 GLU ( 56 ) 19 2 1325 TYR ( 52 ) 20 2 1334 ALA ( 61 ) 20 2 # 136 # Error: Backbone conformation Z-score very low A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is very unusual. Backbone conformation Z-score : -4.807 # 137 # Note: Per-model averages for the backbone conformation check The table below gives the per-model Z-scores for the backbone conformation check. Model 1 : -4.397 Model 2 : -6.250 Model 3 : -4.722 Model 4 : -4.360 Model 5 : -4.777 Model 6 : -4.635 Model 7 : -6.686 Model 8 : -5.226 Model 9 : -3.243 Model 10 : -5.873 Model 11 : -4.337 Model 12 : -4.603 Model 13 : -3.867 Model 14 : -4.515 Model 15 : -7.273 Model 16 : -5.306 Model 17 : -4.463 Model 18 : -3.248 Model 19 : -4.959 Model 20 : -3.403 # 138 # 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 favorable 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. If a residue is marked ``flexible'' the flipped conformation is only slightly better than the non-flipped conformation. 3 ASN ( 3 ) 1 716 GLN ( 46 ) 11 807 ASN ( 3 ) 13 1142 ASN ( 3 ) 18 1209 ASN ( 3 ) 19 # 139 # 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. 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. 16 HIS ( 16 ) 1 HIS-E 1.01 34 HIS ( 34 ) 1 HIS-E 1.39 40 HIS ( 40 ) 1 HIS-D 2.95 HIS-E 3.01 83 HIS ( 16 ) 2 HIS-D 1.10 HIS-E 1.19 101 HIS ( 34 ) 2 HIS-E 1.58 107 HIS ( 40 ) 2 HIS-D 3.22 HIS-E 3.25 150 HIS ( 16 ) 3 HIS-E 1.10 168 HIS ( 34 ) 3 HIS-E 1.43 174 HIS ( 40 ) 3 HIS-D 3.26 HIS-E 3.32 217 HIS ( 16 ) 4 HIS-D 1.00 HIS-E 1.13 235 HIS ( 34 ) 4 HIS-E 1.49 241 HIS ( 40 ) 4 HIS-D 2.47 HIS-E 2.52 284 HIS ( 16 ) 5 HIS-H 0.94 HIS-E 1.03 302 HIS ( 34 ) 5 HIS-E 1.38 308 HIS ( 40 ) 5 HIS-D 3.69 HIS-E 3.75 351 HIS ( 16 ) 6 HIS-H 0.55 HIS-E 0.67 369 HIS ( 34 ) 6 HIS-D 1.20 HIS-E 1.22 375 HIS ( 40 ) 6 HIS-H 3.90 HIS-E 3.90 418 HIS ( 16 ) 7 HIS-H 0.81 HIS-D 1.04 436 HIS ( 34 ) 7 HIS-E 1.47 442 HIS ( 40 ) 7 HIS-D 3.28 HIS-E 3.44 485 HIS ( 16 ) 8 HIS-E 1.38 HIS-D 1.64 503 HIS ( 34 ) 8 HIS-E 1.41 509 HIS ( 40 ) 8 HIS-D 2.93 HIS-E 2.95 552 HIS ( 16 ) 9 HIS-H 0.82 HIS-D 1.03 570 HIS ( 34 ) 9 HIS-E 1.43 576 HIS ( 40 ) 9 HIS-D 2.68 HIS-E 2.74 619 HIS ( 16 ) 10 HIS-H 1.31 HIS-D 1.39 637 HIS ( 34 ) 10 HIS-E 1.42 643 HIS ( 40 ) 10 HIS-D 2.93 HIS-E 2.96 686 HIS ( 16 ) 11 HIS-H 1.06 HIS-D 1.10 704 HIS ( 34 ) 11 HIS-E 1.48 710 HIS ( 40 ) 11 HIS-D 3.05 HIS-E 3.08 753 HIS ( 16 ) 12 HIS-H 0.99 HIS-D 1.15 771 HIS ( 34 ) 12 HIS-E 1.36 777 HIS ( 40 ) 12 HIS-D 3.38 HIS-E 3.38 820 HIS ( 16 ) 13 HIS-E 1.06 838 HIS ( 34 ) 13 HIS-E 1.61 844 HIS ( 40 ) 13 HIS-D 3.06 HIS-E 3.08 887 HIS ( 16 ) 14 HIS-H 1.05 HIS-E 1.14 905 HIS ( 34 ) 14 HIS-E 1.36 911 HIS ( 40 ) 14 HIS-D 2.90 HIS-E 2.95 954 HIS ( 16 ) 15 HIS-H 1.06 HIS-E 1.11 972 HIS ( 34 ) 15 HIS-D 1.22 HIS-E 1.26 978 HIS ( 40 ) 15 HIS-D 3.14 HIS-E 3.17 1021 HIS ( 16 ) 16 HIS-H 0.76 HIS-E 0.83 1039 HIS ( 34 ) 16 HIS-D 1.29 HIS-E 1.29 1045 HIS ( 40 ) 16 HIS-D 3.49 HIS-E 3.53 1088 HIS ( 16 ) 17 HIS-H 0.44 HIS-E 0.75 1106 HIS ( 34 ) 17 HIS-E 1.44 1112 HIS ( 40 ) 17 HIS-D 3.17 HIS-E 3.21 1155 HIS ( 16 ) 18 HIS-H 1.00 HIS-D 1.07 1173 HIS ( 34 ) 18 HIS-E 1.62 1179 HIS ( 40 ) 18 HIS-D 2.99 HIS-E 2.99 1222 HIS ( 16 ) 19 HIS-E 0.97 1240 HIS ( 34 ) 19 HIS-E 1.69 1246 HIS ( 40 ) 19 HIS-D 3.46 HIS-E 3.50 1289 HIS ( 16 ) 20 HIS-H 0.92 HIS-E 0.92 1307 HIS ( 34 ) 20 HIS-D 1.28 HIS-E 1.28 1313 HIS ( 40 ) 20 HIS-D 4.47 # 140 # 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. 5 GLU ( 5 ) 1 N 27 ASP ( 27 ) 1 N 28 SER ( 28 ) 1 N 58 GLU ( 58 ) 1 N 82 LEU ( 15 ) 2 N 84 ARG ( 17 ) 2 N 90 ARG ( 23 ) 2 N 92 PHE ( 25 ) 2 N 94 ASP ( 27 ) 2 N 95 SER ( 28 ) 2 N 104 SER ( 37 ) 2 N 117 GLU ( 50 ) 2 N 124 ALA ( 57 ) 2 N 141 ASP ( 7 ) 3 N 146 GLY ( 12 ) 3 N 151 ARG ( 17 ) 3 N 158 TYR ( 24 ) 3 N 159 PHE ( 25 ) 3 N 161 ASP ( 27 ) 3 N 162 SER ( 28 ) 3 N 191 ALA ( 57 ) 3 N 197 MET ( 63 ) 3 N 206 GLU ( 5 ) 4 N 218 ARG ( 17 ) 4 N 226 PHE ( 25 ) 4 N 228 ASP ( 27 ) 4 N 229 SER ( 28 ) 4 N 253 TYR ( 52 ) 4 N 295 ASP ( 27 ) 5 N 296 SER ( 28 ) 5 N 305 SER ( 37 ) 5 N 318 GLU ( 50 ) 5 N 324 GLU ( 56 ) 5 N 350 LEU ( 15 ) 6 N 352 ARG ( 17 ) 6 N 355 ALA ( 20 ) 6 N 360 PHE ( 25 ) 6 N 362 ASP ( 27 ) 6 N 363 SER ( 28 ) 6 N 418 HIS ( 16 ) 7 N 419 ARG ( 17 ) 7 N 427 PHE ( 25 ) 7 N 429 ASP ( 27 ) 7 N 430 SER ( 28 ) 7 N 492 ARG ( 23 ) 8 N 496 ASP ( 27 ) 8 N 506 SER ( 37 ) 8 N 563 ASP ( 27 ) 9 N 564 SER ( 28 ) 9 N 594 GLU ( 58 ) 9 N 595 ARG ( 59 ) 9 N 620 ARG ( 17 ) 10 N 626 ARG ( 23 ) 10 N 628 PHE ( 25 ) 10 N 630 ASP ( 27 ) 10 N 642 ASP ( 39 ) 10 N 693 ARG ( 23 ) 11 N 697 ASP ( 27 ) 11 N 709 ASP ( 39 ) 11 N 753 HIS ( 16 ) 12 N 757 ALA ( 20 ) 12 N 760 ARG ( 23 ) 12 N 764 ASP ( 27 ) 12 N 765 SER ( 28 ) 12 N 792 GLU ( 55 ) 12 N 794 ALA ( 57 ) 12 N 821 ARG ( 17 ) 13 N 829 PHE ( 25 ) 13 N 831 ASP ( 27 ) 13 N 832 SER ( 28 ) 13 N 834 ASN ( 30 ) 13 N 843 ASP ( 39 ) 13 N 854 GLU ( 50 ) 13 N 859 GLU ( 55 ) 13 N 888 ARG ( 17 ) 14 NH2 898 ASP ( 27 ) 14 N 899 SER ( 28 ) 14 N 926 GLU ( 55 ) 14 N 955 ARG ( 17 ) 15 NE 961 ARG ( 23 ) 15 N 965 ASP ( 27 ) 15 N 991 SER ( 53 ) 15 N 1017 GLY ( 12 ) 16 N 1022 ARG ( 17 ) 16 N 1028 ARG ( 23 ) 16 N 1030 PHE ( 25 ) 16 N 1032 ASP ( 27 ) 16 N 1033 SER ( 28 ) 16 N 1044 ASP ( 39 ) 16 N 1055 GLU ( 50 ) 16 N 1057 TYR ( 52 ) 16 N 1092 ALA ( 20 ) 17 N 1095 ARG ( 23 ) 17 N 1099 ASP ( 27 ) 17 N 1100 SER ( 28 ) 17 N 1122 GLU ( 50 ) 17 N 1148 ASP ( 9 ) 18 N 1149 LEU ( 10 ) 18 N 1156 ARG ( 17 ) 18 NE 1166 ASP ( 27 ) 18 N 1167 SER ( 28 ) 18 N 1176 SER ( 37 ) 18 N 1178 ASP ( 39 ) 18 N 1223 ARG ( 17 ) 19 N 1231 PHE ( 25 ) 19 N 1233 ASP ( 27 ) 19 N 1234 SER ( 28 ) 19 N 1243 SER ( 37 ) 19 N 1258 TYR ( 52 ) 19 N 1267 ALA ( 61 ) 19 N 1290 ARG ( 17 ) 20 N 1296 ARG ( 23 ) 20 N 1298 PHE ( 25 ) 20 N 1300 ASP ( 27 ) 20 N 1301 SER ( 28 ) 20 N 1329 GLU ( 56 ) 20 N # 141 # 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 that are 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. 1319 GLN ( 46 ) 20 OE1 # 142 # Note: Summary report for users of a structure This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations. The second part of the table mostly gives an impression of how well the model conforms to common refinement constraint values. The first part of the table shows a number of constraint-independent quality indicators. Structure Z-scores, positive is better than average: 1st generation packing quality : -4.286 (poor) 2nd generation packing quality : -5.178 (bad) Ramachandran plot appearance : -4.849 (bad) chi-1/chi-2 rotamer normality : -1.327 Backbone conformation : -4.807 (bad) RMS Z-scores, should be close to 1.0: Bond lengths : 0.831 Bond angles : 0.768 Omega angle restraints : 0.686 (tight) Side chain planarity : 0.801 Improper dihedral distribution : 1.508 (loose) Inside/Outside distribution : 1.135 REFERENCES ========== 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). Bond lengths and angles, protein residues R.Engh and R.Huber, Accurate bond and angle parameters for X-ray protein structure refinement, Acta Crystallogr. A47, 392--400 (1991). Bond lengths and angles, DNA/RNA G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman, New parameters for the refinement of nucleic acid-containing structures Acta Crystallogr. D52, 57--64 (1996). DSSP W.Kabsch and C.Sander, Dictionary of protein secondary structure: pattern recognition of hydrogen bond and geometrical features Biopolymers 22, 2577--2637 (1983). Hydrogen bond networks R.W.W.Hooft, C.Sander and G.Vriend, Positioning hydrogen atoms by optimizing hydrogen bond networks in protein structures PROTEINS, 26, 363--376 (1996). Matthews' Coefficient B.W.Matthews Solvent content of Protein Crystals J. Mol. Biol. 33, 491--497 (1968). Protein side chain planarity R.W.W. Hooft, C. Sander and G. Vriend, Verification of protein structures: side-chain planarity J. Appl. Cryst. 29, 714--716 (1996). Puckering parameters D.Cremer and J.A.Pople, A general definition of ring puckering coordinates J. Am. Chem. Soc. 97, 1354--1358 (1975). Quality Control G.Vriend and C.Sander, Quality control of protein models: directional atomic contact analysis, J. Appl. Cryst. 26, 47--60 (1993). Ramachandran plot G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan, Stereochemistry of Polypeptide Chain Conformations J. Mol. Biol. 7, 95--99 (1963). Symmetry Checks R.W.W.Hooft, C.Sander and G.Vriend, Reconstruction of symmetry related molecules from protein data bank (PDB) files J. Appl. Cryst. 27, 1006--1009 (1994).