It seems that the cause for this error can be seen from the coordinates:
ATOM 878 N GLU 119 -5.942 37.105 -26.991 0.00 25.50 N ATOM 879 CA GLU 119 -6.964 36.071 -27.094 0.00 24.21 C ATOM 880 C GLU 119 -8.272 36.467 -26.410 0.00 23.33 C ATOM 881 O GLU 119 -8.527 36.079 -25.269 0.00 23.17 O ATOM 882 CB GLU 119 -6.440 34.757 -26.521 0.00 24.06 C ATOM 883 N GLN 120 -9.074 37.268 -27.107 0.00 22.51 N ATOM 884 CA GLN 120 -10.377 37.732 -26.624 0.00 21.81 C ATOM 885 C GLN 120 -10.353 38.713 -25.450 0.00 21.36 C ATOM 886 O GLN 120 -10.917 39.804 -25.545 0.00 21.25 O ATOM 887 CB GLN 120 -11.282 36.542 -26.303 0.00 21.69 C ATOM 888 N PRO 121 -9.690 38.333 -24.359 0.00 20.99 N ATOM 889 CA PRO 121 -9.597 39.157 -23.152 0.00 20.70 C ATOM 890 C PRO 121 -9.219 40.622 -23.382 0.00 20.54 C ATOM 891 O PRO 121 -9.418 41.462 -22.499 0.00 20.48 O ATOM 892 CB PRO 121 -8.641 38.515 -22.156 0.00 20.62 C ATOM 893 N ASN 122 -8.658 40.924 -24.549 0.00 20.47 N ATOM 894 CA ASN 122 -8.272 42.290 -24.889 0.00 20.46 C ATOM 895 C ASN 122 -9.475 43.226 -24.785 0.00 20.53 C ATOM 896 O ASN 122 -9.345 44.377 -24.362 0.00 20.47 O ATOM 897 CB ASN 122 -7.686 42.337 -26.295 0.00 20.38 C ATOM 898 N PRO 123 -10.647 42.720 -25.155 0.00 20.72 N ATOM 899 CA PRO 123 -11.875 43.503 -25.103 0.00 20.99 C ATOM 900 C PRO 123 -12.442 43.484 -23.688 0.00 21.32 C ATOM 901 O PRO 123 -12.399 42.458 -23.008 0.00 21.24 O ATOM 902 CB PRO 123 -12.893 42.948 -26.088 0.00 20.88 C ATOM 903 N ASN 124 -12.960 44.630 -23.252 0.00 21.86 N ATOM 904 CA ASN 124 -13.554 44.793 -21.925 0.00 22.52 C ATOM 905 C ASN 124 -12.549 44.691 -20.777 0.00 23.22 C ATOM 906 O ASN 124 -12.283 45.680 -20.096 0.00 23.12 O ATOM 907 CB ASN 124 -14.702 43.801 -21.723 0.00 22.34 C ATOM 908 N PRO 125 -11.990 43.501 -20.573 0.00 24.26 N ATOM 909 CA PRO 125 -11.026 43.270 -19.501 0.00 25.45 C ATOM 910 C PRO 125 -9.734 44.066 -19.680 0.00 26.65 C ATOM 911 O PRO 125 -9.390 44.900 -18.842 0.00 26.53 O ATOM 912 CB PRO 125 -10.719 41.781 -19.384 0.00 25.22 C ATOM 913 N GLY 126 -9.010 43.791 -20.761 0.00 28.31 N ATOM 914 CA GLY 126 -7.755 44.483 -21.036 0.00 30.13 C ATOM 915 C GLY 126 -7.951 45.840 -21.710 0.00 31.86 C ATOM 916 O GLY 126 -6.995 46.607 -21.859 0.00 31.79 O ATOM 917 CB GLY 126 -6.843 43.600 -21.877 0.00 29.88 C ATOM 918 N ALA 127 -9.185 46.141 -22.105 0.00 34.12 N ATOM 919 CA ALA 127 -9.504 47.406 -22.764 0.00 36.52 C ATOM 920 C ALA 127 -9.400 48.576 -21.787 0.00 38.56 C ATOM 921 O ALA 127 -10.403 49.186 -21.415 0.00 38.62 O ATOM 922 CB ALA 127 -10.897 47.343 -23.376 0.00 36.32 C ATOM 923 N ASN 128 -8.169 48.901 -21.405 1.00 41.67 N ATOM 924 CA ASN 128 -7.892 49.981 -20.461 1.00 41.34 C ATOM 925 C ASN 128 -6.381 50.200 -20.351 1.00 39.02 C ATOM 926 O ASN 128 -5.922 51.182 -19.762 1.00 39.04 O ATOM 927 CB ASN 128 -8.468 49.624 -19.090 1.00 43.19 C |
Obviously, there must have been a reason to only build alanines in this loop, perhaps because of poor density. And then somebody forgot to remove the Cβ from the Glycine that was initially modeeled as an Alanine.