seq.B99990001.pdb -- The packing quality control per amino acid: Average for range 1 - 182 : -2.231 If a residue has a score of -5.0 or lower, something is really going on: the residue makes symmetry contacts, is contacting a ligand or an ion, or something is wrong. Bond lengths that deviate more than 4 sigma: The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given. Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length. 157 GLN ( 157 ) A N CA 1.55 4.7 157 GLN ( 157 ) A CA C 1.81 13.8 157 GLN ( 157 ) A N -C 1.44 5.6 158 LEU ( 158 ) A N CA 1.64 9.8 158 LEU ( 158 ) A N -C 1.55 10.9 Bond lengths were found to deviate normally from the standard bond lengths (values for Protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). RMS Z-score for bond lengths: 1.023 RMS-deviation in bond distances: 0.021 Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation. You have most probably seen symmetry problems earlier. Please correct these and rerun this check to see the possible implications on the X-ray cell axes. Planarity validation results: The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect. 98 TRP ( 98 ) A 4.86 All of the atoms that are connected to planar aromatic rings in side chains of amino-acid residues are in the plane within expected RMS deviations. Since there is no DNA and no protein with hydrogens, no uncalibrated planarity check was performed. The packing quality control per amino acid: ----Residue------- State AllAll BB-BB BB-SC SC-BB SC-SC --------------------------------------------------------------------------- 1 MET ( 1 ) A 3 -0.791 -0.688 -0.478 -0.944 -0.642 2 ARG ( 2 ) A 3 -1.516 -0.994 -0.816 -0.952 -1.203 3 ILE ( 3 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 4 ALA ( 4 ) A 3 -0.971 -1.078 -0.794 0.000 0.000 5 PHE ( 5 ) A 3 -1.356 -0.801 -0.898 -1.026 -0.958 6 PHE ( 6 ) A 3 -1.353 -0.801 -0.898 -1.017 -0.958 7 LEU ( 7 ) A 3 -1.547 -1.068 -1.105 -1.015 -1.030 8 LEU ( 8 ) A 3 -2.110 -1.233 -1.533 -1.174 -1.419 9 ILE ( 9 ) A 3 -1.049 -0.719 -1.143 -1.207 -1.585 10 LEU ( 10 ) A 3 -0.826 -0.754 -0.770 -0.470 -1.030 11 SER ( 11 ) A 3 -0.753 -0.534 -0.763 -0.826 -0.580 12 ILE ( 12 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 13 ILE ( 13 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 14 VAL ( 14 ) A 3 -1.352 -0.821 -0.810 -0.825 -1.086 15 GLY ( 15 ) A 3 -1.413 -1.020 -0.877 0.000 0.000 16 LEU ( 16 ) A 3 -0.826 -0.754 -0.770 -0.470 -1.030 17 ALA ( 17 ) A 3 -0.971 -1.078 -0.794 0.000 0.000 18 TYR ( 18 ) A 3 -1.539 -0.859 -1.134 -1.153 -1.399 19 GLY ( 19 ) A 3 -1.413 -1.020 -0.877 0.000 0.000 20 TYR ( 20 ) A 3 -1.481 -0.798 -1.079 -1.153 -1.380 21 SER ( 21 ) A 3 -1.497 -0.891 -1.400 -0.581 -1.030 22 CYS ( 22 ) A 3 -1.678 -1.207 -1.754 -1.379 -2.034 23 PRO ( 23 ) A 3 -1.194 -0.710 -0.817 -0.752 -0.830 24 LYS ( 24 ) A 3 -1.581 -1.490 -1.227 -1.088 -0.210 25 PRO ( 25 ) A 3 -0.245 -0.710 0.586 -0.752 0.110 26 CYS ( 26 ) A 3 -1.601 -1.778 -0.229 -1.475 -1.646 27 TYR ( 27 ) A 3 0.111 0.813 -0.209 0.212 -1.052 28 GLY ( 28 ) A 3 -0.528 -0.177 -0.606 0.000 0.000 29 ASN ( 29 ) A 3 -0.879 -0.273 -0.306 -1.270 -0.936 30 MET ( 30 ) A 3 -0.052 1.564 -1.140 0.758 -0.798 31 CYS ( 31 ) A 3 -0.060 0.753 0.185 -0.652 -1.296 32 CYS ( 32 ) A 3 -1.193 -0.683 -1.177 -1.133 -1.920 33 SER ( 33 ) A 2 -0.859 -1.055 0.964 -1.628 -0.327 34 THR ( 34 ) A 2 -0.988 -1.073 0.223 -1.113 -1.221 35 SER ( 35 ) A 2 -0.113 0.180 -0.156 -0.915 -0.992 36 PRO ( 36 ) A 2 -0.627 0.529 -1.586 -0.213 -1.984 37 ASP ( 37 ) A 2 -0.225 0.436 -0.028 -0.531 -0.905 38 HIS ( 38 ) A 2 2.133 1.591 2.712 0.406 1.266 39 LYS ( 39 ) A 2 0.015 0.805 0.603 -0.821 -0.776 40 TYR ( 40 ) A 2 -0.259 0.326 -0.266 -0.223 -1.234 41 TYR ( 41 ) A 2 0.310 0.149 -0.216 0.499 0.911 42 LEU ( 42 ) A 2 -0.651 -0.311 -1.315 -0.352 -0.491 43 THR ( 43 ) A 3 -0.866 -0.830 -0.916 -0.788 0.063 44 ASP ( 44 ) A 3 -0.526 0.997 -1.088 -0.619 -0.866 45 PHE ( 45 ) A 2 -1.573 -1.159 -1.730 -1.157 -0.816 46 CYS ( 46 ) A 3 -1.616 -0.890 -1.777 -1.533 -1.584 47 GLY ( 47 ) A 3 -0.075 0.843 -1.555 0.000 0.000 48 SER ( 48 ) A 3 -0.869 -0.488 -1.329 -0.115 -0.169 49 THR ( 49 ) A 3 -1.075 -1.274 -0.823 -0.853 -0.299 50 SER ( 50 ) A 3 0.134 1.090 -0.757 -0.447 -0.580 51 ALA ( 51 ) A 3 -0.618 -0.253 -0.585 0.000 0.000 52 CYS ( 52 ) A 3 -0.946 -0.400 -0.850 -1.215 -1.433 53 GLY ( 53 ) A 2 -1.782 -1.797 -1.096 0.000 0.000 54 PRO ( 54 ) A 2 -1.200 -1.207 -0.557 -0.729 -0.815 55 LYS ( 55 ) A 2 -1.452 -1.276 -0.296 -1.578 -0.944 56 PRO ( 56 ) A 2 -1.347 -0.721 -1.758 -0.631 -1.415 57 SER ( 57 ) A 2 -0.291 -0.031 0.081 -1.173 -0.978 58 CYS ( 58 ) A 2 -0.089 0.254 -0.358 -0.556 0.719 59 SER ( 59 ) A 2 0.159 0.806 -1.087 -0.138 -0.523 60 GLY ( 60 ) A 2 -0.169 0.386 -1.279 0.000 0.000 61 LYS ( 61 ) A 2 -1.249 -0.701 -1.322 -0.666 -1.689 62 LEU ( 62 ) A 2 -1.286 -0.955 -1.290 -0.911 -1.304 63 TYR ( 63 ) A 2 -1.312 -0.960 -1.317 -0.137 -1.812 64 PHE ( 64 ) A 3 0.050 0.197 0.501 -0.162 -0.250 65 THR ( 65 ) A 3 -0.466 -0.194 -0.447 -0.664 -0.648 66 ALA ( 66 ) A 3 -0.895 -0.479 -0.721 0.000 0.000 67 ASP ( 67 ) A 3 0.689 1.767 -0.350 1.078 -0.792 68 SER ( 68 ) A 3 0.431 1.228 -1.094 1.872 -1.584 69 GLN ( 69 ) A 3 -0.781 -0.232 -0.764 0.009 -0.845 70 ARG ( 70 ) A 3 0.575 0.838 0.061 0.285 0.194 71 PHE ( 71 ) A 3 -0.158 0.464 -0.654 -1.206 0.321 72 GLY ( 72 ) A 1 -0.846 -0.627 -0.980 0.000 0.000 73 CYS ( 73 ) A 3 -1.028 -0.579 -0.668 -1.195 -1.773 74 GLY ( 74 ) A 3 -1.777 -0.734 -2.014 0.000 0.000 75 LYS ( 75 ) A 3 -1.227 -0.706 -0.605 -1.058 -1.346 76 HIS ( 76 ) A 3 -1.555 -1.823 -0.768 -1.533 -0.479 77 LEU ( 77 ) A 3 -0.641 -0.335 0.606 -0.453 -1.119 78 ASN ( 78 ) A 3 -1.254 -0.123 -0.913 -0.923 -1.165 79 LEU ( 79 ) A 3 0.110 0.556 0.453 -0.067 -0.512 80 CYS ( 80 ) A 1 -1.075 -0.209 -1.919 -1.085 -1.810 81 ARG ( 81 ) A 1 -1.040 -0.818 -1.077 -0.532 -0.734 82 GLY ( 82 ) A 3 0.898 1.615 -0.688 0.000 0.000 83 LYS ( 83 ) A 3 0.780 1.005 -0.113 0.830 0.170 84 LYS ( 84 ) A 3 -0.502 0.880 -0.128 -0.136 -1.517 85 CYS ( 85 ) A 3 0.482 0.426 -0.383 1.636 -0.782 86 VAL ( 86 ) A 3 -0.222 -0.433 0.268 -0.720 0.340 87 LYS ( 87 ) A 3 -0.659 -0.426 -1.136 1.172 -1.414 88 ALA ( 88 ) A 3 -0.148 0.167 -0.392 0.000 0.000 89 LYS ( 89 ) A 3 -1.141 -0.405 -0.999 0.531 -1.941 90 VAL ( 90 ) A 3 -0.604 0.650 -1.963 1.419 -2.088 91 TYR ( 91 ) A 3 -0.898 -0.838 -0.244 -0.806 -0.110 92 ASP ( 92 ) A 3 -0.756 -1.025 -0.656 -0.120 -0.167 93 ALA ( 93 ) A 1 -1.928 -1.858 -1.481 0.000 0.000 94 GLY ( 94 ) A 3 -0.107 0.464 -0.777 0.000 0.000 95 PRO ( 95 ) A 3 0.703 -0.130 0.845 1.513 -0.177 96 ALA ( 96 ) A 3 -0.482 -0.394 -0.242 0.000 0.000 97 GLU ( 97 ) A 3 -1.251 0.110 -0.660 0.268 -1.578 98 TRP ( 98 ) A 2 -2.190 -1.616 -1.700 -0.645 -2.545 99 VAL ( 99 ) A 3 0.376 0.484 1.026 -0.794 -0.030 100 GLU ( 100 ) A 3 -0.871 -0.110 0.090 -0.326 -1.070 101 LYS ( 101 ) A 3 -1.542 -1.096 -1.439 -0.825 -0.858 102 ASP ( 102 ) A 3 -1.558 -0.895 -1.268 -0.488 -1.066 103 ALA ( 103 ) A 3 -1.113 -1.403 -0.162 0.000 0.000 104 GLY ( 104 ) A 3 -1.208 -1.387 -0.101 0.000 0.000 105 LYS ( 105 ) A 3 -1.595 -1.401 -1.422 -0.857 -0.389 106 MET ( 106 ) A 3 -2.024 -0.686 -1.472 -1.119 -1.244 107 ILE ( 107 ) A 3 -1.660 -0.174 -1.691 -0.227 -1.895 108 ILE ( 108 ) A 3 -1.218 -0.278 -0.865 -0.933 -1.043 109 ASP ( 109 ) A 3 -1.471 -0.800 -1.278 -0.083 -1.369 110 ALA ( 110 ) A 3 -1.063 -0.889 -0.489 0.000 0.000 111 SER ( 111 ) A 3 -1.811 -1.452 -1.124 -1.112 -0.978 112 PRO ( 112 ) A 3 -0.272 -0.154 0.257 -0.400 -0.513 113 THR ( 113 ) A 3 -0.994 -0.533 -0.352 -1.402 -0.590 114 ILE ( 114 ) A 3 -1.301 -0.538 -0.023 -1.096 -1.247 115 CYS ( 115 ) A 3 -1.227 -1.034 -0.663 -1.031 -1.049 116 HIS ( 116 ) A 2 -1.341 -0.711 -1.011 -1.404 -1.117 117 GLU ( 117 ) A 2 -2.114 -1.971 -1.618 -1.250 -1.296 118 LEU ( 118 ) A 2 -2.372 -1.903 -2.275 -1.090 -1.774 119 THR ( 119 ) A 2 -1.839 -1.362 -2.124 -1.329 -1.894 120 GLY ( 120 ) A 3 -0.484 0.343 -1.306 0.000 0.000 121 GLY ( 121 ) A 3 0.235 -0.005 0.383 0.000 0.000 122 SER ( 122 ) A 3 -0.792 -0.969 -0.424 -1.011 0.402 123 SER ( 123 ) A 3 -0.424 -0.901 0.184 0.437 -0.182 124 CYS ( 124 ) A 3 -1.443 -1.768 0.067 -1.807 -0.364 125 GLY ( 125 ) A 3 -0.834 -1.122 0.388 0.000 0.000 126 TRP ( 126 ) A 3 -1.451 -0.620 -1.638 -1.101 -1.100 127 SER ( 127 ) A 3 -1.096 -1.060 -0.760 -1.057 -0.659 128 ASP ( 128 ) A 3 -0.790 -0.337 -0.865 -0.658 -0.325 129 LYS ( 129 ) A 3 -1.887 -0.917 -0.966 -1.180 -1.553 130 PHE ( 130 ) A 2 -1.163 -0.598 -0.627 -1.001 -1.867 131 GLU ( 131 ) A 2 -0.131 0.370 0.169 -0.399 -0.620 132 ILE ( 132 ) A 2 -0.410 -0.681 0.345 -0.764 0.442 133 THR ( 133 ) A 2 -0.582 -0.022 -0.386 -1.176 -1.541 134 ALA ( 134 ) A 2 -0.380 0.501 -1.725 0.000 0.000 135 THR ( 135 ) A 2 0.266 1.426 -0.437 -1.739 0.060 136 VAL ( 136 ) A 2 0.356 0.606 -0.166 0.152 0.401 137 THR ( 137 ) A 2 -0.252 0.334 0.046 -1.391 -1.517 138 SER ( 138 ) A 2 -0.527 -0.120 -1.042 0.114 -1.564 139 LEU ( 139 ) A 2 -1.571 -0.681 -1.582 -1.244 -1.441 140 THR ( 140 ) A 2 -1.177 -1.160 -0.673 -1.040 -0.272 141 ASP ( 141 ) A 3 -1.305 -0.797 -0.775 -0.966 -0.755 142 SER ( 142 ) A 3 -0.732 -0.528 -0.721 -0.826 -0.580 143 ARG ( 143 ) A 3 -0.701 -0.271 -0.274 -0.684 -0.488 144 PRO ( 144 ) A 3 -0.261 -0.202 0.083 0.067 -0.523 145 LEU ( 145 ) A 3 -1.110 -0.671 0.817 -1.141 -1.168 146 GLY ( 146 ) A 3 -1.764 -0.953 -1.555 0.000 0.000 147 PRO ( 147 ) A 3 -0.112 -0.216 0.275 -0.367 -0.016 148 PHE ( 148 ) A 3 -0.968 -1.116 -0.664 -0.609 -0.033 149 ASN ( 149 ) A 3 -1.092 -1.362 0.038 -1.363 0.024 150 VAL ( 150 ) A 3 -1.195 -0.821 -0.733 -0.825 -1.064 151 THR ( 151 ) A 3 -1.251 -1.078 -0.992 -1.082 -0.153 152 GLU ( 152 ) A 3 -2.160 -1.248 -1.465 -1.148 -1.240 153 GLU ( 153 ) A 3 -0.897 -0.612 -0.894 -1.148 -0.727 154 GLU ( 154 ) A 3 -2.097 -1.495 -1.080 -1.425 -1.237 155 MET ( 155 ) A 3 -1.388 -0.240 -0.874 -0.211 -1.363 156 ASP ( 156 ) A 3 -1.608 -1.046 -1.009 -1.028 -0.929 157 GLN ( 157 ) A 3 0.205 -0.288 -0.108 2.344 -1.004 158 LEU ( 158 ) A 3 -1.180 -0.242 -1.327 0.456 -1.541 159 PHE ( 159 ) A 3 -0.406 0.385 -0.802 -0.111 -0.516 160 ILE ( 160 ) A 2 -0.970 -0.350 0.239 -1.692 -0.774 161 ASP ( 161 ) A 2 -1.017 -0.469 -1.268 -0.656 -1.163 162 HIS ( 162 ) A 3 -0.623 0.471 -1.438 0.383 -1.046 163 GLU ( 163 ) A 2 -1.269 -0.346 -1.691 -0.177 -1.960 164 ILE ( 164 ) A 2 -1.217 -0.793 -1.098 -1.146 0.176 165 ALA ( 165 ) A 2 -1.190 -1.191 -0.745 0.000 0.000 166 MET ( 166 ) A 3 -1.073 -0.092 -0.751 -0.457 -1.221 167 ALA ( 167 ) A 3 -1.117 -0.673 -0.969 0.000 0.000 168 GLN ( 168 ) A 3 -0.632 -0.023 -0.734 -0.888 -1.186 169 CYS ( 169 ) A 3 -1.133 -1.099 -1.372 -1.010 0.399 170 GLU ( 170 ) A 3 -0.604 -0.057 -1.086 0.104 -0.810 171 ALA ( 171 ) A 2 -1.983 -2.095 -0.786 0.000 0.000 172 GLU ( 172 ) A 2 -1.612 -0.979 -0.964 -0.987 -0.940 173 LYS ( 173 ) A 2 -0.770 -0.625 0.072 -0.685 -0.754 174 THR ( 174 ) A 2 -1.839 -1.624 -1.493 -1.408 -1.826 175 CYS ( 175 ) A 3 -1.374 -0.943 -1.379 -1.451 -0.865 176 ASN ( 176 ) A 3 -0.564 -0.756 -0.926 0.253 0.160 177 GLY ( 177 ) A 3 -1.158 -0.985 -0.364 0.000 0.000 178 PHE ( 178 ) A 2 -2.820 -2.350 -1.813 -1.746 -2.357 179 ASP ( 179 ) A 3 -1.358 -0.853 -0.447 -0.883 -0.866 180 LEU ( 180 ) A 3 -1.598 -1.403 -0.756 -1.278 -0.436 181 GLU ( 181 ) A 3 0.411 -0.612 3.138 -1.148 -0.561 All contacts : Average = -0.907 Z-score = -5.87 BB-BB contacts : Average = -0.493 Z-score = -3.26 BB-SC contacts : Average = -0.701 Z-score = -5.37 SC-BB contacts : Average = -0.624 Z-score = -3.70 SC-SC contacts : Average = -0.912 Z-score = -5.22 If an individual residue has a quality control value of -2.5 or worse, you should take a look at it. It can mean that the residue: is involved in symmetry contacts, or is binding a co-factor, ligand or ion, or is an active site residue, or is wrong. Average protein values ("Z-score for all contacts") can be read as follows: -5.0 Guaranteed wrong structure. Bad structure or poor model -3.0 Probably bad structure or unrefined model. Doubtful structure or model -2.0 Structure OK or good model. Good structures 0.0 Good structures. 2.0 Good structures. Unusually Good structures 4.0 Probably a strange model of a perfect helix ------------------------------------- seq.B99990002.pdb -- The packing quality control per amino acid: Average for range 1 - 182 : -2.249 If a residue has a score of -5.0 or lower, something is really going on: the residue makes symmetry contacts, is contacting a ligand or an ion, or something is wrong. Bond lengths that deviate more than 4 sigma: The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given. Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length. 85 CYS ( 85 ) A CA C 1.42 -4.9 157 GLN ( 157 ) A CA C 1.83 14.6 157 GLN ( 157 ) A N -C 1.44 5.5 158 LEU ( 158 ) A N CA 1.64 9.7 158 LEU ( 158 ) A N -C 1.55 11.1 159 PHE ( 159 ) A N -C 1.41 4.3 Bond lengths were found to deviate normally from the standard bond lengths (values for Protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). RMS Z-score for bond lengths: 1.046 RMS-deviation in bond distances: 0.021 Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation. You have most probably seen symmetry problems earlier. Please correct these and rerun this check to see the possible implications on the X-ray cell axes. Planarity validation results: The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect. 157 GLN ( 157 ) A 4.90 All of the atoms that are connected to planar aromatic rings in side chains of amino-acid residues are in the plane within expected RMS deviations. Since there is no DNA and no protein with hydrogens, no uncalibrated planarity check was performed. The packing quality control per amino acid: ----Residue------- State AllAll BB-BB BB-SC SC-BB SC-SC --------------------------------------------------------------------------- 1 MET ( 1 ) A 3 -0.791 -0.688 -0.478 -0.944 -0.642 2 ARG ( 2 ) A 3 -1.516 -0.994 -0.572 -0.952 -1.203 3 ILE ( 3 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 4 ALA ( 4 ) A 3 -0.764 -1.078 -0.668 0.000 0.000 5 PHE ( 5 ) A 3 -1.356 -0.801 -0.898 -1.026 -0.958 6 PHE ( 6 ) A 3 -1.410 -0.948 -0.779 -1.083 -1.044 7 LEU ( 7 ) A 3 -2.110 -1.233 -1.533 -1.174 -1.419 8 LEU ( 8 ) A 3 -1.547 -1.068 -1.105 -1.015 -1.030 9 ILE ( 9 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 10 LEU ( 10 ) A 3 -0.826 -0.754 -0.770 -0.470 -1.030 11 SER ( 11 ) A 3 -1.635 -0.986 -1.431 -0.826 -1.098 12 ILE ( 12 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 13 ILE ( 13 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 14 VAL ( 14 ) A 3 -1.352 -0.821 -0.810 -0.825 -1.086 15 GLY ( 15 ) A 3 -1.413 -1.020 -0.590 0.000 0.000 16 LEU ( 16 ) A 3 -0.826 -0.754 -0.770 -0.470 -1.030 17 ALA ( 17 ) A 3 -0.971 -1.078 -0.794 0.000 0.000 18 TYR ( 18 ) A 3 -1.539 -0.859 -1.134 -1.153 -1.399 19 GLY ( 19 ) A 3 -1.692 -1.399 -0.891 0.000 0.000 20 TYR ( 20 ) A 3 -1.417 -0.784 -0.969 -1.153 -1.324 21 SER ( 21 ) A 3 -1.143 -0.729 -1.005 -0.826 -0.742 22 CYS ( 22 ) A 3 -1.654 -1.207 -1.754 -1.379 -1.835 23 PRO ( 23 ) A 3 -0.690 -0.102 -0.271 -0.752 -0.702 24 LYS ( 24 ) A 3 -2.526 -1.558 -1.230 -2.011 -1.358 25 PRO ( 25 ) A 3 -1.370 -1.183 -0.711 -1.416 -0.609 26 CYS ( 26 ) A 3 -1.369 -1.180 -0.606 -1.357 -1.801 27 TYR ( 27 ) A 3 -0.656 -0.174 0.161 -1.136 -0.933 28 GLY ( 28 ) A 3 -0.381 0.072 -0.762 0.000 0.000 29 ASN ( 29 ) A 3 -0.794 0.176 -0.684 -0.760 -1.204 30 MET ( 30 ) A 3 2.626 3.912 -0.412 2.876 -0.626 31 CYS ( 31 ) A 3 -0.528 -0.151 -0.676 -0.880 -0.032 32 CYS ( 32 ) A 3 -0.917 -0.446 -0.553 -1.166 -1.694 33 SER ( 33 ) A 3 0.182 -0.147 0.719 -0.553 0.715 34 THR ( 34 ) A 2 -0.559 -0.723 1.216 -1.283 -1.072 35 SER ( 35 ) A 2 -0.711 -0.685 -0.475 -0.432 -0.202 36 PRO ( 36 ) A 2 -1.462 -0.386 -1.509 -1.956 -1.314 37 ASP ( 37 ) A 2 -0.374 0.063 -0.390 -0.360 -0.663 38 HIS ( 38 ) A 2 1.094 1.015 1.241 -0.271 0.623 39 LYS ( 39 ) A 2 -0.843 0.924 -1.118 -1.602 -2.258 40 TYR ( 40 ) A 2 -0.645 0.266 -1.470 -0.352 -1.303 41 TYR ( 41 ) A 2 0.171 0.334 -0.431 0.206 0.112 42 LEU ( 42 ) A 2 -0.193 0.793 -1.158 -0.797 -0.897 43 THR ( 43 ) A 2 -1.539 -1.203 -1.469 -1.471 -1.134 44 ASP ( 44 ) A 3 -0.938 0.278 -1.272 -0.508 -1.059 45 PHE ( 45 ) A 2 -1.804 -1.045 -1.871 -1.402 -1.509 46 CYS ( 46 ) A 3 -1.010 -0.427 -1.293 -1.032 -1.494 47 GLY ( 47 ) A 3 0.462 1.195 -1.312 0.000 0.000 48 SER ( 48 ) A 3 -1.040 -0.500 -1.314 -0.649 -0.646 49 THR ( 49 ) A 3 -1.075 -1.278 -0.820 -0.891 -0.256 50 SER ( 50 ) A 3 -0.234 0.545 -0.793 -0.447 -0.742 51 ALA ( 51 ) A 3 -0.568 -0.082 -0.702 0.000 0.000 52 CYS ( 52 ) A 3 -1.254 -0.682 -1.406 -1.252 -1.676 53 GLY ( 53 ) A 3 -1.811 -0.621 -2.064 0.000 0.000 54 PRO ( 54 ) A 2 -1.404 -1.261 -1.031 -0.791 -0.975 55 LYS ( 55 ) A 2 -1.678 -1.033 -0.834 -1.895 -1.364 56 PRO ( 56 ) A 2 -1.294 -0.931 -1.385 -0.541 -1.340 57 SER ( 57 ) A 2 -0.575 0.067 -1.102 -0.882 -1.497 58 CYS ( 58 ) A 2 -0.773 0.109 -0.588 -1.698 -6.552 59 SER ( 59 ) A 2 0.273 0.722 0.059 -0.984 -0.768 60 GLY ( 60 ) A 2 -0.023 0.276 -0.647 0.000 0.000 61 LYS ( 61 ) A 2 -1.066 -0.610 -0.979 -1.057 -0.689 62 LEU ( 62 ) A 2 -2.174 -1.178 -1.281 -1.396 -1.957 63 TYR ( 63 ) A 2 -1.674 -1.269 -1.413 -0.178 -2.046 64 PHE ( 64 ) A 3 -0.261 0.114 0.413 -0.540 -0.670 65 THR ( 65 ) A 3 -0.670 -0.804 -0.199 -0.972 -0.542 66 ALA ( 66 ) A 3 -0.735 -0.640 -0.324 0.000 0.000 67 ASP ( 67 ) A 3 -0.074 1.482 -0.837 -0.245 -0.965 68 SER ( 68 ) A 3 0.122 0.917 -1.264 1.520 -1.405 69 GLN ( 69 ) A 3 -0.872 -0.228 -0.673 0.306 -1.464 70 ARG ( 70 ) A 3 -0.923 0.053 -0.045 -0.183 -1.198 71 PHE ( 71 ) A 3 0.457 0.166 1.097 -0.438 0.353 72 GLY ( 72 ) A 1 -0.394 -0.322 -0.388 0.000 0.000 73 CYS ( 73 ) A 3 -1.060 -0.391 -1.234 -1.107 -1.983 74 GLY ( 74 ) A 3 -1.325 -0.781 -1.187 0.000 0.000 75 LYS ( 75 ) A 3 -0.898 -0.677 0.475 -1.045 -1.282 76 HIS ( 76 ) A 3 -1.643 -1.823 -1.077 -1.411 -0.523 77 LEU ( 77 ) A 3 -0.562 0.185 -0.074 -0.280 -1.222 78 ASN ( 78 ) A 3 -1.837 -0.150 -1.079 -1.126 -2.300 79 LEU ( 79 ) A 3 -1.307 0.342 -0.334 -1.220 -1.747 80 CYS ( 80 ) A 1 -1.221 -0.431 -2.094 -1.102 -1.844 81 ARG ( 81 ) A 1 -1.409 -1.139 -1.172 -0.704 -1.063 82 GLY ( 82 ) A 3 1.543 1.784 0.116 0.000 0.000 83 LYS ( 83 ) A 3 0.283 0.623 -0.467 1.430 -0.869 84 LYS ( 84 ) A 3 -0.437 0.616 -1.133 0.525 -1.224 85 CYS ( 85 ) A 3 -0.150 0.684 -0.837 -0.118 -1.039 86 VAL ( 86 ) A 3 -0.843 -0.200 -0.628 -0.334 -1.354 87 LYS ( 87 ) A 3 -0.653 0.015 -1.293 0.631 -1.207 88 ALA ( 88 ) A 3 -0.233 -0.202 -0.107 0.000 0.000 89 LYS ( 89 ) A 3 -0.778 -0.620 -0.519 0.484 -1.244 90 VAL ( 90 ) A 3 -1.157 -0.506 -1.324 0.210 -1.555 91 TYR ( 91 ) A 3 -0.764 -0.983 0.390 -0.885 -0.055 92 ASP ( 92 ) A 3 -1.027 -0.629 -0.485 -0.988 -0.590 93 ALA ( 93 ) A 1 -1.601 -1.694 -0.783 0.000 0.000 94 GLY ( 94 ) A 3 -0.245 0.284 -0.761 0.000 0.000 95 PRO ( 95 ) A 3 0.817 0.158 0.223 1.924 -0.068 96 ALA ( 96 ) A 3 -0.556 -0.481 -0.249 0.000 0.000 97 GLU ( 97 ) A 3 -1.184 0.256 -0.924 0.537 -1.568 98 TRP ( 98 ) A 2 -2.234 -1.484 -2.118 -0.584 -2.653 99 VAL ( 99 ) A 3 0.099 0.603 0.190 -0.770 -0.260 100 GLU ( 100 ) A 3 -0.669 0.155 -0.331 -0.191 -0.860 101 LYS ( 101 ) A 3 -1.666 -1.416 -1.647 -1.015 -0.516 102 ASP ( 102 ) A 3 -1.413 -0.974 -0.835 -0.378 -1.098 103 ALA ( 103 ) A 3 -1.994 -1.614 -0.983 0.000 0.000 104 GLY ( 104 ) A 3 -1.202 -1.509 0.068 0.000 0.000 105 LYS ( 105 ) A 3 -1.887 -1.321 -1.404 -1.125 -0.951 106 MET ( 106 ) A 3 -1.449 -0.433 -0.904 -0.341 -1.239 107 ILE ( 107 ) A 3 -0.970 0.032 -1.892 0.702 -1.605 108 ILE ( 108 ) A 3 -1.626 -0.812 -0.657 -1.272 -1.054 109 ASP ( 109 ) A 3 -1.647 -0.972 -1.263 -0.314 -1.434 110 ALA ( 110 ) A 3 -1.120 -1.164 -0.241 0.000 0.000 111 SER ( 111 ) A 3 -1.631 -1.216 -1.467 -0.353 -0.956 112 PRO ( 112 ) A 3 -0.886 -0.730 -1.025 -0.433 -0.265 113 THR ( 113 ) A 3 -0.956 -0.014 -0.860 -0.979 -1.404 114 ILE ( 114 ) A 3 -1.241 -0.639 -0.651 -1.382 -0.765 115 CYS ( 115 ) A 3 -1.024 -1.096 0.104 -1.145 -0.714 116 HIS ( 116 ) A 2 -1.146 -0.989 0.002 -1.957 -1.108 117 GLU ( 117 ) A 3 -0.869 -0.363 -0.564 -0.366 -0.608 118 LEU ( 118 ) A 2 -2.392 -2.373 -1.440 -0.926 -1.975 119 THR ( 119 ) A 3 0.012 0.046 0.150 0.295 -0.705 120 GLY ( 120 ) A 3 -0.373 -0.097 -0.517 0.000 0.000 121 GLY ( 121 ) A 3 -0.102 -0.342 0.440 0.000 0.000 122 SER ( 122 ) A 3 -0.612 -1.111 0.412 -1.011 0.073 123 SER ( 123 ) A 3 -0.099 -1.093 0.959 0.003 1.208 124 CYS ( 124 ) A 3 -0.944 -0.584 -0.746 -1.079 -1.200 125 GLY ( 125 ) A 3 -1.172 -0.935 -0.781 0.000 0.000 126 TRP ( 126 ) A 3 -1.447 -0.561 -1.157 -1.103 -1.411 127 SER ( 127 ) A 3 -1.635 -0.986 -1.431 -0.826 -1.098 128 ASP ( 128 ) A 3 -1.195 -0.450 -1.021 -0.889 -0.754 129 LYS ( 129 ) A 3 -0.518 -0.229 -0.158 -0.092 -0.735 130 PHE ( 130 ) A 2 -1.317 -0.769 -0.981 -0.872 -2.074 131 GLU ( 131 ) A 2 -0.599 0.227 -1.016 -0.233 -1.159 132 ILE ( 132 ) A 2 -0.914 -0.096 0.104 -1.870 -0.944 133 THR ( 133 ) A 2 -0.689 0.284 -1.181 -1.394 -1.792 134 ALA ( 134 ) A 2 -0.347 0.433 -1.534 0.000 0.000 135 THR ( 135 ) A 2 0.414 1.453 -0.578 -1.095 -0.224 136 VAL ( 136 ) A 2 0.046 1.015 -0.102 -1.537 -1.377 137 THR ( 137 ) A 2 -0.308 0.472 -0.655 -1.400 -1.147 138 SER ( 138 ) A 2 -0.248 -0.087 -0.280 0.031 -1.104 139 LEU ( 139 ) A 2 -2.250 -1.161 -2.027 -1.717 -2.007 140 THR ( 140 ) A 2 -1.239 -1.029 -0.947 -1.282 -0.838 141 ASP ( 141 ) A 3 -1.171 -0.695 -0.776 -0.788 -0.701 142 SER ( 142 ) A 3 -0.297 -0.712 0.622 -0.826 -0.742 143 ARG ( 143 ) A 3 0.610 -0.154 1.467 -1.055 1.320 144 PRO ( 144 ) A 3 0.022 -0.108 0.605 0.209 -0.572 145 LEU ( 145 ) A 3 -0.494 -0.384 1.530 -0.810 -0.880 146 GLY ( 146 ) A 3 -0.788 -0.275 -0.891 0.000 0.000 147 PRO ( 147 ) A 3 -0.776 -0.336 -1.201 0.927 -1.371 148 PHE ( 148 ) A 3 -0.884 -0.901 -0.896 -0.154 -0.318 149 ASN ( 149 ) A 3 -1.051 -0.834 -0.949 -0.979 0.332 150 VAL ( 150 ) A 3 -0.907 -1.490 0.664 -1.120 0.048 151 THR ( 151 ) A 3 -0.293 -1.078 -0.146 -1.082 0.627 152 GLU ( 152 ) A 3 -1.958 -1.166 -0.914 -1.196 -1.390 153 GLU ( 153 ) A 3 -1.329 -1.163 -0.776 -0.809 -0.468 154 GLU ( 154 ) A 3 -1.821 -0.802 -1.158 -1.119 -1.209 155 MET ( 155 ) A 3 -1.249 -0.837 -0.772 -0.560 -1.059 156 ASP ( 156 ) A 3 -1.610 -1.223 -0.875 -0.827 -0.961 157 GLN ( 157 ) A 3 -0.317 -0.217 0.099 1.068 -1.527 158 LEU ( 158 ) A 3 -0.685 -0.530 -0.880 0.851 -1.017 159 PHE ( 159 ) A 3 1.559 1.103 0.666 2.276 -0.048 160 ILE ( 160 ) A 2 -1.335 -0.734 -1.134 -1.379 -1.094 161 ASP ( 161 ) A 2 -0.709 -0.414 -0.794 -0.440 -0.758 162 HIS ( 162 ) A 2 -0.078 -0.158 -0.350 0.137 0.350 163 GLU ( 163 ) A 2 -1.676 -0.897 -1.456 -0.969 -1.942 164 ILE ( 164 ) A 2 -1.417 -0.755 -1.046 -1.317 -0.939 165 ALA ( 165 ) A 2 -1.388 -1.666 -0.215 0.000 0.000 166 MET ( 166 ) A 2 -2.297 -1.600 -1.412 -1.819 -1.950 167 ALA ( 167 ) A 3 -1.850 -0.882 -1.483 0.000 0.000 168 GLN ( 168 ) A 3 -0.826 -0.636 -0.734 -0.790 -1.186 169 CYS ( 169 ) A 3 -1.424 -1.107 -1.505 -0.977 -1.865 170 GLU ( 170 ) A 3 -0.675 -0.071 -1.255 0.109 -0.810 171 ALA ( 171 ) A 2 -1.696 -1.892 -0.632 0.000 0.000 172 GLU ( 172 ) A 2 -1.759 -1.373 -0.898 -1.106 -1.143 173 LYS ( 173 ) A 2 -0.871 -0.668 -0.127 -0.716 -0.762 174 THR ( 174 ) A 2 -1.747 -1.634 -1.504 -1.121 -1.567 175 CYS ( 175 ) A 3 -1.361 -0.923 -1.415 -1.299 -1.130 176 ASN ( 176 ) A 3 -0.452 -0.715 -0.347 0.050 0.023 177 GLY ( 177 ) A 3 -1.706 -1.382 -0.953 0.000 0.000 178 PHE ( 178 ) A 2 -3.058 -2.358 -2.229 -1.879 -2.707 179 ASP ( 179 ) A 3 -1.457 -0.844 -0.718 -0.887 -0.866 180 LEU ( 180 ) A 3 -1.523 -1.334 -0.827 -0.920 -0.586 181 GLU ( 181 ) A 3 -0.289 -0.595 1.411 -1.148 -0.772 All contacts : Average = -0.947 Z-score = -6.13 BB-BB contacts : Average = -0.509 Z-score = -3.36 BB-SC contacts : Average = -0.708 Z-score = -5.42 SC-BB contacts : Average = -0.670 Z-score = -3.98 SC-SC contacts : Average = -1.033 Z-score = -5.94 If an individual residue has a quality control value of -2.5 or worse, you should take a look at it. It can mean that the residue: is involved in symmetry contacts, or is binding a co-factor, ligand or ion, or is an active site residue, or is wrong. Average protein values ("Z-score for all contacts") can be read as follows: -5.0 Guaranteed wrong structure. Bad structure or poor model -3.0 Probably bad structure or unrefined model. Doubtful structure or model -2.0 Structure OK or good model. Good structures 0.0 Good structures. 2.0 Good structures. Unusually Good structures 4.0 Probably a strange model of a perfect helix ------------------------------------- seq.B99990003.pdb -- The packing quality control per amino acid: Average for range 1 - 182 : -2.281 If a residue has a score of -5.0 or lower, something is really going on: the residue makes symmetry contacts, is contacting a ligand or an ion, or something is wrong. Bond lengths that deviate more than 4 sigma: All bond lengths are in agreement with standard bond lengths using a tolerance of 4 sigma (both standard values and sigma for amino acids have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]) 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: 0.968 RMS-deviation in bond distances: 0.020 Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation. You have most probably seen symmetry problems earlier. Please correct these and rerun this check to see the possible implications on the X-ray cell axes. Planarity validation results: All of the side chains of residues that have a planar group are planar within expected RMS deviations. All of the atoms that are connected to planar aromatic rings in side chains of amino-acid residues are in the plane within expected RMS deviations. Since there is no DNA and no protein with hydrogens, no uncalibrated planarity check was performed. If you have detected any error, or have any question or suggestion, please send an Email to Gert Vriend. Roland Krause, Jens Erik Nielsen, Gert Vriend. The packing quality control per amino acid: ----Residue------- State AllAll BB-BB BB-SC SC-BB SC-SC --------------------------------------------------------------------------- 1 MET ( 1 ) A 3 -0.791 -0.688 -0.478 -0.944 -0.642 2 ARG ( 2 ) A 3 -1.516 -0.994 -0.572 -0.952 -1.203 3 ILE ( 3 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 4 ALA ( 4 ) A 3 -0.971 -1.078 -0.794 0.000 0.000 5 PHE ( 5 ) A 3 -1.356 -0.801 -0.898 -1.027 -0.958 6 PHE ( 6 ) A 3 -1.409 -0.948 -0.779 -1.079 -1.044 7 LEU ( 7 ) A 3 -2.110 -1.233 -1.533 -1.174 -1.419 8 LEU ( 8 ) A 3 -1.547 -1.068 -1.105 -1.015 -1.030 9 ILE ( 9 ) A 3 -1.049 -0.719 -1.144 -1.207 -1.585 10 LEU ( 10 ) A 3 -0.826 -0.754 -0.770 -0.470 -1.030 11 SER ( 11 ) A 3 -1.143 -0.729 -1.005 -0.826 -0.742 12 ILE ( 12 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 13 ILE ( 13 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 14 VAL ( 14 ) A 3 -1.352 -0.821 -0.810 -0.825 -1.086 15 GLY ( 15 ) A 3 -1.413 -1.020 -0.877 0.000 0.000 16 LEU ( 16 ) A 3 -0.826 -0.754 -0.770 -0.470 -1.030 17 ALA ( 17 ) A 3 -0.971 -1.078 -0.794 0.000 0.000 18 TYR ( 18 ) A 3 -1.539 -0.859 -1.134 -1.153 -1.399 19 GLY ( 19 ) A 3 -1.945 -1.399 -1.423 0.000 0.000 20 TYR ( 20 ) A 3 -1.338 -0.772 -0.859 -1.153 -1.209 21 SER ( 21 ) A 3 -0.350 -0.239 -0.636 0.365 0.118 22 CYS ( 22 ) A 3 -1.613 -1.114 -1.706 -1.363 -2.016 23 PRO ( 23 ) A 3 -1.181 -0.710 -0.536 -0.752 -0.493 24 LYS ( 24 ) A 3 -2.484 -1.549 -1.565 -2.202 -0.868 25 PRO ( 25 ) A 3 -0.312 -0.470 0.384 -0.752 -0.071 26 CYS ( 26 ) A 3 -0.979 -1.139 0.061 -1.077 -0.704 27 TYR ( 27 ) A 3 0.270 0.229 0.462 0.588 -0.595 28 GLY ( 28 ) A 3 -1.264 -0.335 -1.570 0.000 0.000 29 ASN ( 29 ) A 3 -0.649 0.194 -1.447 0.941 -1.502 30 MET ( 30 ) A 3 0.853 3.271 -0.755 0.566 -0.726 31 CYS ( 31 ) A 3 -0.725 -0.322 -1.312 -0.276 -0.651 32 CYS ( 32 ) A 3 -1.162 -0.626 -1.164 -1.178 -1.802 33 SER ( 33 ) A 2 -0.698 -0.574 -0.023 -1.273 -1.104 34 THR ( 34 ) A 2 -1.278 -1.070 -0.642 -1.515 -1.070 35 SER ( 35 ) A 2 -0.790 -0.342 -0.939 -1.391 -1.000 36 PRO ( 36 ) A 2 -1.189 -0.013 -1.033 -1.694 -1.807 37 ASP ( 37 ) A 2 -0.397 0.317 -0.850 -0.720 -0.391 38 HIS ( 38 ) A 2 0.486 0.965 0.590 -1.265 -0.884 39 LYS ( 39 ) A 2 0.155 0.783 -0.339 -0.359 -0.127 40 TYR ( 40 ) A 2 -0.423 -0.295 -0.489 -0.213 -0.310 41 TYR ( 41 ) A 2 -0.086 0.209 -0.476 0.196 -0.562 42 LEU ( 42 ) A 2 -1.856 -0.922 -1.796 -1.841 -1.457 43 THR ( 43 ) A 3 -0.571 -0.686 -0.605 0.099 0.079 44 ASP ( 44 ) A 3 -0.628 0.648 -0.994 -0.809 -0.699 45 PHE ( 45 ) A 3 -0.786 0.301 -1.486 0.069 -0.831 46 CYS ( 46 ) A 3 -1.175 -1.078 -0.013 -1.561 -0.847 47 GLY ( 47 ) A 3 0.149 0.819 -1.252 0.000 0.000 48 SER ( 48 ) A 3 -0.784 -0.628 -1.235 0.106 -0.137 49 THR ( 49 ) A 3 -0.857 -0.877 -0.769 0.009 -0.430 50 SER ( 50 ) A 3 0.353 0.211 0.786 -0.701 -0.595 51 ALA ( 51 ) A 3 -0.481 -0.379 -0.258 0.000 0.000 52 CYS ( 52 ) A 3 -0.970 -0.298 -1.276 -0.982 -1.872 53 GLY ( 53 ) A 3 -1.211 -1.034 -0.569 0.000 0.000 54 PRO ( 54 ) A 2 -1.507 -1.149 -1.350 -0.810 -1.302 55 LYS ( 55 ) A 2 -1.223 -1.049 -0.758 -1.337 -0.446 56 PRO ( 56 ) A 2 -0.959 -0.591 -1.167 -0.528 -0.998 57 SER ( 57 ) A 2 -0.392 0.044 -1.015 -0.387 -0.596 58 CYS ( 58 ) A 2 -0.377 0.536 0.346 -1.856 -6.117 59 SER ( 59 ) A 2 0.970 1.125 0.710 -0.601 0.874 60 GLY ( 60 ) A 2 0.292 0.690 -0.656 0.000 0.000 61 LYS ( 61 ) A 2 -0.758 -0.302 -0.740 -0.820 -0.730 62 LEU ( 62 ) A 2 -1.495 -0.802 -1.549 -0.096 -2.046 63 TYR ( 63 ) A 2 -1.610 -1.019 -1.441 -0.322 -2.196 64 PHE ( 64 ) A 3 -0.028 0.510 -0.237 0.532 -0.876 65 THR ( 65 ) A 3 -0.740 -0.733 -0.379 -1.108 -0.639 66 ALA ( 66 ) A 3 -0.649 -0.031 -0.869 0.000 0.000 67 ASP ( 67 ) A 3 0.130 2.093 -0.544 -0.405 -1.274 68 SER ( 68 ) A 3 0.141 0.855 -0.947 1.130 -1.339 69 GLN ( 69 ) A 3 -0.337 0.085 0.014 0.013 -0.842 70 ARG ( 70 ) A 3 -0.721 0.737 -0.977 0.438 -1.415 71 PHE ( 71 ) A 3 0.371 0.076 0.492 -0.443 0.700 72 GLY ( 72 ) A 1 -0.648 -0.648 -0.465 0.000 0.000 73 CYS ( 73 ) A 3 -1.093 -0.433 -1.280 -1.143 -1.903 74 GLY ( 74 ) A 3 -1.725 -0.708 -1.963 0.000 0.000 75 LYS ( 75 ) A 3 -1.234 -0.719 -0.831 -1.058 -1.346 76 HIS ( 76 ) A 3 -1.450 -1.122 -1.559 -0.760 -0.900 77 LEU ( 77 ) A 3 -0.228 0.173 0.358 0.119 -1.083 78 ASN ( 78 ) A 3 -1.212 0.147 -0.878 -1.036 -1.345 79 LEU ( 79 ) A 3 -0.497 0.229 -0.006 -0.669 -0.673 80 CYS ( 80 ) A 1 -1.184 -0.534 -1.786 -1.036 -1.824 81 ARG ( 81 ) A 1 -1.430 -1.174 -1.136 -0.688 -0.737 82 GLY ( 82 ) A 3 1.685 1.687 0.468 0.000 0.000 83 LYS ( 83 ) A 3 0.702 1.250 -0.895 2.077 -0.825 84 LYS ( 84 ) A 3 -0.280 0.802 -1.537 0.586 -0.892 85 CYS ( 85 ) A 3 -1.118 -0.137 -1.814 -0.468 -2.078 86 VAL ( 86 ) A 3 -1.082 0.204 -1.490 -0.283 -1.930 87 LYS ( 87 ) A 3 0.188 0.150 -0.515 2.009 -1.158 88 ALA ( 88 ) A 3 -0.608 -0.554 -0.242 0.000 0.000 89 LYS ( 89 ) A 3 -1.204 -0.731 -0.892 -0.520 -0.989 90 VAL ( 90 ) A 3 -0.802 -0.444 -0.437 0.251 -1.488 91 TYR ( 91 ) A 3 -0.999 -0.765 0.310 -0.991 -0.994 92 ASP ( 92 ) A 3 -0.908 -0.753 0.032 -0.769 -0.707 93 ALA ( 93 ) A 1 -1.342 -1.655 -0.329 0.000 0.000 94 GLY ( 94 ) A 3 0.462 0.631 -0.104 0.000 0.000 95 PRO ( 95 ) A 3 0.420 -0.119 -0.141 1.441 -0.033 96 ALA ( 96 ) A 3 -0.834 -0.437 -0.625 0.000 0.000 97 GLU ( 97 ) A 3 -0.979 0.707 -0.900 -0.648 -1.186 98 TRP ( 98 ) A 2 -1.552 -1.000 -1.532 0.036 -2.349 99 VAL ( 99 ) A 3 0.658 0.578 0.811 0.089 0.184 100 GLU ( 100 ) A 1 -1.169 -1.226 -0.258 -0.609 -0.674 101 LYS ( 101 ) A 3 -1.567 -0.996 -1.393 -0.431 -1.342 102 ASP ( 102 ) A 3 -0.886 -0.759 -1.122 0.873 -0.589 103 ALA ( 103 ) A 3 -1.601 -1.213 -1.116 0.000 0.000 104 GLY ( 104 ) A 3 -1.162 -1.012 -0.520 0.000 0.000 105 LYS ( 105 ) A 3 -0.476 -0.692 -0.838 -0.787 -0.304 106 MET ( 106 ) A 3 -0.696 -0.186 -0.478 -0.944 -0.642 107 ILE ( 107 ) A 3 -1.442 -0.524 -1.599 0.495 -1.724 108 ILE ( 108 ) A 3 -0.330 0.509 -1.101 -0.737 -1.501 109 ASP ( 109 ) A 3 -1.789 -0.720 -1.804 -0.257 -1.657 110 ALA ( 110 ) A 3 -1.107 -0.950 -0.480 0.000 0.000 111 SER ( 111 ) A 3 -1.319 -1.302 -0.738 -0.516 -0.446 112 PRO ( 112 ) A 3 -1.001 -0.746 -1.043 -0.418 -0.563 113 THR ( 113 ) A 1 -1.947 -2.053 -0.926 -1.613 -0.505 114 ILE ( 114 ) A 3 -0.070 0.397 0.484 -0.534 -0.565 115 CYS ( 115 ) A 2 -1.418 -1.338 -0.072 -1.560 -1.543 116 HIS ( 116 ) A 2 -1.090 -0.856 -0.038 -2.531 -0.868 117 GLU ( 117 ) A 2 -2.250 -1.922 -1.597 -1.383 -1.404 118 LEU ( 118 ) A 2 -2.080 -2.203 -1.131 -1.091 -1.228 119 THR ( 119 ) A 3 0.278 0.270 -0.396 1.767 -0.870 120 GLY ( 120 ) A 3 0.028 0.128 -0.148 0.000 0.000 121 GLY ( 121 ) A 3 0.026 -0.882 1.231 0.000 0.000 122 SER ( 122 ) A 3 -0.342 -0.356 -0.189 -0.422 -0.069 123 SER ( 123 ) A 3 -0.404 -0.806 0.541 -1.069 0.532 124 CYS ( 124 ) A 3 -1.215 -1.216 -0.364 -1.567 -0.230 125 GLY ( 125 ) A 3 -2.175 -1.633 -1.318 0.000 0.000 126 TRP ( 126 ) A 3 -1.547 -0.632 -1.449 -1.121 -1.411 127 SER ( 127 ) A 3 -1.309 -1.203 -1.354 -0.848 -0.266 128 ASP ( 128 ) A 3 -0.669 -0.759 -0.565 -0.201 -0.320 129 LYS ( 129 ) A 3 -0.518 -0.379 -0.498 0.694 -1.059 130 PHE ( 130 ) A 2 -2.318 -1.429 -1.798 -1.065 -2.978 131 GLU ( 131 ) A 2 -0.257 0.324 -1.055 0.217 -0.653 132 ILE ( 132 ) A 2 -0.836 -0.390 0.788 -1.816 -0.761 133 THR ( 133 ) A 2 -0.142 0.053 0.258 -0.614 -1.034 134 ALA ( 134 ) A 2 -0.364 0.494 -1.679 0.000 0.000 135 THR ( 135 ) A 2 0.237 1.502 -1.046 -1.621 0.108 136 VAL ( 136 ) A 2 1.079 0.983 0.254 0.556 2.010 137 THR ( 137 ) A 2 -0.583 0.022 -0.274 -1.470 -1.547 138 SER ( 138 ) A 2 -0.065 0.003 0.397 -0.864 -0.509 139 LEU ( 139 ) A 2 -1.627 -0.973 -1.001 -1.046 -1.869 140 THR ( 140 ) A 2 -1.029 -1.069 -0.567 -0.833 -0.039 141 ASP ( 141 ) A 3 -1.365 -0.895 -0.825 -0.671 -0.951 142 SER ( 142 ) A 3 -0.660 -0.607 -0.494 -0.826 0.028 143 ARG ( 143 ) A 3 -1.186 -0.463 -0.212 -0.494 -1.286 144 PRO ( 144 ) A 3 0.061 -0.341 0.715 0.564 -0.483 145 LEU ( 145 ) A 3 -1.262 -1.086 0.042 -1.060 -0.887 146 GLY ( 146 ) A 3 -0.859 -0.781 -0.340 0.000 0.000 147 PRO ( 147 ) A 3 -0.104 -0.386 0.454 -0.037 -0.284 148 PHE ( 148 ) A 3 -0.734 -0.299 -0.262 0.167 -1.044 149 ASN ( 149 ) A 3 -0.257 -0.570 1.178 -1.054 -0.237 150 VAL ( 150 ) A 3 -1.293 -0.888 -0.653 -0.934 -1.058 151 THR ( 151 ) A 3 -0.309 -1.078 -0.038 -1.082 0.155 152 GLU ( 152 ) A 3 -1.921 -1.103 -0.953 -1.027 -1.218 153 GLU ( 153 ) A 3 -0.961 -0.612 -0.609 -1.148 -0.810 154 GLU ( 154 ) A 3 -1.439 -0.930 -1.255 -1.148 -0.810 155 MET ( 155 ) A 3 -0.788 -0.477 -0.447 1.009 -1.275 156 ASP ( 156 ) A 3 -0.996 -0.503 -0.292 -1.205 -0.669 157 GLN ( 157 ) A 3 -0.997 -0.342 -0.688 -0.088 -1.509 158 LEU ( 158 ) A 3 -0.396 -0.681 -0.386 0.559 -0.359 159 PHE ( 159 ) A 2 -2.965 -2.376 -1.831 -2.032 -2.547 160 ILE ( 160 ) A 3 -0.971 -0.843 0.104 -0.448 -0.695 161 ASP ( 161 ) A 2 -0.726 -0.413 0.210 -1.113 -0.961 162 HIS ( 162 ) A 2 -0.562 -0.271 -0.753 -0.719 -0.284 163 GLU ( 163 ) A 3 -0.787 -0.117 -1.160 0.407 -0.740 164 ILE ( 164 ) A 3 0.973 0.818 -0.586 0.232 0.325 165 ALA ( 165 ) A 2 -1.417 -1.703 -0.215 0.000 0.000 166 MET ( 166 ) A 2 -2.196 -1.565 -1.270 -1.938 -1.721 167 ALA ( 167 ) A 3 -1.884 -0.878 -1.533 0.000 0.000 168 GLN ( 168 ) A 3 -0.923 -0.635 -0.733 -0.900 -1.186 169 CYS ( 169 ) A 3 -1.488 -1.097 -1.708 -1.016 -1.951 170 GLU ( 170 ) A 3 -0.331 -0.037 -1.255 0.598 -0.507 171 ALA ( 171 ) A 2 -2.011 -1.961 -1.265 0.000 0.000 172 GLU ( 172 ) A 2 -1.596 -1.002 -0.842 -0.997 -0.809 173 LYS ( 173 ) A 3 -0.477 -0.090 -0.505 -0.243 -0.683 174 THR ( 174 ) A 2 -1.924 -1.482 -1.966 -1.243 -2.071 175 CYS ( 175 ) A 2 -1.851 -0.997 -2.119 -1.732 0.000 176 ASN ( 176 ) A 3 -0.614 -0.567 -0.331 -0.127 -0.633 177 GLY ( 177 ) A 3 -0.740 -0.853 0.299 0.000 0.000 178 PHE ( 178 ) A 3 -1.382 -0.832 -0.691 -0.795 -0.986 179 ASP ( 179 ) A 3 -1.322 -0.821 -0.431 -0.889 -0.825 180 LEU ( 180 ) A 3 -1.797 -1.364 -0.952 -1.299 -0.738 181 GLU ( 181 ) A 3 0.063 -0.311 1.760 -1.148 -0.585 All contacts : Average = -0.877 Z-score = -5.68 BB-BB contacts : Average = -0.477 Z-score = -3.16 BB-SC contacts : Average = -0.675 Z-score = -5.17 SC-BB contacts : Average = -0.567 Z-score = -3.35 SC-SC contacts : Average = -0.990 Z-score = -5.69 If an individual residue has a quality control value of -2.5 or worse, you should take a look at it. It can mean that the residue: is involved in symmetry contacts, or is binding a co-factor, ligand or ion, or is an active site residue, or is wrong. Average protein values ("Z-score for all contacts") can be read as follows: -5.0 Guaranteed wrong structure. Bad structure or poor model -3.0 Probably bad structure or unrefined model. Doubtful structure or model -2.0 Structure OK or good model. Good structures 0.0 Good structures. 2.0 Good structures. Unusually Good structures 4.0 Probably a strange model of a perfect helix ------------------------------------- seq.B99990004.pdb -- The packing quality control per amino acid: Average for range 1 - 182 : -2.347 If a residue has a score of -5.0 or lower, something is really going on: the residue makes symmetry contacts, is contacting a ligand or an ion, or something is wrong. Bond lengths that deviate more than 4 sigma: All bond lengths are in agreement with standard bond lengths using a tolerance of 4 sigma (both standard values and sigma for amino acids have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]) 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: 0.968 RMS-deviation in bond distances: 0.020 Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation. You have most probably seen symmetry problems earlier. Please correct these and rerun this check to see the possible implications on the X-ray cell axes. Planarity validation results: The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect. 98 TRP ( 98 ) A 4.54 All of the atoms that are connected to planar aromatic rings in side chains of amino-acid residues are in the plane within expected RMS deviations. Since there is no DNA and no protein with hydrogens, no uncalibrated planarity check was performed. The packing quality control per amino acid: ----Residue------- State AllAll BB-BB BB-SC SC-BB SC-SC --------------------------------------------------------------------------- 1 MET ( 1 ) A 3 -0.791 -0.688 -0.478 -0.944 -0.642 2 ARG ( 2 ) A 3 -1.516 -0.994 -0.572 -0.952 -1.203 3 ILE ( 3 ) A 3 -1.834 -1.013 -1.146 -1.207 -1.585 4 ALA ( 4 ) A 3 -1.669 -1.078 -1.201 0.000 0.000 5 PHE ( 5 ) A 3 -1.356 -0.801 -0.898 -1.027 -0.958 6 PHE ( 6 ) A 3 -1.356 -0.801 -0.898 -1.027 -0.958 7 LEU ( 7 ) A 3 -2.110 -1.233 -1.533 -1.174 -1.419 8 LEU ( 8 ) A 3 -2.110 -1.233 -1.533 -1.174 -1.419 9 ILE ( 9 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 10 LEU ( 10 ) A 3 -0.826 -0.754 -0.770 -0.470 -1.030 11 SER ( 11 ) A 3 -1.143 -0.729 -1.005 -0.826 -0.742 12 ILE ( 12 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 13 ILE ( 13 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 14 VAL ( 14 ) A 3 -1.352 -0.821 -0.810 -0.825 -1.086 15 GLY ( 15 ) A 3 -1.413 -1.020 -0.877 0.000 0.000 16 LEU ( 16 ) A 3 -0.786 -0.754 -0.737 -0.470 -1.030 17 ALA ( 17 ) A 3 -0.764 -1.078 -0.668 0.000 0.000 18 TYR ( 18 ) A 3 -1.539 -0.859 -1.134 -1.153 -1.399 19 GLY ( 19 ) A 3 -1.413 -1.020 -0.877 0.000 0.000 20 TYR ( 20 ) A 3 -1.512 -0.859 -1.074 -1.153 -1.382 21 SER ( 21 ) A 3 -1.183 -0.903 -1.060 -0.248 -0.477 22 CYS ( 22 ) A 3 -1.678 -1.207 -1.754 -1.379 -2.034 23 PRO ( 23 ) A 3 -1.194 -0.710 -0.817 -0.752 -0.831 24 LYS ( 24 ) A 3 -2.062 -1.532 -1.511 -1.344 -0.862 25 PRO ( 25 ) A 3 -0.591 -0.710 0.386 -0.752 -0.618 26 CYS ( 26 ) A 3 -1.147 -1.154 -0.305 -1.166 -1.124 27 TYR ( 27 ) A 3 -0.485 0.043 -0.212 -0.464 -0.920 28 GLY ( 28 ) A 3 -1.101 -0.763 -0.749 0.000 0.000 29 ASN ( 29 ) A 3 -0.509 0.362 -0.092 -0.926 -1.191 30 MET ( 30 ) A 3 1.663 3.846 0.228 1.012 -0.562 31 CYS ( 31 ) A 3 -0.607 0.124 -1.077 -0.646 -0.805 32 CYS ( 32 ) A 3 -0.926 -0.374 -0.801 -1.168 -1.594 33 SER ( 33 ) A 3 -0.332 -0.669 0.380 -0.774 0.164 34 THR ( 34 ) A 2 -0.855 -0.958 0.511 -1.402 -0.868 35 SER ( 35 ) A 2 -0.612 -0.580 -0.558 -0.256 -0.020 36 PRO ( 36 ) A 2 -1.283 -0.064 -1.175 -1.801 -1.810 37 ASP ( 37 ) A 2 -0.708 -0.149 -0.250 -0.825 -1.030 38 HIS ( 38 ) A 2 0.969 0.981 1.545 -0.982 0.239 39 LYS ( 39 ) A 2 -0.418 0.662 -0.672 -0.381 -1.691 40 TYR ( 40 ) A 2 -0.775 -0.010 -1.423 0.070 -1.585 41 TYR ( 41 ) A 2 0.202 -0.040 0.037 0.062 1.047 42 LEU ( 42 ) A 2 -0.268 0.602 -0.907 -0.931 -0.498 43 THR ( 43 ) A 3 -0.998 -0.662 -1.027 -0.886 -0.728 44 ASP ( 44 ) A 3 -0.993 0.154 -1.197 -0.725 -0.972 45 PHE ( 45 ) A 2 -1.717 -1.027 -1.942 -1.224 -1.336 46 CYS ( 46 ) A 3 -1.107 -0.602 -1.429 -1.052 -1.263 47 GLY ( 47 ) A 3 -0.564 0.396 -1.794 0.000 0.000 48 SER ( 48 ) A 2 -1.226 -1.395 -0.641 -0.403 0.430 49 THR ( 49 ) A 3 -0.955 -1.341 -0.718 -0.436 0.377 50 SER ( 50 ) A 3 -0.278 -0.018 -0.305 -0.684 -0.346 51 ALA ( 51 ) A 3 -0.471 -0.412 -0.208 0.000 0.000 52 CYS ( 52 ) A 3 -1.293 -0.702 -1.506 -1.196 -1.885 53 GLY ( 53 ) A 3 -1.392 -0.513 -1.540 0.000 0.000 54 PRO ( 54 ) A 2 -1.675 -1.571 -1.022 -1.337 -1.197 55 LYS ( 55 ) A 2 -1.438 -1.255 -0.578 -1.379 -0.950 56 PRO ( 56 ) A 2 -1.028 -0.410 -1.196 -0.728 -1.399 57 SER ( 57 ) A 2 -0.348 0.060 -0.582 -0.493 -1.353 58 CYS ( 58 ) A 2 0.057 0.365 0.071 -0.840 4.039 59 SER ( 59 ) A 2 1.208 1.037 0.442 1.125 1.769 60 GLY ( 60 ) A 2 0.166 0.465 -0.527 0.000 0.000 61 LYS ( 61 ) A 2 -1.254 -0.646 -0.563 -1.434 -1.393 62 LEU ( 62 ) A 2 -1.538 -0.938 -1.439 -0.814 -1.733 63 TYR ( 63 ) A 2 -1.224 -0.823 -1.579 0.167 -1.735 64 PHE ( 64 ) A 3 0.102 0.308 0.150 0.330 -0.354 65 THR ( 65 ) A 3 -0.500 -0.727 0.183 -0.889 -0.255 66 ALA ( 66 ) A 3 -0.358 -0.602 0.156 0.000 0.000 67 ASP ( 67 ) A 3 0.896 2.126 0.269 0.791 -0.980 68 SER ( 68 ) A 3 -0.028 0.840 -1.258 1.150 -1.521 69 GLN ( 69 ) A 3 -0.520 -0.121 -0.397 0.218 -0.909 70 ARG ( 70 ) A 3 0.126 0.902 -0.200 -0.063 -0.265 71 PHE ( 71 ) A 3 -0.472 0.574 -1.282 -0.967 -0.186 72 GLY ( 72 ) A 1 -1.473 -1.441 -1.107 0.000 0.000 73 CYS ( 73 ) A 3 -0.250 -0.809 0.182 -0.341 1.342 74 GLY ( 74 ) A 3 -1.292 -0.971 -0.964 0.000 0.000 75 LYS ( 75 ) A 3 -1.260 -0.770 -0.831 -1.059 -1.346 76 HIS ( 76 ) A 3 -0.770 -1.241 -0.452 -1.305 0.768 77 LEU ( 77 ) A 3 -1.847 -0.475 -1.402 -0.847 -1.631 78 ASN ( 78 ) A 3 -1.493 -0.120 -1.558 -1.061 -0.986 79 LEU ( 79 ) A 3 -1.668 -0.239 -1.092 -0.953 -1.736 80 CYS ( 80 ) A 1 -0.522 0.429 -1.810 -0.769 -0.845 81 ARG ( 81 ) A 1 -1.943 -1.320 -1.359 -1.487 -1.217 82 GLY ( 82 ) A 3 1.163 1.870 -0.600 0.000 0.000 83 LYS ( 83 ) A 3 0.043 1.160 -1.397 1.743 -1.556 84 LYS ( 84 ) A 3 -0.388 0.490 -1.084 0.822 -1.302 85 CYS ( 85 ) A 3 -0.267 0.277 -1.444 0.483 -1.562 86 VAL ( 86 ) A 3 -0.970 0.177 -1.742 0.150 -1.637 87 LYS ( 87 ) A 3 0.010 0.583 -1.248 1.199 -0.799 88 ALA ( 88 ) A 3 0.292 0.036 0.361 0.000 0.000 89 LYS ( 89 ) A 3 -1.094 -0.590 -0.862 0.320 -1.596 90 VAL ( 90 ) A 3 -1.126 -0.168 -1.455 -0.037 -1.685 91 TYR ( 91 ) A 3 -0.847 -0.672 -0.481 -0.676 -0.125 92 ASP ( 92 ) A 3 -1.029 -1.115 -1.297 0.025 -0.332 93 ALA ( 93 ) A 1 -1.575 -1.844 -0.524 0.000 0.000 94 GLY ( 94 ) A 3 -0.205 0.122 -0.485 0.000 0.000 95 PRO ( 95 ) A 3 -0.551 0.001 -0.182 -0.092 -0.958 96 ALA ( 96 ) A 3 -0.812 -0.489 -0.596 0.000 0.000 97 GLU ( 97 ) A 3 -1.808 0.123 -1.474 -0.274 -1.831 98 TRP ( 98 ) A 2 -2.306 -1.583 -2.146 -0.580 -2.679 99 VAL ( 99 ) A 3 0.184 0.566 -0.385 0.038 -0.012 100 GLU ( 100 ) A 1 -1.021 -1.006 -0.620 -0.314 -0.654 101 LYS ( 101 ) A 3 -1.023 -0.905 -0.275 -0.629 -0.753 102 ASP ( 102 ) A 3 -0.936 -0.840 -0.779 0.016 -0.789 103 ALA ( 103 ) A 3 -1.608 -1.669 -0.347 0.000 0.000 104 GLY ( 104 ) A 3 -1.106 -1.164 -0.231 0.000 0.000 105 LYS ( 105 ) A 3 -1.269 -1.066 -1.215 -0.932 -0.181 106 MET ( 106 ) A 3 -0.707 -0.243 -0.477 -0.944 -0.642 107 ILE ( 107 ) A 3 -1.590 -0.073 -1.711 -0.389 -1.743 108 ILE ( 108 ) A 3 -0.331 0.436 -0.818 0.389 -1.129 109 ASP ( 109 ) A 3 -1.414 -0.821 -0.952 -0.129 -1.427 110 ALA ( 110 ) A 3 -0.991 -0.788 -0.505 0.000 0.000 111 SER ( 111 ) A 3 -1.696 -1.594 -0.934 -0.402 -1.123 112 PRO ( 112 ) A 3 0.349 -0.122 0.543 0.282 0.250 113 THR ( 113 ) A 1 -1.324 -1.398 -0.263 -1.425 -0.591 114 ILE ( 114 ) A 3 -0.824 0.155 -0.312 -0.912 -1.086 115 CYS ( 115 ) A 2 -1.568 -1.493 -0.504 -1.389 -1.441 116 HIS ( 116 ) A 2 -1.456 -1.068 -0.577 -1.579 -0.808 117 GLU ( 117 ) A 2 -2.279 -1.879 -1.737 -1.232 -1.597 118 LEU ( 118 ) A 2 -2.410 -2.355 -1.248 -1.119 -1.988 119 THR ( 119 ) A 2 -1.764 -1.575 -1.552 -1.239 -1.652 120 GLY ( 120 ) A 3 -0.268 -0.650 0.416 0.000 0.000 121 GLY ( 121 ) A 3 -0.537 -1.077 0.547 0.000 0.000 122 SER ( 122 ) A 3 -0.837 -0.698 -0.737 -0.572 -0.771 123 SER ( 123 ) A 3 -0.865 -1.237 -0.190 -0.844 0.849 124 CYS ( 124 ) A 3 -1.050 -0.732 -0.424 -1.331 -1.415 125 GLY ( 125 ) A 3 -2.042 -1.599 -1.151 0.000 0.000 126 TRP ( 126 ) A 3 -1.648 -0.795 -1.573 -1.121 -1.406 127 SER ( 127 ) A 3 -1.212 -1.037 -1.290 -0.828 -0.578 128 ASP ( 128 ) A 3 -1.180 -0.775 -0.193 -0.875 -0.758 129 LYS ( 129 ) A 3 -1.414 -1.190 -0.553 -0.903 -0.844 130 PHE ( 130 ) A 2 -2.296 -1.237 -1.941 -1.221 -2.998 131 GLU ( 131 ) A 2 -0.305 0.510 -0.584 0.044 -1.185 132 ILE ( 132 ) A 2 -0.728 -0.279 0.819 -1.772 -0.575 133 THR ( 133 ) A 2 -0.593 -0.119 -0.867 -0.666 -1.621 134 ALA ( 134 ) A 2 -0.332 0.366 -1.384 0.000 0.000 135 THR ( 135 ) A 2 1.076 1.474 -0.800 1.128 1.203 136 VAL ( 136 ) A 2 -0.029 0.848 0.147 -1.551 -0.521 137 THR ( 137 ) A 2 -0.439 0.250 -0.563 -1.165 -1.606 138 SER ( 138 ) A 2 -0.615 -0.334 -0.826 0.041 -1.482 139 LEU ( 139 ) A 2 -1.134 -0.468 -1.525 -0.601 -1.139 140 THR ( 140 ) A 2 -1.379 -1.178 -1.048 -1.284 -1.179 141 ASP ( 141 ) A 3 -1.490 -0.861 -0.996 -0.931 -0.966 142 SER ( 142 ) A 3 -1.124 -0.721 -0.977 -0.826 -0.742 143 ARG ( 143 ) A 3 -0.226 -0.073 0.223 -0.936 0.105 144 PRO ( 144 ) A 3 -0.408 -0.245 0.224 -0.202 -0.707 145 LEU ( 145 ) A 3 -1.015 -0.750 -0.315 -0.693 -0.718 146 GLY ( 146 ) A 3 -1.966 -1.249 -1.487 0.000 0.000 147 PRO ( 147 ) A 3 -1.347 -0.483 -1.414 0.588 -1.820 148 PHE ( 148 ) A 3 -1.761 -1.051 -0.915 -1.485 -1.086 149 ASN ( 149 ) A 3 -1.205 -1.224 -0.179 -0.979 -0.713 150 VAL ( 150 ) A 3 -1.275 -1.356 -0.854 -0.640 0.418 151 THR ( 151 ) A 3 -1.051 -1.078 -0.973 -1.082 -0.813 152 GLU ( 152 ) A 3 -1.748 -1.176 -1.021 -1.134 -1.030 153 GLU ( 153 ) A 3 -0.961 -0.612 -0.894 -1.148 -0.810 154 GLU ( 154 ) A 3 -2.188 -1.239 -1.546 -1.148 -1.240 155 MET ( 155 ) A 3 -1.266 -0.583 -1.533 0.559 -1.561 156 ASP ( 156 ) A 3 -1.968 -1.271 -1.459 -0.699 -1.434 157 GLN ( 157 ) A 3 0.356 -0.378 -0.203 2.886 -0.887 158 LEU ( 158 ) A 3 -1.357 -0.384 -1.435 0.065 -1.558 159 PHE ( 159 ) A 3 -0.374 0.250 -0.958 0.299 -0.494 160 ILE ( 160 ) A 2 -0.794 -0.633 0.422 -1.324 -0.065 161 ASP ( 161 ) A 2 -0.865 -0.135 0.055 -1.109 -1.525 162 HIS ( 162 ) A 3 0.579 0.862 -0.872 1.154 0.164 163 GLU ( 163 ) A 2 -1.057 -0.307 -1.383 -0.328 -1.417 164 ILE ( 164 ) A 2 -0.783 -1.064 -0.756 -0.395 0.865 165 ALA ( 165 ) A 2 -1.640 -1.674 -0.874 0.000 0.000 166 MET ( 166 ) A 2 -2.716 -1.646 -1.176 -1.903 -1.612 167 ALA ( 167 ) A 3 -1.036 -0.446 -0.985 0.000 0.000 168 GLN ( 168 ) A 3 -0.921 -0.628 -0.734 -0.900 -1.186 169 CYS ( 169 ) A 3 -2.094 -1.843 -2.027 -1.638 -1.367 170 GLU ( 170 ) A 3 1.488 -0.237 0.415 -0.316 2.383 171 ALA ( 171 ) A 2 -1.681 -1.914 -0.539 0.000 0.000 172 GLU ( 172 ) A 2 -1.529 -1.370 -0.337 -1.171 -0.782 173 LYS ( 173 ) A 2 -0.383 -0.631 -0.426 0.092 0.113 174 THR ( 174 ) A 2 -1.704 -1.577 -1.371 -1.119 -1.305 175 CYS ( 175 ) A 3 -1.692 -1.491 -1.151 -1.616 -0.995 176 ASN ( 176 ) A 3 -1.737 -1.206 -1.423 -0.790 -0.675 177 GLY ( 177 ) A 3 -1.344 -0.984 -0.484 0.000 0.000 178 PHE ( 178 ) A 2 -2.948 -2.345 -2.176 -1.810 -2.447 179 ASP ( 179 ) A 3 -1.470 -0.860 -0.734 -0.888 -0.866 180 LEU ( 180 ) A 3 -1.663 -1.311 -0.996 -1.211 -0.569 181 GLU ( 181 ) A 3 0.052 -0.605 2.203 -1.148 -0.647 All contacts : Average = -0.980 Z-score = -6.34 BB-BB contacts : Average = -0.561 Z-score = -3.69 BB-SC contacts : Average = -0.770 Z-score = -5.89 SC-BB contacts : Average = -0.634 Z-score = -3.76 SC-SC contacts : Average = -0.946 Z-score = -5.42 If an individual residue has a quality control value of -2.5 or worse, you should take a look at it. It can mean that the residue: is involved in symmetry contacts, or is binding a co-factor, ligand or ion, or is an active site residue, or is wrong. Average protein values ("Z-score for all contacts") can be read as follows: -5.0 Guaranteed wrong structure. Bad structure or poor model -3.0 Probably bad structure or unrefined model. Doubtful structure or model -2.0 Structure OK or good model. Good structures 0.0 Good structures. 2.0 Good structures. Unusually Good structures 4.0 Probably a strange model of a perfect helix ------------------------------------- seq.B99990005.pdb -- The packing quality control per amino acid: Average for range 1 - 182 : -2.203 If a residue has a score of -5.0 or lower, something is really going on: the residue makes symmetry contacts, is contacting a ligand or an ion, or something is wrong. Bond lengths that deviate more than 4 sigma: The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given. Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length. 157 GLN ( 157 ) A N CA 1.55 4.7 157 GLN ( 157 ) A CA C 1.83 14.5 157 GLN ( 157 ) A N -C 1.46 6.7 158 LEU ( 158 ) A N CA 1.64 9.6 158 LEU ( 158 ) A N -C 1.55 10.9 Bond lengths were found to deviate normally from the standard bond lengths (values for Protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). RMS Z-score for bond lengths: 1.031 RMS-deviation in bond distances: 0.021 Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation. You have most probably seen symmetry problems earlier. Please correct these and rerun this check to see the possible implications on the X-ray cell axes. Planarity validation results: All of the side chains of residues that have a planar group are planar within expected RMS deviations. All of the atoms that are connected to planar aromatic rings in side chains of amino-acid residues are in the plane within expected RMS deviations. Since there is no DNA and no protein with hydrogens, no uncalibrated planarity check was performed. The packing quality control per amino acid: ----Residue------- State AllAll BB-BB BB-SC SC-BB SC-SC --------------------------------------------------------------------------- 1 MET ( 1 ) A 3 -0.790 -0.688 -0.478 -0.940 -0.642 2 ARG ( 2 ) A 3 -1.516 -0.994 -0.816 -0.952 -1.203 3 ILE ( 3 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 4 ALA ( 4 ) A 3 -1.669 -1.078 -1.201 0.000 0.000 5 PHE ( 5 ) A 3 -1.356 -0.801 -0.898 -1.027 -0.958 6 PHE ( 6 ) A 3 -1.356 -0.801 -0.898 -1.027 -0.958 7 LEU ( 7 ) A 3 -2.110 -1.233 -1.533 -1.174 -1.419 8 LEU ( 8 ) A 3 -1.547 -1.068 -1.105 -1.015 -1.030 9 ILE ( 9 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 10 LEU ( 10 ) A 3 -0.826 -0.754 -0.770 -0.470 -1.030 11 SER ( 11 ) A 3 -1.143 -0.729 -1.005 -0.826 -0.742 12 ILE ( 12 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 13 ILE ( 13 ) A 3 -1.049 -0.719 -1.145 -1.207 -1.585 14 VAL ( 14 ) A 3 -1.352 -0.821 -0.810 -0.825 -1.086 15 GLY ( 15 ) A 3 -1.413 -1.020 -0.877 0.000 0.000 16 LEU ( 16 ) A 3 -0.826 -0.754 -0.770 -0.470 -1.030 17 ALA ( 17 ) A 3 -0.971 -1.078 -0.794 0.000 0.000 18 TYR ( 18 ) A 3 -1.539 -0.859 -1.134 -1.153 -1.399 19 GLY ( 19 ) A 3 -1.413 -1.020 -0.877 0.000 0.000 20 TYR ( 20 ) A 3 -1.502 -0.859 -1.127 -1.153 -1.276 21 SER ( 21 ) A 3 -1.632 -0.986 -1.429 -0.826 -1.085 22 CYS ( 22 ) A 3 -1.678 -1.207 -1.754 -1.379 -2.034 23 PRO ( 23 ) A 3 -1.137 -0.710 -0.817 -0.752 -0.668 24 LYS ( 24 ) A 3 -1.857 -1.526 -1.285 -1.350 -0.552 25 PRO ( 25 ) A 3 -0.376 -0.710 0.438 -0.752 -0.077 26 CYS ( 26 ) A 3 -1.253 -1.207 -0.676 -1.310 -0.699 27 TYR ( 27 ) A 3 -0.116 0.547 -0.481 0.544 -1.119 28 GLY ( 28 ) A 3 -0.989 -0.419 -1.117 0.000 0.000 29 ASN ( 29 ) A 3 -1.374 0.265 -1.529 -0.776 -1.989 30 MET ( 30 ) A 3 -0.839 1.469 -1.312 -0.350 -1.123 31 CYS ( 31 ) A 3 -0.410 0.249 -1.195 -0.270 -1.088 32 CYS ( 32 ) A 3 -0.870 -0.259 -0.896 -1.144 -1.483 33 SER ( 33 ) A 2 -0.731 -1.103 0.878 -1.565 0.668 34 THR ( 34 ) A 2 -0.563 -0.811 1.453 -1.326 -0.972 35 SER ( 35 ) A 2 -0.101 0.091 -0.288 -0.888 0.452 36 PRO ( 36 ) A 2 -0.604 0.634 -1.154 -0.712 -1.869 37 ASP ( 37 ) A 2 -0.387 0.449 -0.246 -0.630 -1.192 38 HIS ( 38 ) A 2 1.347 1.041 2.755 -0.912 0.634 39 LYS ( 39 ) A 2 -0.164 1.131 -0.534 -0.235 -1.865 40 TYR ( 40 ) A 2 -0.716 0.473 -1.794 -0.538 -1.554 41 TYR ( 41 ) A 2 -0.040 0.178 -0.542 0.256 -0.208 42 LEU ( 42 ) A 2 -0.136 0.127 -0.990 0.200 -0.840 43 THR ( 43 ) A 2 -0.979 -0.918 -0.707 -1.350 0.092 44 ASP ( 44 ) A 3 -0.948 0.142 -0.987 -0.741 -1.038 45 PHE ( 45 ) A 2 -1.437 -1.198 -1.323 -1.027 -0.727 46 CYS ( 46 ) A 3 -0.812 -0.612 0.116 -1.407 -0.510 47 GLY ( 47 ) A 3 -0.114 0.775 -1.519 0.000 0.000 48 SER ( 48 ) A 3 -0.445 -0.414 -0.478 -0.891 0.959 49 THR ( 49 ) A 3 -0.955 -0.973 -0.721 -0.402 -0.293 50 SER ( 50 ) A 3 0.226 0.530 0.013 -0.447 -0.473 51 ALA ( 51 ) A 3 -0.588 -0.200 -0.601 0.000 0.000 52 CYS ( 52 ) A 3 -0.917 -0.315 -1.203 -0.929 -1.630 53 GLY ( 53 ) A 3 -1.951 -1.309 -1.385 0.000 0.000 54 PRO ( 54 ) A 2 -1.022 -1.065 -0.158 -0.840 -0.670 55 LYS ( 55 ) A 2 -1.127 -1.110 0.275 -1.337 -0.884 56 PRO ( 56 ) A 2 -0.939 -0.873 -0.392 -0.740 -0.828 57 SER ( 57 ) A 2 -0.507 0.001 -0.549 -1.104 -1.616 58 CYS ( 58 ) A 2 -0.052 0.320 -0.700 -0.040 -0.786 59 SER ( 59 ) A 2 0.527 0.672 -0.371 0.742 0.499 60 GLY ( 60 ) A 2 -0.041 0.319 -0.785 0.000 0.000 61 LYS ( 61 ) A 2 -1.517 -0.568 -1.237 -1.632 -1.519 62 LEU ( 62 ) A 2 -1.603 -0.906 -1.524 -0.816 -2.016 63 TYR ( 63 ) A 2 -1.503 -1.159 -1.213 -0.209 -1.807 64 PHE ( 64 ) A 3 -0.588 0.200 -0.230 -0.224 -0.948 65 THR ( 65 ) A 3 -0.823 -0.611 -0.585 -1.144 -1.020 66 ALA ( 66 ) A 3 -0.629 -0.350 -0.494 0.000 0.000 67 ASP ( 67 ) A 3 0.106 1.952 -0.836 -0.155 -1.127 68 SER ( 68 ) A 3 0.132 0.664 -1.104 1.813 -1.211 69 GLN ( 69 ) A 3 -1.186 -0.023 -1.049 -0.291 -1.576 70 ARG ( 70 ) A 3 -0.330 0.553 -0.966 0.352 -0.740 71 PHE ( 71 ) A 3 -0.624 -0.298 -0.219 -1.034 -0.189 72 GLY ( 72 ) A 1 -0.451 -0.331 -0.499 0.000 0.000 73 CYS ( 73 ) A 3 -1.176 -0.564 -1.336 -1.169 -1.871 74 GLY ( 74 ) A 3 -1.769 -0.702 -2.046 0.000 0.000 75 LYS ( 75 ) A 3 -1.235 -0.721 -0.605 -1.058 -1.346 76 HIS ( 76 ) A 3 -1.375 -1.704 -0.115 -1.671 -0.428 77 LEU ( 77 ) A 3 -0.478 -0.392 0.513 0.062 -1.085 78 ASN ( 78 ) A 3 -1.115 -0.006 -0.774 -0.866 -1.168 79 LEU ( 79 ) A 3 -1.499 -0.022 -0.457 -1.418 -1.630 80 CYS ( 80 ) A 1 -1.330 -0.809 -1.950 -0.985 -1.843 81 ARG ( 81 ) A 3 -0.533 0.362 -0.081 -0.578 -0.675 82 GLY ( 82 ) A 3 0.698 1.576 -0.955 0.000 0.000 83 LYS ( 83 ) A 3 0.834 1.173 -1.060 2.046 -0.387 84 LYS ( 84 ) A 3 -0.088 0.898 -0.878 0.618 -0.941 85 CYS ( 85 ) A 3 -1.326 -0.684 -1.440 -0.851 -1.658 86 VAL ( 86 ) A 3 -0.883 -0.173 -1.048 0.027 -1.283 87 LYS ( 87 ) A 3 -0.494 -0.199 -0.658 0.342 -0.801 88 ALA ( 88 ) A 3 0.199 -0.441 0.752 0.000 0.000 89 LYS ( 89 ) A 3 -1.162 -0.721 -0.343 0.191 -1.790 90 VAL ( 90 ) A 3 -1.089 -0.493 -1.106 0.147 -1.535 91 TYR ( 91 ) A 3 -0.912 -0.890 0.388 -0.939 -0.396 92 ASP ( 92 ) A 3 -0.932 -1.008 0.495 -1.226 -0.512 93 ALA ( 93 ) A 3 -0.729 -0.638 -0.318 0.000 0.000 94 GLY ( 94 ) A 3 -0.304 0.400 -1.007 0.000 0.000 95 PRO ( 95 ) A 3 0.747 0.172 -0.057 1.413 0.347 96 ALA ( 96 ) A 3 -0.193 -0.432 0.200 0.000 0.000 97 GLU ( 97 ) A 3 -1.158 0.159 -0.582 0.352 -1.537 98 TRP ( 98 ) A 2 -2.170 -1.563 -1.816 -0.651 -2.473 99 VAL ( 99 ) A 3 0.800 0.541 0.927 -0.058 0.683 100 GLU ( 100 ) A 1 -1.173 -1.245 -0.574 -0.523 -0.532 101 LYS ( 101 ) A 3 -0.995 -1.314 -0.573 -0.594 -0.092 102 ASP ( 102 ) A 3 -1.392 -0.862 -1.017 -0.857 -0.861 103 ALA ( 103 ) A 3 -1.450 -1.455 -0.619 0.000 0.000 104 GLY ( 104 ) A 3 -0.787 -1.457 0.659 0.000 0.000 105 LYS ( 105 ) A 3 -1.826 -1.458 -1.182 -1.146 -1.023 106 MET ( 106 ) A 3 -1.109 -0.306 -1.089 -0.553 -0.744 107 ILE ( 107 ) A 3 -1.488 -0.125 -1.729 0.116 -1.793 108 ILE ( 108 ) A 3 -1.145 -0.507 -0.887 -0.650 -1.015 109 ASP ( 109 ) A 3 -1.614 -0.900 -1.049 -0.486 -1.482 110 ALA ( 110 ) A 3 -1.051 -1.000 -0.337 0.000 0.000 111 SER ( 111 ) A 3 -1.745 -1.607 -1.218 -0.475 -0.669 112 PRO ( 112 ) A 3 -0.678 -0.218 -1.001 0.192 -0.764 113 THR ( 113 ) A 1 -1.316 -1.636 -0.089 -1.419 0.413 114 ILE ( 114 ) A 3 -0.339 0.378 0.730 -0.705 -1.158 115 CYS ( 115 ) A 2 -1.343 -1.226 -0.315 -1.363 -1.367 116 HIS ( 116 ) A 2 -1.524 -0.920 -1.043 -1.499 -1.126 117 GLU ( 117 ) A 2 -1.509 -1.307 -0.449 -1.171 -1.246 118 LEU ( 118 ) A 2 -1.864 -2.017 -0.089 -1.323 -1.380 119 THR ( 119 ) A 3 -0.494 0.327 -1.305 0.415 -1.210 120 GLY ( 120 ) A 3 -0.507 0.139 -1.067 0.000 0.000 121 GLY ( 121 ) A 3 -0.253 -0.449 0.326 0.000 0.000 122 SER ( 122 ) A 3 -1.040 -1.070 -0.770 -1.242 0.116 123 SER ( 123 ) A 3 -0.708 -1.006 0.070 -0.200 -0.338 124 CYS ( 124 ) A 3 -1.100 -0.651 -1.065 -1.240 -1.191 125 GLY ( 125 ) A 3 -0.620 -0.649 -0.145 0.000 0.000 126 TRP ( 126 ) A 2 -2.679 -1.705 -2.216 -2.166 -2.574 127 SER ( 127 ) A 3 -1.635 -0.986 -1.431 -0.826 -1.098 128 ASP ( 128 ) A 3 -1.300 -0.474 -0.734 -0.889 -0.866 129 LYS ( 129 ) A 3 -0.498 -0.460 -0.926 0.320 -0.224 130 PHE ( 130 ) A 2 -2.109 -1.272 -2.107 -1.258 -2.090 131 GLU ( 131 ) A 2 -0.765 0.298 -1.150 -1.338 -0.704 132 ILE ( 132 ) A 2 -1.512 -0.406 -1.313 -1.701 -1.503 133 THR ( 133 ) A 2 -0.151 0.415 -0.943 -0.178 -1.336 134 ALA ( 134 ) A 2 -0.231 0.570 -1.509 0.000 0.000 135 THR ( 135 ) A 2 0.492 1.378 -0.272 -1.036 0.019 136 VAL ( 136 ) A 2 0.250 0.879 0.926 -1.575 0.019 137 THR ( 137 ) A 2 -0.706 -0.047 -0.607 -1.492 -1.549 138 SER ( 138 ) A 2 -0.367 0.131 -1.188 -0.131 -0.856 139 LEU ( 139 ) A 2 -1.695 -0.617 -1.407 -1.885 -1.287 140 THR ( 140 ) A 3 -0.737 -0.526 -0.652 -0.426 -0.776 141 ASP ( 141 ) A 3 -0.554 -0.572 -0.451 -0.445 0.082 142 SER ( 142 ) A 3 -0.999 -0.718 -0.792 -0.826 -0.602 143 ARG ( 143 ) A 3 0.525 -0.305 0.452 -0.135 1.258 144 PRO ( 144 ) A 3 -0.125 0.048 0.069 0.240 -0.662 145 LEU ( 145 ) A 3 -1.630 -0.585 -0.699 -1.066 -1.463 146 GLY ( 146 ) A 3 -1.743 -0.934 -1.546 0.000 0.000 147 PRO ( 147 ) A 3 -0.148 -0.408 1.061 -0.856 -0.203 148 PHE ( 148 ) A 3 -0.696 -0.563 -0.093 -0.039 -0.707 149 ASN ( 149 ) A 3 -0.154 -0.394 0.158 -0.919 -0.181 150 VAL ( 150 ) A 3 -1.311 -0.821 -1.327 -0.825 -0.906 151 THR ( 151 ) A 3 -0.921 -1.050 -0.415 -0.903 -0.008 152 GLU ( 152 ) A 3 -1.594 -1.098 -0.779 -0.868 -1.069 153 GLU ( 153 ) A 3 0.476 -0.599 0.663 -1.094 1.067 154 GLU ( 154 ) A 3 -0.877 -0.240 -0.599 -1.133 -0.753 155 MET ( 155 ) A 3 -1.852 -1.039 -1.555 -0.589 -1.676 156 ASP ( 156 ) A 3 -1.528 -1.251 -0.849 -0.796 -0.780 157 GLN ( 157 ) A 3 -0.301 -0.368 0.001 1.535 -1.617 158 LEU ( 158 ) A 3 -0.404 -0.268 -0.119 0.201 -0.641 159 PHE ( 159 ) A 3 0.690 0.599 1.289 0.358 -0.294 160 ILE ( 160 ) A 2 -1.162 -0.542 -0.848 -1.437 -1.160 161 ASP ( 161 ) A 2 -0.809 -0.362 -1.089 -0.399 -1.030 162 HIS ( 162 ) A 2 -0.539 -0.125 -1.224 0.173 -0.808 163 GLU ( 163 ) A 2 -1.792 -0.975 -1.927 -0.939 -1.574 164 ILE ( 164 ) A 2 -1.303 -0.697 -1.016 -1.314 -0.353 165 ALA ( 165 ) A 2 -1.360 -1.603 -0.313 0.000 0.000 166 MET ( 166 ) A 2 -2.404 -1.604 -1.511 -1.737 -2.226 167 ALA ( 167 ) A 3 -1.958 -0.932 -1.572 0.000 0.000 168 GLN ( 168 ) A 3 -0.925 -0.636 -0.734 -0.900 -1.186 169 CYS ( 169 ) A 3 -1.219 -1.115 -1.101 -0.959 -0.923 170 GLU ( 170 ) A 3 0.974 -0.711 1.348 -0.211 1.537 171 ALA ( 171 ) A 2 -1.940 -2.104 -0.656 0.000 0.000 172 GLU ( 172 ) A 2 -1.820 -1.073 -1.074 -1.168 -1.060 173 LYS ( 173 ) A 2 -0.521 -0.619 -0.606 -0.131 0.014 174 THR ( 174 ) A 3 -0.822 -0.623 -0.562 -0.581 -1.076 175 CYS ( 175 ) A 2 -1.563 -1.047 -0.782 -1.737 -9.554 176 ASN ( 176 ) A 3 -0.260 -0.066 -0.819 0.044 -0.646 177 GLY ( 177 ) A 3 -1.364 -0.998 -0.814 0.000 0.000 178 PHE ( 178 ) A 2 -2.931 -2.368 -2.059 -1.847 -2.410 179 ASP ( 179 ) A 3 -1.430 -0.859 -1.071 -0.887 -0.866 180 LEU ( 180 ) A 3 -1.883 -1.438 -0.927 -1.576 -0.638 181 GLU ( 181 ) A 3 -0.734 -0.612 -0.464 -1.148 -0.790 All contacts : Average = -0.925 Z-score = -5.98 BB-BB contacts : Average = -0.504 Z-score = -3.33 BB-SC contacts : Average = -0.692 Z-score = -5.30 SC-BB contacts : Average = -0.680 Z-score = -4.04 SC-SC contacts : Average = -0.981 Z-score = -5.63 If an individual residue has a quality control value of -2.5 or worse, you should take a look at it. It can mean that the residue: is involved in symmetry contacts, or is binding a co-factor, ligand or ion, or is an active site residue, or is wrong. Average protein values ("Z-score for all contacts") can be read as follows: -5.0 Guaranteed wrong structure. Bad structure or poor model -3.0 Probably bad structure or unrefined model. Doubtful structure or model -2.0 Structure OK or good model. Good structures 0.0 Good structures. 2.0 Good structures. Unusually Good structures 4.0 Probably a strange model of a perfect helix