/Applications/phenix-1.18.2-3874/build/bin/phenix.clashscore ../test/1xjrA.pdb Using electron cloud x-H distances and vdW radii Adding H/D atoms with reduce... Bad Clashes >= 0.4 Angstrom: A 17 A N1 A 34 G N1 :0.430 clashscore = 0.66 ../test/1xjrA.pdb 0.66 /Applications/phenix-1.18.2-3874/build/bin/phenix.clashscore ../test/1xjrA_M1.pdb Using electron cloud x-H distances and vdW radii Adding H/D atoms with reduce... Bad Clashes >= 0.4 Angstrom: A 41 G H2' A 42 U OP1 :0.738 A 25 U H6 A 25 U HO2' :0.659 A 46 U H2' A 47 U OP2 :0.656 A 29 A H5'' A 30 U O2' :0.623 A 45 A H8 A 45 A O5' :0.593 A 3 A H8 A 3 A O5' :0.558 A 42 U H6 A 42 U OP1 :0.526 A 24 G H2' A 25 U O2' :0.484 A 40 A C4 A 40 A O2' :0.452 A 45 A O2' A 46 U H5' :0.445 A 42 U C6 A 42 U OP1 :0.440 A 40 A O2' A 41 G C8 :0.436 A 5 U O2' A 6 U C6 :0.429 A 46 U C2' A 47 U OP2 :0.423 A 42 U O2' A 43 G C8 :0.418 A 17 A N1 A 34 G N1 :0.418 A 3 A C8 A 3 A O5' :0.418 A 2 G O2' A 3 A C8 :0.415 A 25 U H6 A 25 U O2' :0.412 A 24 G O2' A 26 A C8 :0.410 A 42 U O2' A 43 G H8 :0.409 A 43 G H2' A 44 A O4' :0.408 A 28 G C8 A 28 G O2' :0.403 clashscore = 15.45 ../test/1xjrA_M1.pdb 15.45 /Applications/phenix-1.18.2-3874/build/bin/phenix.clashscore ../test/6TNA.pdb Using electron cloud x-H distances and vdW radii Adding H/D atoms with reduce... Bad Clashes >= 0.4 Angstrom: A 46 7MG H4' A 102 HOH O :1.205 A 46 7MG P A 102 HOH O :1.155 A 37 YG H1' A 37 YG H31 :1.099 A 73 A OP2 A 111 HOH O :1.083 A 57 G H5' A 57 G H8 :1.077 A 36 A H2' A 37 YG H5'' :0.996 A 75 C C5' A 76 A H5' :0.991 A 36 A C2' A 37 YG H5'' :0.985 A 37 YG C1' A 37 YG H31 :0.944 A 57 G C8 A 57 G H5' :0.931 A 12 U OP2 A 157 HOH O :0.930 A 25 C P A 92 HOH O :0.916 A 46 7MG C4' A 102 HOH O :0.877 A 59 U H5' A 59 U H6 :0.861 A 75 C H5'' A 76 A OP1 :0.836 A 75 C H5'' A 76 A H5' :0.831 A 4 G OP2 A 140 HOH O :0.804 A 47 U OP2 A 116 HOH O :0.795 A 40 5MC C2' A 41 U H5' :0.779 A 2 C O2 A 105 HOH O :0.778 A 10 2MG C5 A 26 M2G HM13 :0.778 A 56 C C3' A 57 G H5'' :0.775 A 25 C O5' A 92 HOH O :0.769 A 75 C H5' A 76 A H5' :0.760 A 45 G O3' A 102 HOH O :0.738 A 45 G O6 A 112 HOH O :0.737 A 40 5MC H2' A 41 U H5' :0.715 A 45 G O3' A 128 HOH O :0.705 A 16 H2U H4' A 17 H2U OP1 :0.704 A 17 H2U H2' A 17 H2U O2 :0.697 A 11 C OP2 A 133 HOH O :0.690 A 26 M2G C2' A 27 C H5' :0.685 A 46 7MG OP1 A 102 HOH O :0.685 A 39 PSU H3' A 40 5MC HM51 :0.682 A 70 C H2' A 71 G H8 :0.681 A 14 A H2' A 15 G H5' :0.677 A 37 YG N7 A 163 HOH O :0.676 A 54 5MU H73 A 55 PSU O2 :0.674 A 57 G C5' A 57 G H8 :0.667 A 37 YG C3 A 37 YG H1' :0.665 A 4 G N2 A 107 HOH O :0.665 A 14 A C2' A 15 G H5' :0.665 A 1 G C5 A 2 C C5 :0.658 A 70 C H2' A 71 G C8 :0.652 A 16 H2U OP2 A 139 HOH O :0.649 A 56 C C2' A 57 G H5'' :0.629 A 25 C OP2 A 92 HOH O :0.624 A 10 2MG C6 A 26 M2G HM13 :0.624 A 26 M2G H2' A 27 C H6 :0.622 A 14 A C3' A 15 G H5' :0.608 A 45 G H5'' A 46 7MG OP2 :0.601 A 59 U C6 A 59 U H5' :0.592 A 26 M2G HM23 A 27 C C2 :0.590 A 56 C H2' A 57 G H5'' :0.576 A 12 U H5'' A 129 HOH O :0.575 A 75 C H5'' A 76 A C5' :0.574 A 14 A H5'' A 115 HOH O :0.566 A 37 YG C2' A 37 YG H31 :0.556 A 39 PSU H2' A 40 5MC C6 :0.555 A 25 C H3' A 26 M2G H8 :0.555 A 59 U C5' A 59 U H6 :0.552 A 26 M2G C4 A 27 C C5 :0.551 A 23 A H2' A 24 G C8 :0.546 A 26 M2G C5 A 27 C C5 :0.543 A 10 2MG N7 A 26 M2G HM13 :0.543 A 8 U C2 A 15 G O6 :0.539 A 52 U H2' A 53 G O4' :0.537 A 68 U C4 A 69 U C4 :0.534 A 35 A H8 A 35 A OP2 :0.533 A 30 G H2' A 31 A O4' :0.532 A 57 G C5' A 57 G C8 :0.530 A 37 YG C1' A 37 YG C3 :0.530 A 31 A H3' A 32 OMC C6 :0.527 A 2 C H2' A 105 HOH O :0.527 A 46 7MG O5' A 102 HOH O :0.515 A 1 G H5' A 142 HOH O :0.512 A 1 G C6 A 2 C C4 :0.504 A 26 M2G H2' A 27 C C6 :0.503 A 23 A H2' A 24 G H8 :0.503 A 72 C C4 A 73 A N7 :0.499 A 17 H2U C2' A 17 H2U O2 :0.498 A 26 M2G O2' A 27 C H5' :0.496 A 75 C H5'' A 76 A P :0.494 A 49 5MC H2' A 50 U H6 :0.491 A 10 2MG H2' A 11 C C6 :0.485 A 36 A C3' A 37 YG H5'' :0.484 A 10 2MG C4 A 11 C C5 :0.483 A 59 U C2' A 60 C O5' :0.482 A 10 2MG H2' A 11 C H6 :0.481 A 11 C C2' A 12 U O5' :0.478 A 19 G N1 A 56 C N3 :0.478 A 34 OMG H8 A 34 OMG OP1 :0.473 A 68 U C4 A 69 U C5 :0.471 A 1 G C6 A 2 C C5 :0.468 A 69 U H2' A 70 C C6 :0.468 A 31 A H3' A 32 OMC H6 :0.463 A 33 U O2 A 36 A H8 :0.459 A 46 7MG H3' A 47 U H5'' :0.457 A 39 PSU H2' A 39 PSU O4 :0.456 A 10 2MG C2' A 11 C O5' :0.451 A 42 G H2' A 43 G O5' :0.450 A 50 U H2' A 50 U O2 :0.448 A 26 M2G HM22 A 27 C H1' :0.448 A 26 M2G H2' A 27 C H5' :0.446 A 56 C C3' A 57 G C5' :0.445 A 49 5MC C2 A 50 U C5 :0.444 A 9 A C2 A 45 G C6 :0.442 A 26 M2G C6 A 27 C C4 :0.442 A 71 G H2' A 72 C O4' :0.441 A 24 G C6 A 25 C C4 :0.439 A 69 U H2' A 70 C H6 :0.437 A 1 G H2' A 2 C O4' :0.437 A 35 A C8 A 35 A OP2 :0.433 A 26 M2G CM2 A 44 A C2 :0.430 A 25 C C5' A 92 HOH O :0.428 A 11 C H6 A 11 C O5' :0.421 A 31 A H2' A 81 HOH O :0.416 A 46 7MG P A 128 HOH O :0.415 A 1 G C4 A 2 C C6 :0.413 A 10 2MG H2' A 11 C O5' :0.412 A 59 U H2' A 60 C O5' :0.407 A 42 G C2' A 43 G O5' :0.406 A 55 PSU H6 A 55 PSU O5' :0.406 A 2 C H2' A 2 C O2 :0.405 A 63 C C2 A 64 A C8 :0.401 A 1 G C4 A 2 C C5 :0.400 A 33 U H5'' A 34 OMG OP2 :0.400 clashscore = 50.48 ../test/6TNA.pdb 50.48