Hi Chris, Not a direct answer to your question, but I notice that there are two TER records for the same residue. We've been noticing a lot of problems with leftover TER records. Any idea where they came from? It probably won't help, but try deleting those.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Chris Ulens > Sent: Monday, June 19, 2017 10:54 > To: [email protected] > Subject: Re: [ccp4bb] N-linked glycosylation check > > Good morning, > I am looking to get feedback from others who have recently built and refined > bond lengths and angles of an N-linked glycosyl chain in Refmac. > I observed in Coot that the bond between O3 of BMA303 and C1 of MAN304 > does show while the bond between O6 of BMA303 and C1 of MAN305 does > not and I wonder why. > Molprobity issues warnings for bond length and angle outliers for the entire > chain. I have copied the relevant PDB lines below. > > Thank you for your help. > Best regards > Chris > > > > LINKR C1 NAG B 301 ND2 ASN B 108 > NAG-ASN > LINKR O4 NAG B 301 1.439 C1 NAG B 302 > BETA1-4 > LINKR O4 NAG B 302 1.439 C1 BMA B 303 > ALPHA1-4 > LINKR O3 BMA B 303 1.439 C1 MAN B 304 > BETA1-3 > LINKR O6 BMA B 303 1.439 C1 MAN B 305 > BETA1-6 > ATOM 2609 N ASN B 108 14.827 -15.743 -7.774 1.00 68.73 N > ATOM 2610 CA ASN B 108 14.379 -16.001 -9.161 1.00 68.24 C > ATOM 2611 CB ASN B 108 15.440 -16.789 -9.973 1.00 68.43 C > ATOM 2612 CG ASN B 108 15.523 -18.271 -9.618 1.00 70.34 C > ATOM 2613 OD1 ASN B 108 14.776 -18.790 -8.780 1.00 68.94 O > ATOM 2614 ND2 ASN B 108 16.451 -18.966 -10.296 1.00 74.17 N > ATOM 2615 C ASN B 108 12.982 -16.637 -9.178 1.00 68.93 C > ATOM 2616 O ASN B 108 12.427 -16.943 -8.116 1.00 66.58 O > HETATM 3393 C1 NAG B 301 16.707 -20.385 -10.157 1.00 77.65 C > HETATM 3394 O5 NAG B 301 18.065 -20.635 -9.781 1.00 78.99 O > HETATM 3395 C5 NAG B 301 18.330 -22.011 -9.454 1.00 80.39 C > HETATM 3396 C6 NAG B 301 19.783 -22.145 -9.032 1.00 78.67 C > HETATM 3397 O6 NAG B 301 20.614 -21.561 -10.039 1.00 78.50 O > HETATM 3398 C4 NAG B 301 18.025 -22.927 -10.646 1.00 82.50 C > HETATM 3399 O4 NAG B 301 18.039 -24.305 -10.255 1.00 85.12 O > HETATM 3400 C3 NAG B 301 16.640 -22.661 -11.203 1.00 81.09 C > HETATM 3401 O3 NAG B 301 16.488 -23.414 -12.412 1.00 81.20 O > HETATM 3402 C2 NAG B 301 16.428 -21.169 -11.448 1.00 79.40 C > HETATM 3403 N2 NAG B 301 15.066 -21.042 -11.942 1.00 79.12 N > HETATM 3404 C7 NAG B 301 14.706 -20.379 -13.047 1.00 78.12 C > HETATM 3405 C8 NAG B 301 13.243 -20.422 -13.354 1.00 78.57 C > HETATM 3406 O7 NAG B 301 15.476 -19.768 -13.766 1.00 76.05 O > HETATM 3407 C1 NAG B 302 19.037 -25.083 -10.947 1.00 87.76 C > HETATM 3408 O5 NAG B 302 18.655 -25.448 -12.270 1.00 87.97 O > HETATM 3409 C5 NAG B 302 19.667 -26.160 -12.982 1.00 89.21 C > HETATM 3410 C6 NAG B 302 19.082 -26.481 -14.347 1.00 90.71 C > HETATM 3411 O6 NAG B 302 19.210 -25.325 -15.180 1.00 95.46 O > HETATM 3412 C4 NAG B 302 20.094 -27.444 -12.263 1.00 90.51 C > HETATM 3413 O4 NAG B 302 21.315 -27.940 -12.855 1.00 93.27 O > HETATM 3414 C3 NAG B 302 20.319 -27.252 -10.763 1.00 89.34 C > HETATM 3415 O3 NAG B 302 20.255 -28.506 -10.070 1.00 88.92 O > HETATM 3416 C2 NAG B 302 19.285 -26.337 -10.120 1.00 88.56 C > HETATM 3417 N2 NAG B 302 19.762 -25.958 -8.795 1.00 88.35 N > HETATM 3418 C7 NAG B 302 19.037 -26.050 -7.679 1.00 86.04 C > HETATM 3419 C8 NAG B 302 19.763 -25.594 -6.443 1.00 86.11 C > HETATM 3420 O7 NAG B 302 17.885 -26.464 -7.647 1.00 81.74 O > HETATM 3421 C1 BMA B 303 21.616 -29.338 -12.590 1.00 96.54 C > HETATM 3422 O5 BMA B 303 20.446 -30.174 -12.479 1.00 98.08 O > HETATM 3423 C5 BMA B 303 20.540 -31.614 -12.489 1.00 99.62 C > HETATM 3424 C6 BMA B 303 20.256 -32.208 -11.107 1.00100.50 C > HETATM 3425 O6 BMA B 303 20.931 -31.469 -10.075 1.00100.33 O > HETATM 3426 C4 BMA B 303 21.875 -32.103 -13.039 1.00 97.91 C > HETATM 3427 O4 BMA B 303 21.772 -33.482 -13.431 1.00 95.77 O > HETATM 3428 C3 BMA B 303 22.244 -31.206 -14.216 1.00 96.33 C > HETATM 3429 O3 BMA B 303 23.273 -31.875 -14.962 1.00 94.34 O > HETATM 3430 C2 BMA B 303 22.598 -29.814 -13.669 1.00 96.74 C > HETATM 3431 O2 BMA B 303 23.919 -29.813 -13.104 1.00 97.73 O > HETATM 3432 C1 MAN B 304 23.970 -31.058 -15.921 1.00 93.13 C > HETATM 3433 O5 MAN B 304 23.200 -30.504 -16.999 1.00 92.48 O > HETATM 3434 C5 MAN B 304 23.937 -29.452 -17.653 1.00 94.03 C > HETATM 3435 C6 MAN B 304 23.073 -28.788 -18.726 1.00 93.77 C > HETATM 3436 O6 MAN B 304 22.666 -29.744 -19.708 1.00 94.64 O > HETATM 3437 C4 MAN B 304 25.272 -29.993 -18.201 1.00 93.08 C > HETATM 3438 O4 MAN B 304 26.089 -28.900 -18.655 1.00 90.68 O > HETATM 3439 C3 MAN B 304 26.034 -30.834 -17.160 1.00 92.23 C > HETATM 3440 O3 MAN B 304 27.106 -31.570 -17.732 1.00 94.34 O > HETATM 3441 C2 MAN B 304 25.134 -31.859 -16.488 1.00 92.52 C > HETATM 3442 O2 MAN B 304 24.723 -32.907 -17.396 1.00 89.90 O > HETATM 3443 C1 MAN B 305 21.455 -32.294 -9.018 1.00102.01 C > HETATM 3444 O5 MAN B 305 21.325 -33.695 -8.914 1.00102.85 O > HETATM 3445 C5 MAN B 305 22.576 -34.203 -9.377 1.00101.34 C > HETATM 3446 C6 MAN B 305 22.439 -35.713 -9.516 1.00 99.57 C > HETATM 3447 O6 MAN B 305 21.964 -36.012 -10.842 1.00 99.10 O > HETATM 3448 C4 MAN B 305 23.716 -33.690 -8.465 1.00101.06 C > HETATM 3449 O4 MAN B 305 24.981 -34.109 -8.996 1.00 99.42 O > HETATM 3450 C3 MAN B 305 23.720 -32.144 -8.347 1.00101.15 C > HETATM 3451 O3 MAN B 305 24.692 -31.689 -7.399 1.00100.86 O > HETATM 3452 C2 MAN B 305 22.336 -31.620 -7.977 1.00101.26 C > HETATM 3453 O2 MAN B 305 22.004 -32.090 -6.664 1.00 99.36 O > TER 3454 MAN B 305 > TER 3455 MAN B 305
