Error when processing PDB file: LYS atoms not the same

Trying to dock on the HADDOCK webserver using a PDB file manipulated in Pymol. However, I keep getting this error:
The following error occurred when processing one of your PDB file: Instances of ligand LYS do not contain the same atoms

Despite multiple checks on my LYS residues, there seems to be no inconsistency in the atoms between different LYS. What is exactly going on here with the error message? Copying the lines containing LYS over below.

ATOM 88 N LYS 30 36.320 24.990 38.790 0.00 0.00 N
ATOM 89 CA LYS 30 36.560 24.390 40.120 0.00 0.00 C
ATOM 90 C LYS 30 35.710 25.150 41.150 0.00 0.00 C
ATOM 91 O LYS 30 35.510 26.350 40.990 0.00 0.00 O
ATOM 92 CB LYS 30 38.060 24.400 40.480 0.00 0.00 C
ATOM 93 CG LYS 30 38.930 23.670 39.440 0.00 0.00 C
ATOM 94 CD LYS 30 40.400 23.540 39.890 0.00 0.00 C
ATOM 95 CE LYS 30 41.280 22.850 38.840 0.00 0.00 C
ATOM 96 NZ LYS 30 42.670 22.660 39.310 0.00 0.00 N1+
ATOM 97 H LYS 30 36.890 25.780 38.510 0.00 0.00 H
ATOM 98 HA LYS 30 36.210 23.350 40.110 0.00 0.00 H
ATOM 99 HB1 LYS 30 38.190 23.920 41.450 0.00 0.00 H
ATOM 100 HB2 LYS 30 38.410 25.430 40.560 0.00 0.00 H
ATOM 101 HG1 LYS 30 38.900 24.220 38.500 0.00 0.00 H
ATOM 102 HG2 LYS 30 38.520 22.660 39.280 0.00 0.00 H
ATOM 103 HD1 LYS 30 40.420 22.960 40.810 0.00 0.00 H
ATOM 104 HD2 LYS 30 40.790 24.540 40.070 0.00 0.00 H
ATOM 105 HE1 LYS 30 41.280 23.450 37.920 0.00 0.00 H
ATOM 106 HE2 LYS 30 40.840 21.880 38.600 0.00 0.00 H
ATOM 107 HZ1 LYS 30 43.250 22.200 38.610 0.00 0.00 H
ATOM 108 HZ2 LYS 30 43.100 23.550 39.560 0.00 0.00 H
ATOM 109 HZ3 LYS 30 42.700 22.090 40.150 0.00 0.00 H

ATOM 181 N LYS 35 31.910 29.460 43.080 0.00 0.00 N
ATOM 182 CA LYS 35 31.530 30.500 44.050 0.00 0.00 C
ATOM 183 C LYS 35 31.540 31.920 43.470 0.00 0.00 C
ATOM 184 O LYS 35 30.610 32.690 43.710 0.00 0.00 O
ATOM 185 CB LYS 35 32.470 30.450 45.270 0.00 0.00 C
ATOM 186 CG LYS 35 32.090 29.360 46.280 0.00 0.00 C
ATOM 187 CD LYS 35 32.950 29.480 47.550 0.00 0.00 C
ATOM 188 CE LYS 35 32.300 28.740 48.720 0.00 0.00 C
ATOM 189 NZ LYS 35 32.970 29.070 50.000 0.00 0.00 N1+
ATOM 190 H LYS 35 32.690 28.850 43.310 0.00 0.00 H
ATOM 191 HA LYS 35 30.520 30.310 44.380 0.00 0.00 H
ATOM 192 HB1 LYS 35 32.410 31.420 45.790 0.00 0.00 H
ATOM 193 HB2 LYS 35 33.500 30.310 44.950 0.00 0.00 H
ATOM 194 HG1 LYS 35 32.210 28.380 45.840 0.00 0.00 H
ATOM 195 HG2 LYS 35 31.040 29.500 46.560 0.00 0.00 H
ATOM 196 HD1 LYS 35 33.050 30.530 47.820 0.00 0.00 H
ATOM 197 HD2 LYS 35 33.950 29.080 47.360 0.00 0.00 H
ATOM 198 HE1 LYS 35 32.300 27.660 48.550 0.00 0.00 H
ATOM 199 HE2 LYS 35 31.260 29.070 48.780 0.00 0.00 H
ATOM 200 HZ1 LYS 35 32.340 28.990 50.800 0.00 0.00 H
ATOM 201 HZ2 LYS 35 33.800 28.530 50.200 0.00 0.00 H
ATOM 202 HZ3 LYS 35 33.260 30.050 50.020 0.00 0.00 H

ATOM 401 N LYS 50 34.950 31.830 26.150 0.00 0.00 N
ATOM 402 CA LYS 50 34.360 33.160 25.890 0.00 0.00 C
ATOM 403 C LYS 50 33.280 33.540 26.910 0.00 0.00 C
ATOM 404 O LYS 50 33.190 34.700 27.300 0.00 0.00 O
ATOM 405 CB LYS 50 33.820 33.190 24.440 0.00 0.00 C
ATOM 406 CG LYS 50 33.170 34.540 24.070 0.00 0.00 C
ATOM 407 CD LYS 50 32.770 34.590 22.600 0.00 0.00 C
ATOM 408 CE LYS 50 31.910 35.840 22.320 0.00 0.00 C
ATOM 409 NZ LYS 50 31.490 35.900 20.900 0.00 0.00 N1+
ATOM 410 H LYS 50 34.830 31.100 25.450 0.00 0.00 H
ATOM 411 HA LYS 50 35.150 33.910 25.980 0.00 0.00 H
ATOM 412 HB1 LYS 50 33.080 32.400 24.320 0.00 0.00 H
ATOM 413 HB2 LYS 50 34.650 33.000 23.760 0.00 0.00 H
ATOM 414 HG1 LYS 50 33.870 35.350 24.280 0.00 0.00 H
ATOM 415 HG2 LYS 50 32.280 34.680 24.680 0.00 0.00 H
ATOM 416 HD1 LYS 50 32.190 33.700 22.350 0.00 0.00 H
ATOM 417 HD2 LYS 50 33.660 34.610 21.970 0.00 0.00 H
ATOM 418 HE1 LYS 50 32.490 36.730 22.580 0.00 0.00 H
ATOM 419 HE2 LYS 50 31.020 35.800 22.960 0.00 0.00 H
ATOM 420 HZ1 LYS 50 30.880 36.690 20.710 0.00 0.00 H
ATOM 421 HZ2 LYS 50 32.280 35.910 20.260 0.00 0.00 H
ATOM 422 HZ3 LYS 50 30.950 35.080 20.640 0.00 0.00 H

ATOM 625 N LYS 63 32.860 43.290 44.240 0.00 0.00 N
ATOM 626 CA LYS 63 33.680 43.410 45.460 0.00 0.00 C
ATOM 627 C LYS 63 34.730 44.530 45.380 0.00 0.00 C
ATOM 628 O LYS 63 35.660 44.570 46.190 0.00 0.00 O
ATOM 629 CB LYS 63 34.270 42.030 45.830 0.00 0.00 C
ATOM 630 CG LYS 63 33.210 40.920 45.860 0.00 0.00 C
ATOM 631 CD LYS 63 33.730 39.600 46.440 0.00 0.00 C
ATOM 632 CE LYS 63 33.770 39.610 47.970 0.00 0.00 C
ATOM 633 NZ LYS 63 34.230 38.300 48.480 0.00 0.00 N1+
ATOM 634 H LYS 63 33.260 42.820 43.440 0.00 0.00 H
ATOM 635 HA LYS 63 33.020 43.700 46.280 0.00 0.00 H
ATOM 636 HB1 LYS 63 34.740 42.110 46.810 0.00 0.00 H
ATOM 637 HB2 LYS 63 35.050 41.760 45.110 0.00 0.00 H
ATOM 638 HG1 LYS 63 32.890 40.720 44.830 0.00 0.00 H
ATOM 639 HG2 LYS 63 32.340 41.250 46.430 0.00 0.00 H
ATOM 640 HD1 LYS 63 34.730 39.410 46.050 0.00 0.00 H
ATOM 641 HD2 LYS 63 33.070 38.800 46.110 0.00 0.00 H
ATOM 642 HE1 LYS 63 32.770 39.830 48.360 0.00 0.00 H
ATOM 643 HE2 LYS 63 34.450 40.400 48.300 0.00 0.00 H
ATOM 644 HZ1 LYS 63 34.310 38.310 49.490 0.00 0.00 H
ATOM 645 HZ2 LYS 63 33.600 37.550 48.220 0.00 0.00 H
ATOM 646 HZ3 LYS 63 35.150 38.090 48.090 0.00 0.00 H

ATOM 1094 N LYS 93 46.990 46.070 32.630 0.00 0.00 N
ATOM 1095 CA LYS 93 46.980 46.110 31.160 0.00 0.00 C
ATOM 1096 C LYS 93 45.920 45.200 30.510 0.00 0.00 C
ATOM 1097 O LYS 93 45.870 45.110 29.290 0.00 0.00 O
ATOM 1098 CB LYS 93 48.400 45.910 30.600 0.00 0.00 C
ATOM 1099 CG LYS 93 48.800 47.030 29.620 0.00 0.00 C
ATOM 1100 CD LYS 93 49.490 48.250 30.270 0.00 0.00 C
ATOM 1101 CE LYS 93 48.590 49.130 31.150 0.00 0.00 C
ATOM 1102 NZ LYS 93 47.640 49.950 30.370 0.00 0.00 N1+
ATOM 1103 H LYS 93 47.390 45.260 33.110 0.00 0.00 H
ATOM 1104 HA LYS 93 46.650 47.100 30.860 0.00 0.00 H
ATOM 1105 HB1 LYS 93 48.450 44.960 30.080 0.00 0.00 H
ATOM 1106 HB2 LYS 93 49.130 45.860 31.410 0.00 0.00 H
ATOM 1107 HG1 LYS 93 47.930 47.360 29.060 0.00 0.00 H
ATOM 1108 HG2 LYS 93 49.500 46.600 28.910 0.00 0.00 H
ATOM 1109 HD1 LYS 93 49.910 48.860 29.470 0.00 0.00 H
ATOM 1110 HD2 LYS 93 50.320 47.890 30.880 0.00 0.00 H
ATOM 1111 HE1 LYS 93 49.250 49.810 31.710 0.00 0.00 H
ATOM 1112 HE2 LYS 93 48.060 48.520 31.880 0.00 0.00 H
ATOM 1113 HZ1 LYS 93 47.390 50.780 30.890 0.00 0.00 H
ATOM 1114 HZ2 LYS 93 48.030 50.270 29.480 0.00 0.00 H
ATOM 1115 HZ3 LYS 93 46.780 49.450 30.140 0.00 0.00 H

ATOM 1279 N LYS 104 39.060 34.750 36.780 0.00 0.00 N
ATOM 1280 CA LYS 104 40.200 33.770 36.680 0.00 0.00 C
ATOM 1281 C LYS 104 39.860 32.290 36.300 0.00 0.00 C
ATOM 1282 O LYS 104 39.880 31.980 35.120 0.00 0.00 O
ATOM 1283 CB LYS 104 41.230 33.810 37.840 0.00 0.00 C
ATOM 1284 CG LYS 104 42.560 33.210 37.300 0.00 0.00 C
ATOM 1285 CD LYS 104 43.520 32.630 38.340 0.00 0.00 C
ATOM 1286 CE LYS 104 44.520 31.710 37.630 0.00 0.00 C
ATOM 1287 NZ LYS 104 45.550 31.200 38.550 0.00 0.00 N1+
ATOM 1288 H LYS 104 38.280 34.450 36.210 0.00 0.00 H
ATOM 1289 HA LYS 104 40.770 34.120 35.810 0.00 0.00 H
ATOM 1290 HB1 LYS 104 40.860 33.250 38.690 0.00 0.00 H
ATOM 1291 HB2 LYS 104 41.420 34.840 38.160 0.00 0.00 H
ATOM 1292 HG1 LYS 104 43.080 33.990 36.750 0.00 0.00 H
ATOM 1293 HG2 LYS 104 42.340 32.410 36.600 0.00 0.00 H
ATOM 1294 HD1 LYS 104 42.970 32.060 39.090 0.00 0.00 H
ATOM 1295 HD2 LYS 104 44.040 33.440 38.840 0.00 0.00 H
ATOM 1296 HE1 LYS 104 45.000 32.260 36.810 0.00 0.00 H
ATOM 1297 HE2 LYS 104 43.960 30.880 37.190 0.00 0.00 H
ATOM 1298 HZ1 LYS 104 45.920 30.310 38.230 0.00 0.00 H
ATOM 1299 HZ2 LYS 104 46.310 31.870 38.620 0.00 0.00 H
ATOM 1300 HZ3 LYS 104 45.180 31.080 39.490 0.00 0.00 H

Appreciate any help.

What is the error message?

Are you submitting an ensemble of conformations?

If that’s the case all models within the ensemble should have the same atoms.