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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Chris Ulens
> Sent: Monday, June 19, 2017 10:54
> To: CCP4BB@JISCMAIL.AC.UK
> 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

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