************************************************************************ ********** 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//@19434.1//====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 90.0 283 TYR ( 24 ) 7 327 TYR ( 24 ) 8 459 TYR ( 24 ) 11 591 TYR ( 24 ) 14 679 TYR ( 24 ) 16 723 TYR ( 24 ) 17 767 TYR ( 24 ) 18 # 14 # Warning: Phenylalanine convention problem The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0. 1 PHE ( 6 ) 1 74 PHE ( 35 ) 2 89 PHE ( 6 ) 3 108 PHE ( 25 ) 3 152 PHE ( 25 ) 4 177 PHE ( 6 ) 5 196 PHE ( 25 ) 5 221 PHE ( 6 ) 6 250 PHE ( 35 ) 6 265 PHE ( 6 ) 7 284 PHE ( 25 ) 7 328 PHE ( 25 ) 8 338 PHE ( 35 ) 8 372 PHE ( 25 ) 9 382 PHE ( 35 ) 9 416 PHE ( 25 ) 10 441 PHE ( 6 ) 11 470 PHE ( 35 ) 11 504 PHE ( 25 ) 12 548 PHE ( 25 ) 13 558 PHE ( 35 ) 13 573 PHE ( 6 ) 14 602 PHE ( 35 ) 14 646 PHE ( 35 ) 15 661 PHE ( 6 ) 16 690 PHE ( 35 ) 16 705 PHE ( 6 ) 17 724 PHE ( 25 ) 17 734 PHE ( 35 ) 17 749 PHE ( 6 ) 18 793 PHE ( 6 ) 19 812 PHE ( 25 ) 19 837 PHE ( 6 ) 20 856 PHE ( 25 ) 20 866 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. 22 ASP ( 27 ) 1 46 ASP ( 7 ) 2 48 ASP ( 9 ) 2 66 ASP ( 27 ) 2 110 ASP ( 27 ) 3 122 ASP ( 39 ) 3 136 ASP ( 9 ) 4 166 ASP ( 39 ) 4 180 ASP ( 9 ) 5 210 ASP ( 39 ) 5 224 ASP ( 9 ) 6 242 ASP ( 27 ) 6 254 ASP ( 39 ) 6 286 ASP ( 27 ) 7 354 ASP ( 7 ) 9 374 ASP ( 27 ) 9 398 ASP ( 7 ) 10 400 ASP ( 9 ) 10 418 ASP ( 27 ) 10 442 ASP ( 7 ) 11 444 ASP ( 9 ) 11 462 ASP ( 27 ) 11 518 ASP ( 39 ) 12 530 ASP ( 7 ) 13 532 ASP ( 9 ) 13 620 ASP ( 9 ) 15 662 ASP ( 7 ) 16 706 ASP ( 7 ) 17 726 ASP ( 27 ) 17 750 ASP ( 7 ) 18 770 ASP ( 27 ) 18 794 ASP ( 7 ) 19 814 ASP ( 27 ) 19 858 ASP ( 27 ) 20 # 16 # Note: Heavy atom naming OK No errors were detected in the atom names for non-hydrogen atoms. # 17 # 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. 339 ARG ( 36 ) 8 CA -6.0 24.5 34.0 # 18 # 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 : 1.492 # 19 # Note: Per-model averages for chirality check The table below gives the per-model improper dihedral RMS Z-scores. Model 1 : 1.543 Model 2 : 1.296 Model 3 : 1.342 Model 4 : 1.153 Model 5 : 1.974 Model 6 : 1.422 Model 7 : 1.421 Model 8 : 1.541 Model 9 : 1.440 Model 10 : 1.555 Model 11 : 1.527 Model 12 : 1.356 Model 13 : 1.509 Model 14 : 1.465 Model 15 : 1.319 Model 16 : 1.595 Model 17 : 1.509 Model 18 : 1.478 Model 19 : 1.580 Model 20 : 1.641 # 20 # Note: No missing atoms detected All expected atoms are present. # 21 # Warning: C-terminal oxygen atoms missing The C-atoms listed in the table below belong to a C-terminal residue in a protein chain, but the C-terminal oxygen ("O2" or "OXT") that it should be bound to was not found. 44 VAL ( 49 ) 1 C 88 VAL ( 49 ) 2 C 132 VAL ( 49 ) 3 C 176 VAL ( 49 ) 4 C 220 VAL ( 49 ) 5 C 264 VAL ( 49 ) 6 C 308 VAL ( 49 ) 7 C 352 VAL ( 49 ) 8 C 396 VAL ( 49 ) 9 C 440 VAL ( 49 ) 10 C 484 VAL ( 49 ) 11 C 528 VAL ( 49 ) 12 C 572 VAL ( 49 ) 13 C 616 VAL ( 49 ) 14 C 660 VAL ( 49 ) 15 C 704 VAL ( 49 ) 16 C 748 VAL ( 49 ) 17 C 792 VAL ( 49 ) 18 C 836 VAL ( 49 ) 19 C 880 VAL ( 49 ) 20 C # 22 # Note: No extra C-terminal groups found No C-terminal groups are present for non C-terminal residues # 23 # 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. 35 HIS ( 40 ) 1 CG CD2 1.296 -5.5 79 HIS ( 40 ) 2 CG CD2 1.286 -6.4 123 HIS ( 40 ) 3 CG CD2 1.289 -6.1 211 HIS ( 40 ) 5 CG CD2 1.278 -7.1 255 HIS ( 40 ) 6 CG CD2 1.267 -8.1 299 HIS ( 40 ) 7 CB CG 1.431 -4.7 299 HIS ( 40 ) 7 CG CD2 1.292 -5.8 299 HIS ( 40 ) 7 ND1 CE1 1.263 -4.3 343 HIS ( 40 ) 8 CG CD2 1.295 -5.5 387 HIS ( 40 ) 9 CG CD2 1.304 -4.7 431 HIS ( 40 ) 10 CG CD2 1.294 -5.6 475 HIS ( 40 ) 11 CG CD2 1.290 -6.0 519 HIS ( 40 ) 12 CG CD2 1.279 -7.0 563 HIS ( 40 ) 13 CG CD2 1.291 -5.9 607 HIS ( 40 ) 14 CG CD2 1.296 -5.5 651 HIS ( 40 ) 15 CG CD2 1.288 -6.2 695 HIS ( 40 ) 16 CG CD2 1.278 -7.1 739 HIS ( 40 ) 17 CG CD2 1.289 -6.1 783 HIS ( 40 ) 18 CG CD2 1.292 -5.8 827 HIS ( 40 ) 19 CG CD2 1.282 -6.7 871 HIS ( 40 ) 20 CG CD2 1.252 -9.4 # 24 # 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: 0.865 RMS-deviation in bond distances: 0.017 # 25 # Note: Per-model averages for bond-length check The table below gives the per-model bond-length RMS Z-scores. Model 1 : 0.865 Model 2 : 0.837 Model 3 : 0.845 Model 4 : 0.781 Model 5 : 0.924 Model 6 : 0.935 Model 7 : 0.912 Model 8 : 0.844 Model 9 : 0.862 Model 10 : 0.789 Model 11 : 0.885 Model 12 : 0.868 Model 13 : 0.819 Model 14 : 0.858 Model 15 : 0.835 Model 16 : 0.869 Model 17 : 0.878 Model 18 : 0.863 Model 19 : 0.849 Model 20 : 0.963 # 26 # 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. 11 HIS ( 16 ) 1 CG ND1 CE1 109.753 4.2 69 ASN ( 30 ) 2 CA CB CG 117.626 5.0 99 HIS ( 16 ) 3 CG ND1 CE1 109.602 4.0 162 PHE ( 35 ) 4 CA CB CG 118.255 4.5 231 HIS ( 16 ) 6 CG ND1 CE1 109.730 4.1 245 ASN ( 30 ) 6 CA CB CG 117.937 5.3 363 HIS ( 16 ) 9 CG ND1 CE1 109.635 4.0 519 HIS ( 40 ) 12 CA CB CG 117.873 4.1 539 HIS ( 16 ) 13 CG ND1 CE1 109.809 4.2 627 HIS ( 16 ) 15 CG ND1 CE1 109.602 4.0 715 HIS ( 16 ) 17 CG ND1 CE1 109.697 4.1 803 HIS ( 16 ) 19 CG ND1 CE1 109.708 4.1 822 PHE ( 35 ) 19 CA CB CG 118.901 5.1 847 HIS ( 16 ) 20 CG ND1 CE1 109.605 4.0 # 27 # 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: 0.780 RMS-deviation in bond angles: 1.354 # 28 # Note: Per-model averages for bond-angle check The table below gives the per-model bond-angle RMS Z-scores. Model 1 : 0.750 Model 2 : 0.804 Model 3 : 0.732 Model 4 : 0.747 Model 5 : 0.747 Model 6 : 0.859 Model 7 : 0.773 Model 8 : 0.823 Model 9 : 0.771 Model 10 : 0.741 Model 11 : 0.755 Model 12 : 0.778 Model 13 : 0.764 Model 14 : 0.766 Model 15 : 0.734 Model 16 : 0.870 Model 17 : 0.776 Model 18 : 0.778 Model 19 : 0.788 Model 20 : 0.822 # 29 # Note: Side chain planarity OK All of the side chains of residues that have a planar group are planar within expected RMS deviations. # 30 # 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. 871 HIS ( 40 ) 20 CB 11.305 255 HIS ( 40 ) 6 CB 10.785 695 HIS ( 40 ) 16 CB 10.571 519 HIS ( 40 ) 12 CB 10.245 783 HIS ( 40 ) 18 CB 10.207 431 HIS ( 40 ) 10 CB 10.084 123 HIS ( 40 ) 3 CB 10.079 827 HIS ( 40 ) 19 CB 9.709 739 HIS ( 40 ) 17 CB 9.689 607 HIS ( 40 ) 14 CB 9.589 563 HIS ( 40 ) 13 CB 9.571 475 HIS ( 40 ) 11 CB 9.567 35 HIS ( 40 ) 1 CB 9.483 343 HIS ( 40 ) 8 CB 9.371 651 HIS ( 40 ) 15 CB 9.261 387 HIS ( 40 ) 9 CB 9.119 79 HIS ( 40 ) 2 CB 9.089 211 HIS ( 40 ) 5 CB 8.974 299 HIS ( 40 ) 7 CB 8.605 167 HIS ( 40 ) 4 CB 6.729 # 31 # Note: PRO puckering amplitude OK Puckering amplitudes for all PRO residues are within normal ranges. # 32 # 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. 3 PRO ( 8 ) 1 -42.8 envelop C-alpha (-36 degrees) 355 PRO ( 8 ) 9 -64.4 envelop C-beta (-72 degrees) 443 PRO ( 8 ) 11 -52.7 half-chair C-beta/C-alpha (-54 degrees) 575 PRO ( 8 ) 14 -60.0 half-chair C-beta/C-alpha (-54 degrees) # 33 # 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. 575 PRO ( 8 ) 14 -2.6454 443 PRO ( 8 ) 11 -2.6164 3 PRO ( 8 ) 1 -2.3400 223 PRO ( 8 ) 6 -2.0643 131 SER ( 48 ) 3 -2.0634 355 PRO ( 8 ) 9 -2.0111 778 PHE ( 35 ) 18 -2.0050 # 34 # 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. 3 PRO ( 8 ) 1 Poor PRO-phi 17 ALA ( 22 ) 1 Poor phi/psi 53 GLY ( 14 ) 2 Poor phi/psi 55 HIS ( 16 ) 2 Poor phi/psi 56 ARG ( 17 ) 2 Poor phi/psi 61 ALA ( 22 ) 2 Poor phi/psi 87 SER ( 48 ) 2 Poor phi/psi 91 PRO ( 8 ) 3 Poor PRO-phi 99 HIS ( 16 ) 3 Poor phi/psi 100 ARG ( 17 ) 3 Poor phi/psi 105 ALA ( 22 ) 3 Poor phi/psi 131 SER ( 48 ) 3 Poor phi/psi 143 HIS ( 16 ) 4 Poor phi/psi 144 ARG ( 17 ) 4 Poor phi/psi 149 ALA ( 22 ) 4 Poor phi/psi 193 ALA ( 22 ) 5 Poor phi/psi 219 SER ( 48 ) 5 Poor phi/psi 223 PRO ( 8 ) 6 Poor PRO-phi 237 ALA ( 22 ) 6 Poor phi/psi 263 SER ( 48 ) 6 Poor phi/psi 275 HIS ( 16 ) 7 Poor phi/psi 276 ARG ( 17 ) 7 Poor phi/psi 281 ALA ( 22 ) 7 Poor phi/psi 325 ALA ( 22 ) 8 Poor phi/psi 351 SER ( 48 ) 8 Poor phi/psi 355 PRO ( 8 ) 9 Poor PRO-phi 358 PRO ( 11 ) 9 Poor phi/psi 369 ALA ( 22 ) 9 Poor phi/psi 407 HIS ( 16 ) 10 Poor phi/psi 408 ARG ( 17 ) 10 Poor phi/psi 413 ALA ( 22 ) 10 Poor phi/psi 443 PRO ( 8 ) 11 Poor PRO-phi 457 ALA ( 22 ) 11 Poor phi/psi 487 PRO ( 8 ) 12 Poor PRO-phi 501 ALA ( 22 ) 12 Poor phi/psi 527 SER ( 48 ) 12 Poor phi/psi 539 HIS ( 16 ) 13 Poor phi/psi 540 ARG ( 17 ) 13 Poor phi/psi 545 ALA ( 22 ) 13 Poor phi/psi 575 PRO ( 8 ) 14 Poor PRO-phi 589 ALA ( 22 ) 14 Poor phi/psi 633 ALA ( 22 ) 15 Poor phi/psi 659 SER ( 48 ) 15 Poor phi/psi 663 PRO ( 8 ) 16 Poor PRO-phi 671 HIS ( 16 ) 16 Poor phi/psi 672 ARG ( 17 ) 16 Poor phi/psi 677 ALA ( 22 ) 16 Poor phi/psi 703 SER ( 48 ) 16 Poor phi/psi 721 ALA ( 22 ) 17 Poor phi/psi 765 ALA ( 22 ) 18 Poor phi/psi 801 GLY ( 14 ) 19 Poor phi/psi 803 HIS ( 16 ) 19 Poor phi/psi 804 ARG ( 17 ) 19 Poor phi/psi 809 ALA ( 22 ) 19 Poor phi/psi 839 PRO ( 8 ) 20 Poor PRO-phi 845 GLY ( 14 ) 20 Poor phi/psi 847 HIS ( 16 ) 20 Poor phi/psi 848 ARG ( 17 ) 20 Poor phi/psi 853 ALA ( 22 ) 20 Poor phi/psi # 35 # Warning: Ramachandran Z-score low The score expressing how well the backbone conformations of all residues are corresponding to the known allowed areas in the Ramachandran plot is a bit low. Ramachandran Z-score : -3.500 # 36 # Note: Per-model averages for Ramachandran check The table below gives the per-model Ramachandran Z-scores. Model 1 : -4.362 Model 2 : -3.682 Model 3 : -4.164 Model 4 : -3.438 Model 5 : -3.301 Model 6 : -3.303 Model 7 : -1.650 Model 8 : -4.794 Model 9 : -3.018 Model 10 : -2.876 Model 11 : -2.450 Model 12 : -2.701 Model 13 : -3.685 Model 14 : -3.502 Model 15 : -3.391 Model 16 : -4.248 Model 17 : -3.398 Model 18 : -3.604 Model 19 : -4.345 Model 20 : -4.093 # 37 # 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 : 3.730 # 38 # Note: Per-model averages for omega angle check The table below gives the per-model omega angle standard deviations. Model 1 : 3.733 Model 2 : 3.410 Model 3 : 3.757 Model 4 : 3.652 Model 5 : 3.234 Model 6 : 3.958 Model 7 : 3.642 Model 8 : 3.662 Model 9 : 4.047 Model 10 : 4.015 Model 11 : 3.361 Model 12 : 3.944 Model 13 : 4.005 Model 14 : 3.253 Model 15 : 3.712 Model 16 : 4.316 Model 17 : 3.435 Model 18 : 3.623 Model 19 : 3.903 Model 20 : 4.139 # 39 # 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 : -1.774 # 40 # 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 : -2.732 Model 2 : 0.358 Model 3 : -2.502 Model 4 : -0.542 Model 5 : -1.420 Model 6 : -1.836 Model 7 : -1.151 Model 8 : -2.303 Model 9 : -2.698 Model 10 : -1.191 Model 11 : -2.439 Model 12 : -1.587 Model 13 : -1.922 Model 14 : -1.398 Model 15 : -1.100 Model 16 : -2.971 Model 17 : -3.382 Model 18 : -2.458 Model 19 : -0.490 Model 20 : -1.711 # 41 # 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 # 42 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 2 # 43 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 3 # 44 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 4 # 45 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 5 # 46 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 6 # 47 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 7 # 48 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 8 # 49 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 9 # 50 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 10 # 51 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 11 # 52 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 12 # 53 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 13 # 54 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 14 # 55 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 15 # 56 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 16 # 57 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 17 # 58 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 18 # 59 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 19 # 60 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Model number 20 # 61 # 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 : 1.121 # 62 # 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 : 1.139 Model 2 : 1.115 Model 3 : 1.110 Model 4 : 1.105 Model 5 : 1.126 Model 6 : 1.115 Model 7 : 1.083 Model 8 : 1.109 Model 9 : 1.156 Model 10 : 1.146 Model 11 : 1.084 Model 12 : 1.126 Model 13 : 1.165 Model 14 : 1.120 Model 15 : 1.043 Model 16 : 1.126 Model 17 : 1.126 Model 18 : 1.158 Model 19 : 1.127 Model 20 : 1.133 # 63 # 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 # 64 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 2 # 65 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 3 # 66 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 4 # 67 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 5 # 68 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 6 # 69 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 7 # 70 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 8 # 71 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 9 # 72 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 10 # 73 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 11 # 74 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 12 # 75 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 13 # 76 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 14 # 77 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 15 # 78 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 16 # 79 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 17 # 80 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 18 # 81 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 19 # 82 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Model number 20 # 83 # 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 | | | | 1 - 44 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 1 - 44 TTT3333TTSSTTTTSS TTHHHHHHHTT HHHHHHHHHH 50 60 70 80 | | | | 45 - 88 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 45 - 88 TTTTTTTTT TTTT TTHHHHHHHTT HHHHHHHHHH 90 100 110 120 130 | | | | | 89 - 132 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 89 - 132 TTT3333TT TTTT TTHHHHHHHTT HHHHHHHHHHT 140 150 160 170 | | | | 133 - 176 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 133 - 176 TTT3333TT 333T TTHHHHHHHTT HHHHHHHHHH 180 190 200 210 220 | | | | | 177 - 220 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 177 - 220 TTT3333TTSS333TSS TTHHHHHHHTTTHHHHHHHHHHT 230 240 250 260 | | | | 221 - 264 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 221 - 264 TTTTTTTTT TTTT TTHHHHHHHTT HHHHHHHHHH 270 280 290 300 | | | | 265 - 308 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 265 - 308 TTTTTTTTT TTTT TTHHHHHHHTT HHHHHHHHHHH 310 320 330 340 350 | | | | | 309 - 352 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 309 - 352 TTT3333T SSTTTTSS TTHHHHHHHHT HHHHHHHHHH 360 370 380 390 | | | | 353 - 396 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 353 - 396 TTTTTTTTTSSTTTTSS TTHHHHHHHTT HHHHHHHHHHT 400 410 420 430 440 | | | | | 397 - 440 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 397 - 440 TTT3333TT TTTT TTHHHHHHHTT HHHHHHHHHH 450 460 470 480 | | | | 441 - 484 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 441 - 484 TTTTT TTTSSTTTTSS T HHHHHHHT HHHHHHHHHHH 490 500 510 520 | | | | 485 - 528 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 485 - 528 TTTT333 SSTTTTSS TTHHHHHHHTT HHHHHHHHHH 530 540 550 560 570 | | | | | 529 - 572 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 529 - 572 TTTT333TT TTTT TTHHHHHHHTT HHHHHHHHHH 580 590 600 610 | | | | 573 - 616 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 573 - 616 TTTT333TTSSTTTTSS TTHHHHHHHT HHHHHHHHHHH 620 630 640 650 660 | | | | | 617 - 660 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 617 - 660 TTT3333 TSSTTTTSS TTHHHHHHHTT HHHHHHHHHH 670 680 690 700 | | | | 661 - 704 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 661 - 704 TTTTTTTT TTTT TTHHHHHHHTT HHHHHHHHHHT 710 720 730 740 | | | | 705 - 748 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 705 - 748 TTT3333TTSSTTTTSS TTHHHHHHHTT HHHHHHHHHH 750 760 770 780 790 | | | | | 749 - 792 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 749 - 792 TTTT333TTSSTTTTSS TTHHHHHHHT HHHHHHHHHHH 800 810 820 830 | | | | 793 - 836 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 793 - 836 TTT3333TTT TTTT TTHHHHHHHH HHHHHHHHHH 840 850 860 870 880 | | | | | 837 - 880 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV 837 - 880 TTTTTTTTT TTTT TTHHHHHHHHT HHHHHHHHHTT # 84 # 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. 66 ASP ( 27 ) 2 CG -- 67 SER ( 28 ) 2 N 0.251 2.849 INTRA 22 ASP ( 27 ) 1 CG -- 23 SER ( 28 ) 1 N 0.230 2.870 INTRA 682 ASP ( 27 ) 16 CG -- 683 SER ( 28 ) 16 N 0.201 2.899 INTRA 761 CYS ( 18 ) 18 SG -- 778 PHE ( 35 ) 18 CE1 0.197 3.203 INTRA 814 ASP ( 27 ) 19 CG -- 815 SER ( 28 ) 19 N 0.197 2.903 INTRA 453 CYS ( 18 ) 11 SG -- 470 PHE ( 35 ) 11 CE1 0.190 3.210 INTRA 409 CYS ( 18 ) 10 SG -- 426 PHE ( 35 ) 10 CE1 0.173 3.227 INTRA 286 ASP ( 27 ) 7 CG -- 287 SER ( 28 ) 7 N 0.172 2.928 INTRA 805 CYS ( 18 ) 19 SG -- 822 PHE ( 35 ) 19 CE1 0.164 3.236 INTRA 321 CYS ( 18 ) 8 SG -- 338 PHE ( 35 ) 8 CE1 0.155 3.245 INTRA 550 ASP ( 27 ) 13 CG -- 551 SER ( 28 ) 13 N 0.153 2.947 INTRA 717 CYS ( 18 ) 17 SG -- 734 PHE ( 35 ) 17 CE1 0.152 3.248 INTRA 726 ASP ( 27 ) 17 CG -- 727 SER ( 28 ) 17 N 0.146 2.954 INTRA 154 ASP ( 27 ) 4 CG -- 155 SER ( 28 ) 4 N 0.145 2.955 INTRA 330 ASP ( 27 ) 8 CG -- 331 SER ( 28 ) 8 N 0.138 2.962 INTRA 242 ASP ( 27 ) 6 CG -- 243 SER ( 28 ) 6 N 0.134 2.966 INTRA 506 ASP ( 27 ) 12 CG -- 507 SER ( 28 ) 12 N 0.127 2.973 INTRA 581 GLY ( 14 ) 14 CA -- 584 ARG ( 17 ) 14 NH2 0.116 2.984 INTRA 319 HIS ( 16 ) 8 CE1 -- 331 SER ( 28 ) 8 OG 0.107 2.693 INTRA 374 ASP ( 27 ) 9 CG -- 375 SER ( 28 ) 9 N 0.107 2.993 INTRA 585 CYS ( 18 ) 14 SG -- 602 PHE ( 35 ) 14 CE1 0.103 3.297 INTRA 57 CYS ( 18 ) 2 SG -- 74 PHE ( 35 ) 2 CE1 0.102 3.298 INTRA 198 ASP ( 27 ) 5 CG -- 199 SER ( 28 ) 5 N 0.100 3.000 INTRA 594 ASP ( 27 ) 14 CG -- 595 SER ( 28 ) 14 N 0.093 3.007 INTRA 104 CYS ( 21 ) 3 SG -- 123 HIS ( 40 ) 3 CE1 0.091 3.309 INTRA 145 CYS ( 18 ) 4 SG -- 162 PHE ( 35 ) 4 CE1 0.089 3.311 INTRA 598 LEU ( 31 ) 14 CD1 -- 602 PHE ( 35 ) 14 CE2 0.084 3.116 INTRA 858 ASP ( 27 ) 20 CG -- 859 SER ( 28 ) 20 N 0.080 3.020 INTRA 334 LEU ( 31 ) 8 CD1 -- 338 PHE ( 35 ) 8 CE2 0.079 3.121 INTRA 280 CYS ( 21 ) 7 SG -- 299 HIS ( 40 ) 7 CE1 0.074 3.326 INTRA 774 LEU ( 31 ) 18 CD1 -- 778 PHE ( 35 ) 18 CE2 0.074 3.126 INTRA 202 LEU ( 31 ) 5 CD1 -- 206 PHE ( 35 ) 5 CE2 0.074 3.126 INTRA 110 ASP ( 27 ) 3 CG -- 111 SER ( 28 ) 3 N 0.073 3.027 INTRA 849 CYS ( 18 ) 20 SG -- 866 PHE ( 35 ) 20 CE1 0.072 3.328 INTRA 290 LEU ( 31 ) 7 CD1 -- 294 PHE ( 35 ) 7 CE2 0.072 3.128 INTRA 192 CYS ( 21 ) 5 SG -- 211 HIS ( 40 ) 5 CE1 0.069 3.331 INTRA 70 LEU ( 31 ) 2 CD1 -- 74 PHE ( 35 ) 2 CE2 0.068 3.132 INTRA 158 LEU ( 31 ) 4 CD1 -- 162 PHE ( 35 ) 4 CE2 0.066 3.134 INTRA 770 ASP ( 27 ) 18 CG -- 771 SER ( 28 ) 18 N 0.064 3.036 INTRA 430 ASP ( 39 ) 10 CG -- 431 HIS ( 40 ) 10 N 0.063 3.037 INTRA 541 CYS ( 18 ) 13 SG -- 558 PHE ( 35 ) 13 CE1 0.060 3.340 INTRA 148 CYS ( 21 ) 4 SG -- 167 HIS ( 40 ) 4 CE1 0.057 3.343 INTRA 554 LEU ( 31 ) 13 CD1 -- 558 PHE ( 35 ) 13 CE2 0.053 3.147 INTRA 510 LEU ( 31 ) 12 CD1 -- 514 PHE ( 35 ) 12 CE2 0.051 3.149 INTRA 818 LEU ( 31 ) 19 CD1 -- 822 PHE ( 35 ) 19 CE2 0.048 3.152 INTRA 843 GLY ( 12 ) 20 N -- 844 GLY ( 13 ) 20 N 0.046 2.554 INTRA B3 583 HIS ( 16 ) 14 ND1 -- 595 SER ( 28 ) 14 CB 0.041 3.059 INTRA 242 ASP ( 27 ) 6 OD1 -- 243 SER ( 28 ) 6 N 0.040 2.660 INTRA 497 CYS ( 18 ) 12 SG -- 514 PHE ( 35 ) 12 CE1 0.040 3.360 INTRA 713 GLY ( 14 ) 17 N -- 714 LEU ( 15 ) 17 N 0.039 2.561 INTRA B3 60 CYS ( 21 ) 2 SG -- 79 HIS ( 40 ) 2 CE1 0.036 3.364 INTRA 466 LEU ( 31 ) 11 CD1 -- 470 PHE ( 35 ) 11 CE2 0.033 3.167 INTRA 730 LEU ( 31 ) 17 CD1 -- 734 PHE ( 35 ) 17 CE2 0.031 3.169 INTRA 378 LEU ( 31 ) 9 CD1 -- 382 PHE ( 35 ) 9 CE2 0.031 3.169 INTRA 51 GLY ( 12 ) 2 N -- 52 GLY ( 13 ) 2 N 0.031 2.569 INTRA B3 862 LEU ( 31 ) 20 CD1 -- 866 PHE ( 35 ) 20 CE2 0.031 3.169 INTRA 808 CYS ( 21 ) 19 SG -- 827 HIS ( 40 ) 19 CE1 0.030 3.370 INTRA 251 ARG ( 36 ) 6 N -- 252 SER ( 37 ) 6 N 0.030 2.570 INTRA B3 702 LEU ( 47 ) 16 N -- 703 SER ( 48 ) 16 N 0.029 2.571 INTRA B3 588 CYS ( 21 ) 14 N -- 589 ALA ( 22 ) 14 N 0.028 2.572 INTRA B3 720 CYS ( 21 ) 17 SG -- 739 HIS ( 40 ) 17 CE1 0.023 3.377 INTRA 808 CYS ( 21 ) 19 N -- 809 ALA ( 22 ) 19 N 0.023 2.577 INTRA B3 16 CYS ( 21 ) 1 SG -- 35 HIS ( 40 ) 1 CE1 0.023 3.377 INTRA 324 CYS ( 21 ) 8 SG -- 343 HIS ( 40 ) 8 CE1 0.022 3.378 INTRA 31 ARG ( 36 ) 1 N -- 32 SER ( 37 ) 1 N 0.021 2.579 INTRA B3 114 LEU ( 31 ) 3 CD1 -- 118 PHE ( 35 ) 3 CE2 0.020 3.180 INTRA 412 CYS ( 21 ) 10 SG -- 431 HIS ( 40 ) 10 CE1 0.019 3.381 INTRA 588 CYS ( 21 ) 14 SG -- 607 HIS ( 40 ) 14 CE1 0.019 3.381 INTRA 246 LEU ( 31 ) 6 CD1 -- 250 PHE ( 35 ) 6 CE2 0.019 3.181 INTRA 271 GLY ( 12 ) 7 N -- 272 GLY ( 13 ) 7 N 0.018 2.582 INTRA B3 686 LEU ( 31 ) 16 CD1 -- 690 PHE ( 35 ) 16 CE2 0.018 3.182 INTRA 799 GLY ( 12 ) 19 N -- 800 GLY ( 13 ) 19 N 0.018 2.582 INTRA B3 277 CYS ( 18 ) 7 SG -- 294 PHE ( 35 ) 7 CE1 0.018 3.382 INTRA 368 CYS ( 21 ) 9 SG -- 387 HIS ( 40 ) 9 CE1 0.017 3.383 INTRA 403 GLY ( 12 ) 10 N -- 404 GLY ( 13 ) 10 N 0.017 2.583 INTRA B3 603 ARG ( 36 ) 14 N -- 604 SER ( 37 ) 14 N 0.017 2.583 INTRA B3 676 CYS ( 21 ) 16 SG -- 695 HIS ( 40 ) 16 CE1 0.016 3.384 INTRA 718 LEU ( 19 ) 17 CG -- 719 ALA ( 20 ) 17 N 0.012 3.088 INTRA 579 GLY ( 12 ) 14 N -- 580 GLY ( 13 ) 14 N 0.011 2.589 INTRA B3 189 CYS ( 18 ) 5 SG -- 206 PHE ( 35 ) 5 CE1 0.010 3.390 INTRA 365 CYS ( 18 ) 9 SG -- 382 PHE ( 35 ) 9 CE1 0.010 3.390 INTRA 779 ARG ( 36 ) 18 N -- 780 SER ( 37 ) 18 N 0.006 2.594 INTRA B3 233 CYS ( 18 ) 6 SG -- 250 PHE ( 35 ) 6 CE1 0.005 3.395 INTRA 140 GLY ( 13 ) 4 C -- 142 LEU ( 15 ) 4 N 0.003 2.897 INTRA 319 HIS ( 16 ) 8 CE1 -- 331 SER ( 28 ) 8 N 0.003 3.097 INTRA 577 LEU ( 10 ) 14 CB -- 584 ARG ( 17 ) 14 NH2 0.003 3.097 INTRA 658 LEU ( 47 ) 15 N -- 659 SER ( 48 ) 15 N 0.003 2.597 INTRA B3 139 GLY ( 12 ) 4 N -- 140 GLY ( 13 ) 4 N 0.002 2.598 INTRA B3 625 GLY ( 14 ) 15 N -- 626 LEU ( 15 ) 15 N 0.001 2.599 INTRA B3 66 ASP ( 27 ) 2 OD2 -- 67 SER ( 28 ) 2 N 0.001 2.699 INTRA 404 GLY ( 13 ) 10 C -- 406 LEU ( 15 ) 10 N 0.001 2.899 INTRA 234 LEU ( 19 ) 6 N -- 235 ALA ( 20 ) 6 N 0.001 2.599 INTRA B3 493 GLY ( 14 ) 12 N -- 494 LEU ( 15 ) 12 N 0.000 2.600 INTRA B3 # 85 # 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. 98 LEU ( 15 ) 3 -5.93 670 LEU ( 15 ) 16 -5.92 93 LEU ( 10 ) 3 -5.77 63 TYR ( 24 ) 2 -5.62 811 TYR ( 24 ) 19 -5.55 274 LEU ( 15 ) 7 -5.50 406 LEU ( 15 ) 10 -5.44 54 LEU ( 15 ) 2 -5.42 415 TYR ( 24 ) 10 -5.41 107 TYR ( 24 ) 3 -5.40 846 LEU ( 15 ) 20 -5.39 494 LEU ( 15 ) 12 -5.38 549 ILE ( 26 ) 13 -5.37 582 LEU ( 15 ) 14 -5.37 417 ILE ( 26 ) 10 -5.37 538 LEU ( 15 ) 13 -5.34 109 ILE ( 26 ) 3 -5.29 5 LEU ( 10 ) 1 -5.28 445 LEU ( 10 ) 11 -5.28 285 ILE ( 26 ) 7 -5.27 593 ILE ( 26 ) 14 -5.26 637 ILE ( 26 ) 15 -5.25 681 ILE ( 26 ) 16 -5.24 153 ILE ( 26 ) 4 -5.24 55 HIS ( 16 ) 2 -5.23 138 PRO ( 11 ) 4 -5.23 94 PRO ( 11 ) 3 -5.20 798 PRO ( 11 ) 19 -5.19 539 HIS ( 16 ) 13 -5.19 709 LEU ( 10 ) 17 -5.17 402 PRO ( 11 ) 10 -5.15 6 PRO ( 11 ) 1 -5.14 314 PRO ( 11 ) 8 -5.11 65 ILE ( 26 ) 2 -5.11 857 ILE ( 26 ) 20 -5.11 142 LEU ( 15 ) 4 -5.10 505 ILE ( 26 ) 12 -5.10 802 LEU ( 15 ) 19 -5.10 665 LEU ( 10 ) 16 -5.07 813 ILE ( 26 ) 19 -5.04 239 TYR ( 24 ) 6 -5.03 225 LEU ( 10 ) 6 -5.00 710 PRO ( 11 ) 17 -5.00 # 86 # 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. 4 ASP ( 9 ) 1 --- 7 GLY ( 12 ) 1 -4.69 92 ASP ( 9 ) 3 --- 96 GLY ( 13 ) 3 -4.68 136 ASP ( 9 ) 4 --- 139 GLY ( 12 ) 4 -4.46 180 ASP ( 9 ) 5 --- 183 GLY ( 12 ) 5 -4.30 312 ASP ( 9 ) 8 --- 315 GLY ( 12 ) 8 -4.58 400 ASP ( 9 ) 10 --- 404 GLY ( 13 ) 10 -4.50 620 ASP ( 9 ) 15 --- 624 GLY ( 13 ) 15 -4.36 708 ASP ( 9 ) 17 --- 711 GLY ( 12 ) 17 -4.61 796 ASP ( 9 ) 19 --- 799 GLY ( 12 ) 19 -4.48 # 87 # Note: Structural average packing environment OK The structural average quality control value is within normal ranges. Average for range 1 - 880 : -1.384 # 88 # 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 # 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 2 # 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 3 # 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 4 # 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 5 # 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 6 # 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 7 # 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 8 # 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 9 # 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 10 # 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 11 # 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 12 # 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 13 # 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 14 # 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 15 # 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 16 # 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 17 # 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 18 # 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 19 # 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 20 # 108 # 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. 150 ARG ( 23 ) 4 -2.62 106 ARG ( 23 ) 3 -2.60 546 ARG ( 23 ) 13 -2.59 238 ARG ( 23 ) 6 -2.57 590 ARG ( 23 ) 14 -2.56 810 ARG ( 23 ) 19 -2.53 440 VAL ( 49 ) 10 -2.51 18 ARG ( 23 ) 1 -2.50 282 ARG ( 23 ) 7 -2.50 # 109 # 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. 367 ALA ( 20 ) 9 --- 370 ARG ( 23 ) 9 -1.68 # 110 # Note: Structural average packing Z-score OK The structural average for the second generation quality control value is within normal ranges. All contacts : Average = -0.239 Z-score = -1.61 BB-BB contacts : Average = 0.291 Z-score = 1.76 BB-SC contacts : Average = -0.538 Z-score = -3.55 SC-BB contacts : Average = -0.005 Z-score = -0.03 SC-SC contacts : Average = -0.526 Z-score = -3.03 # 111 # 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 : -0.281; -1.887 Model 2 : -0.267; -1.796 Model 3 : -0.340; -2.274 Model 4 : -0.254; -1.706 Model 5 : -0.104; -0.723 Model 6 : -0.447; -2.975 Model 7 : -0.152; -1.037 Model 8 : -0.144; -0.985 Model 9 : -0.291; -1.952 Model 10 : -0.257; -1.725 Model 11 : -0.136; -0.933 Model 12 : -0.221; -1.490 Model 13 : -0.384; -2.561 Model 14 : -0.275; -1.846 Model 15 : -0.059; -0.429 Model 16 : -0.123; -0.848 Model 17 : -0.194; -1.316 Model 18 : -0.226; -1.522 Model 19 : -0.233; -1.570 Model 20 : -0.398; -2.656 # 112 # 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 # 113 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 2 # 114 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 3 # 115 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 4 # 116 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 5 # 117 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 6 # 118 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 7 # 119 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 8 # 120 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 9 # 121 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 10 # 122 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 11 # 123 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 12 # 124 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 13 # 125 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 14 # 126 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 15 # 127 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 16 # 128 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 17 # 129 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 18 # 130 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 19 # 131 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Model number 20 # 132 # Note: Backbone oxygen evaluation OK All residues for which the local backbone conformation could be found in the WHAT IF database have a normal backbone oxygen position. # 133 # 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. 205 HIS ( 34 ) 5 0.35 737 LYS ( 38 ) 17 0.36 # 134 # 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! 31 ARG ( 36 ) 1 0 55 HIS ( 16 ) 2 0 56 ARG ( 17 ) 2 0 65 ILE ( 26 ) 2 0 99 HIS ( 16 ) 3 0 100 ARG ( 17 ) 3 0 143 HIS ( 16 ) 4 0 144 ARG ( 17 ) 4 0 236 CYS ( 21 ) 6 0 275 HIS ( 16 ) 7 0 276 ARG ( 17 ) 7 0 359 GLY ( 12 ) 9 0 383 ARG ( 36 ) 9 0 407 HIS ( 16 ) 10 0 408 ARG ( 17 ) 10 0 539 HIS ( 16 ) 13 0 540 ARG ( 17 ) 13 0 581 GLY ( 14 ) 14 0 584 ARG ( 17 ) 14 0 603 ARG ( 36 ) 14 0 665 LEU ( 10 ) 16 0 671 HIS ( 16 ) 16 0 672 ARG ( 17 ) 16 0 720 CYS ( 21 ) 17 0 803 HIS ( 16 ) 19 0 804 ARG ( 17 ) 19 0 847 HIS ( 16 ) 20 0 848 ARG ( 17 ) 20 0 32 SER ( 37 ) 1 1 52 GLY ( 13 ) 2 1 60 CYS ( 21 ) 2 1 119 ARG ( 36 ) 3 1 262 LEU ( 47 ) 6 1 412 CYS ( 21 ) 10 1 456 CYS ( 21 ) 11 1 494 LEU ( 15 ) 12 1 500 CYS ( 21 ) 12 1 582 LEU ( 15 ) 14 1 583 HIS ( 16 ) 14 1 588 CYS ( 21 ) 14 1 647 ARG ( 36 ) 15 1 676 CYS ( 21 ) 16 1 808 CYS ( 21 ) 19 1 852 CYS ( 21 ) 20 1 8 GLY ( 13 ) 1 2 21 ILE ( 26 ) 1 2 93 LEU ( 10 ) 3 2 96 GLY ( 13 ) 3 2 140 GLY ( 13 ) 4 2 142 LEU ( 15 ) 4 2 228 GLY ( 13 ) 6 2 272 GLY ( 13 ) 7 2 315 GLY ( 12 ) 8 2 316 GLY ( 13 ) 8 2 339 ARG ( 36 ) 8 2 361 GLY ( 14 ) 9 2 404 GLY ( 13 ) 10 2 406 LEU ( 15 ) 10 2 413 ALA ( 22 ) 10 2 448 GLY ( 13 ) 11 2 536 GLY ( 13 ) 13 2 625 GLY ( 14 ) 15 2 626 LEU ( 15 ) 15 2 667 GLY ( 12 ) 16 2 668 GLY ( 13 ) 16 2 669 GLY ( 14 ) 16 2 712 GLY ( 13 ) 17 2 735 ARG ( 36 ) 17 2 756 GLY ( 13 ) 18 2 800 GLY ( 13 ) 19 2 # 135 # Note: Backbone conformation Z-score OK The backbone conformation analysis gives a score that is normal for well refined protein structures. Backbone conformation Z-score : -1.478 # 136 # 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 : -2.358 Model 2 : -1.623 Model 3 : -1.912 Model 4 : -2.088 Model 5 : -1.428 Model 6 : -1.504 Model 7 : 0.207 Model 8 : -2.833 Model 9 : -0.310 Model 10 : -2.243 Model 11 : -0.004 Model 12 : -1.488 Model 13 : -1.381 Model 14 : -2.903 Model 15 : -1.789 Model 16 : -2.093 Model 17 : -1.383 Model 18 : -0.218 Model 19 : -1.938 Model 20 : -0.266 # 137 # Note: HIS, ASN, GLN side chains OK All of the side chain conformations of Histidine, Asparagine and Glutamine residues were found to be optimal for hydrogen bonding. # 138 # 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. 11 HIS ( 16 ) 1 HIS-E 1.04 29 HIS ( 34 ) 1 HIS-E 1.40 35 HIS ( 40 ) 1 HIS-D 2.94 HIS-E 3.00 55 HIS ( 16 ) 2 HIS-D 1.09 HIS-E 1.17 73 HIS ( 34 ) 2 HIS-E 1.58 79 HIS ( 40 ) 2 HIS-D 3.22 HIS-E 3.25 99 HIS ( 16 ) 3 HIS-E 1.09 117 HIS ( 34 ) 3 HIS-D 1.43 HIS-E 1.43 123 HIS ( 40 ) 3 HIS-D 3.27 HIS-E 3.33 143 HIS ( 16 ) 4 HIS-D 1.01 HIS-E 1.14 161 HIS ( 34 ) 4 HIS-E 1.49 167 HIS ( 40 ) 4 HIS-D 2.45 HIS-E 2.49 187 HIS ( 16 ) 5 HIS-H 0.96 HIS-E 1.04 205 HIS ( 34 ) 5 HIS-E 1.38 211 HIS ( 40 ) 5 HIS-D 3.72 HIS-E 3.78 231 HIS ( 16 ) 6 HIS-H 0.56 HIS-E 0.68 249 HIS ( 34 ) 6 HIS-D 1.21 HIS-E 1.23 255 HIS ( 40 ) 6 HIS-H 3.87 HIS-E 3.87 275 HIS ( 16 ) 7 HIS-H 0.81 HIS-E 0.95 293 HIS ( 34 ) 7 HIS-E 1.47 299 HIS ( 40 ) 7 HIS-D 3.27 HIS-E 3.42 319 HIS ( 16 ) 8 HIS-E 1.38 337 HIS ( 34 ) 8 HIS-E 1.42 343 HIS ( 40 ) 8 HIS-D 2.94 HIS-E 2.97 363 HIS ( 16 ) 9 HIS-H 0.82 HIS-E 0.96 381 HIS ( 34 ) 9 HIS-E 1.44 387 HIS ( 40 ) 9 HIS-D 2.70 HIS-E 2.76 407 HIS ( 16 ) 10 HIS-H 1.31 HIS-E 1.33 425 HIS ( 34 ) 10 HIS-E 1.43 431 HIS ( 40 ) 10 HIS-D 2.92 HIS-E 2.95 451 HIS ( 16 ) 11 HIS-H 1.04 HIS-E 1.11 469 HIS ( 34 ) 11 HIS-E 1.48 475 HIS ( 40 ) 11 HIS-D 3.06 HIS-E 3.09 495 HIS ( 16 ) 12 HIS-H 0.99 HIS-E 1.15 513 HIS ( 34 ) 12 HIS-E 1.36 519 HIS ( 40 ) 12 HIS-D 3.39 HIS-E 3.39 539 HIS ( 16 ) 13 HIS-E 1.08 557 HIS ( 34 ) 13 HIS-E 1.61 563 HIS ( 40 ) 13 HIS-D 3.05 HIS-E 3.08 583 HIS ( 16 ) 14 HIS-H 1.06 HIS-E 1.15 601 HIS ( 34 ) 14 HIS-E 1.36 607 HIS ( 40 ) 14 HIS-D 2.88 HIS-E 2.92 627 HIS ( 16 ) 15 HIS-H 1.05 HIS-E 1.10 645 HIS ( 34 ) 15 HIS-D 1.23 HIS-E 1.27 651 HIS ( 40 ) 15 HIS-D 3.16 HIS-E 3.19 671 HIS ( 16 ) 16 HIS-H 0.77 HIS-E 0.83 689 HIS ( 34 ) 16 HIS-D 1.30 HIS-E 1.30 695 HIS ( 40 ) 16 HIS-D 3.49 HIS-E 3.52 715 HIS ( 16 ) 17 HIS-H 0.42 HIS-E 0.73 733 HIS ( 34 ) 17 HIS-E 1.45 739 HIS ( 40 ) 17 HIS-D 3.17 HIS-E 3.21 759 HIS ( 16 ) 18 HIS-H 1.01 HIS-E 1.11 777 HIS ( 34 ) 18 HIS-E 1.64 783 HIS ( 40 ) 18 HIS-D 2.98 HIS-E 2.99 803 HIS ( 16 ) 19 HIS-E 0.96 821 HIS ( 34 ) 19 HIS-E 1.70 827 HIS ( 40 ) 19 HIS-D 3.45 HIS-E 3.50 847 HIS ( 16 ) 20 HIS-E 0.91 865 HIS ( 34 ) 20 HIS-D 1.28 HIS-E 1.28 871 HIS ( 40 ) 20 HIS-D 4.47 # 139 # 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. 22 ASP ( 27 ) 1 N 23 SER ( 28 ) 1 N 54 LEU ( 15 ) 2 N 56 ARG ( 17 ) 2 N 62 ARG ( 23 ) 2 N 64 PHE ( 25 ) 2 N 67 SER ( 28 ) 2 N 76 SER ( 37 ) 2 N 95 GLY ( 12 ) 3 N 100 ARG ( 17 ) 3 N 107 TYR ( 24 ) 3 N 108 PHE ( 25 ) 3 N 110 ASP ( 27 ) 3 N 111 SER ( 28 ) 3 N 122 ASP ( 39 ) 3 N 144 ARG ( 17 ) 4 N 152 PHE ( 25 ) 4 N 154 ASP ( 27 ) 4 N 155 SER ( 28 ) 4 N 198 ASP ( 27 ) 5 N 199 SER ( 28 ) 5 N 230 LEU ( 15 ) 6 N 232 ARG ( 17 ) 6 N 240 PHE ( 25 ) 6 N 242 ASP ( 27 ) 6 N 243 SER ( 28 ) 6 N 275 HIS ( 16 ) 7 N 276 ARG ( 17 ) 7 N 284 PHE ( 25 ) 7 N 286 ASP ( 27 ) 7 N 287 SER ( 28 ) 7 N 326 ARG ( 23 ) 8 N 330 ASP ( 27 ) 8 N 340 SER ( 37 ) 8 N 364 ARG ( 17 ) 9 NE 374 ASP ( 27 ) 9 N 375 SER ( 28 ) 9 N 408 ARG ( 17 ) 10 N 414 ARG ( 23 ) 10 N 416 PHE ( 25 ) 10 N 418 ASP ( 27 ) 10 N 430 ASP ( 39 ) 10 N 458 ARG ( 23 ) 11 N 462 ASP ( 27 ) 11 N 495 HIS ( 16 ) 12 N 499 ALA ( 20 ) 12 N 502 ARG ( 23 ) 12 N 505 ILE ( 26 ) 12 N 506 ASP ( 27 ) 12 N 507 SER ( 28 ) 12 N 540 ARG ( 17 ) 13 N 548 PHE ( 25 ) 13 N 550 ASP ( 27 ) 13 N 551 SER ( 28 ) 13 N 553 ASN ( 30 ) 13 N 584 ARG ( 17 ) 14 NH2 593 ILE ( 26 ) 14 N 594 ASP ( 27 ) 14 N 595 SER ( 28 ) 14 N 634 ARG ( 23 ) 15 N 638 ASP ( 27 ) 15 N 667 GLY ( 12 ) 16 N 672 ARG ( 17 ) 16 N 678 ARG ( 23 ) 16 N 680 PHE ( 25 ) 16 N 682 ASP ( 27 ) 16 N 683 SER ( 28 ) 16 N 694 ASP ( 39 ) 16 N 719 ALA ( 20 ) 17 N 722 ARG ( 23 ) 17 N 726 ASP ( 27 ) 17 N 727 SER ( 28 ) 17 N 736 SER ( 37 ) 17 N 752 ASP ( 9 ) 18 N 753 LEU ( 10 ) 18 N 760 ARG ( 17 ) 18 NE 770 ASP ( 27 ) 18 N 771 SER ( 28 ) 18 N 780 SER ( 37 ) 18 N 804 ARG ( 17 ) 19 N 812 PHE ( 25 ) 19 N 814 ASP ( 27 ) 19 N 815 SER ( 28 ) 19 N 824 SER ( 37 ) 19 N 848 ARG ( 17 ) 20 N 854 ARG ( 23 ) 20 N 856 PHE ( 25 ) 20 N 858 ASP ( 27 ) 20 N 859 SER ( 28 ) 20 N # 140 # Note: Buried hydrogen bond acceptors OK All buried polar side-chain hydrogen bond acceptors are involved in a hydrogen bond in the optimized hydrogen bond network. # 141 # 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 : -2.211 2nd generation packing quality : -2.656 Ramachandran plot appearance : -3.500 (poor) chi-1/chi-2 rotamer normality : -1.774 Backbone conformation : -1.478 RMS Z-scores, should be close to 1.0: Bond lengths : 0.865 Bond angles : 0.780 Omega angle restraints : 0.678 (tight) Side chain planarity : 0.939 Improper dihedral distribution : 1.492 Inside/Outside distribution : 1.121 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).