The atoms 3051-3062 cut-n-pasted directly from 1htr.
.... HETATM 3051 O HOH 542 3.598 37.189 21.675 0.50 29.84 1HTR3221 HETATM 3052 O HOH 543 17.340 44.239 20.339 0.40 43.34 1HTR3222 HETATM 3053 O HOH 544 28.073 47.073 10.521 0.40 16.48 1HTR3223 HETATM 3054 O HOH 545 46.581 23.244 17.866 0.55 31.68 1HTR3224 HETATM 3055 O HOH 546 18.170 9.874 27.048 0.45 29.34 1HTR3225 HETATM 3056 O HOH B 547 38.070 6.610 1.430 0.40 31.67 1HTR3226 HETATM 3057 O HOH 548 9.430 30.260 24.949 0.40 39.52 1HTR3227 HETATM 3058 O HOH 549 22.495 32.343 -0.727 0.40 23.64 1HTR3228 HETATM 3059 O HOH 550 21.435 31.394 28.989 0.40 20.77 1HTR3229 HETATM 3060 O HOH 551 27.612 46.250 19.869 0.45 23.42 1HTR3230 HETATM 3061 O HOH 552 39.117 2.140 39.454 0.40 31.03 1HTR3231 HETATM 3062 O HOH 553 10.837 44.972 5.264 0.40 32.71 1HTR3232 .... |
It is unclear what reason there is for this 'problem'. WHAT_CHECK tells us about the waters:
Warning: Water molecules need moving The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given. The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. 380 HOH (HOH ) 497 53.152 1.099 18.605 385 HOH (HOH ) 618 51.553 -0.271 30.320 Error: Water molecules without hydrogen bonds The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file. 382 HOH (HOH ) B 547 383 HOH (HOH ) 564 387 HOH (HOH ) 571 388 HOH (HOH ) 567 |
But please be aware that WHAT_CHECK becomes very forgiving when the occupancy of an atom is less than 0.50.
The table of bumps reveals a bit more:
.... 379 HOH (HOH ) 421 -- 388 HOH (HOH ) 604 0.933 2.267 INTRA 379 HOH (HOH ) 500 -- 388 HOH (HOH ) 604 0.928 2.272 INTRA 379 HOH (HOH ) 486 -- 388 HOH (HOH ) 621 0.892 2.308 INTRA 379 HOH (HOH ) 404 -- 388 HOH (HOH ) 604 0.880 2.320 INTRA 376 HOH (HOH ) 433 -- 385 HOH (HOH ) 619 0.857 2.343 INTRA 380 HOH (HOH ) 403 -- 380 HOH (HOH ) 497 0.812 2.238 INTER HB 377 HOH (HOH ) 535 -- 377 HOH (HOH ) 536 0.802 2.398 INTRA 379 HOH (HOH ) 443 -- 388 HOH (HOH ) 621 0.802 2.398 INTRA 379 HOH (HOH ) 404 -- 379 HOH (HOH ) 467 0.745 2.305 INTRA HB 376 HOH (HOH ) 449 -- 376 HOH (HOH ) 524 0.735 2.315 INTRA HB 379 HOH (HOH ) 451 -- 379 HOH (HOH ) 515 0.726 2.324 INTRA HB 379 HOH (HOH ) 425 -- 379 HOH (HOH ) 490 0.697 2.503 INTRA 379 HOH (HOH ) 477 -- 381 HOH (HOH ) 456 0.675 2.375 INTER HB 379 HOH (HOH ) 401 -- 384 HOH (HOH ) 588 0.663 2.537 INTRA 381 HOH (HOH ) 452 -- 381 HOH (HOH ) 537 0.657 2.543 INTRA 379 HOH (HOH ) 401 -- 388 HOH (HOH ) 587 0.652 2.548 INTRA 380 HOH (HOH ) 497 -- 380 HOH (HOH ) 497 0.637 2.413 INTER HB 381 HOH (HOH ) 428 -- 390 HOH (HOH ) 595 0.614 2.586 INTRA 374 HOH (HOH ) 448 -- 374 HOH (HOH ) 455 0.609 2.441 INTRA HB 380 HOH (HOH ) 531 -- 390 HOH (HOH ) 594 0.607 2.593 INTRA 377 HOH (HOH ) 414 -- 377 HOH (HOH ) 460 0.596 2.454 INTRA HB 379 HOH (HOH ) 523 -- 388 HOH (HOH ) 617 0.590 2.610 INTRA 375 HOH (HOH ) 462 -- 384 HOH (HOH ) 611 0.589 2.611 INTRA And so on for a total of 272 lines |
So the large number of waters with low occupancies have probably been an attempt to model disordered waters. This leads to many bumps. But this still doesn't explain why one single water has chain-id B.