remarks file: relaxation/refine.inp remarks relaxation matrix refinement using the method of remarks Yip and Case (1989), JMR 83, 643-648. set seed 584930 end { seed for random velocity assignemnt } structure PSF 4 !NTITLE REMARKS FILENAME="c2.psf" REMARKS generic parameter file for all-h proteins PARALLHSA.PRO REMARKS based on PARMALLH6.PRO REMARKS DATE:26-Nov-91 15:16:25 created by user: nilges 114 !NATOM 1 1 PHE N NH1 -.360000 14.0070 0 2 1 PHE HN H .260000 1.00800 0 3 1 PHE CA CT .000000 12.0110 0 4 1 PHE HA HA .100000 1.00800 0 5 1 PHE CB CT -.160000 12.0110 0 6 1 PHE HB1 HA .100000 1.00800 0 7 1 PHE HB2 HA .100000 1.00800 0 8 1 PHE CG CA 0.300000E-01 12.0110 0 9 1 PHE CD1 CA -.160000 12.0110 0 10 1 PHE HD1 HA .140000 1.00800 0 11 1 PHE CD2 CA -.160000 12.0110 0 12 1 PHE HD2 HA .140000 1.00800 0 13 1 PHE CE1 CA -.150000 12.0110 0 14 1 PHE HE1 HA .140000 1.00800 0 15 1 PHE CE2 CA -.150000 12.0110 0 16 1 PHE HE2 HA .140000 1.00800 0 17 1 PHE CZ CA -.150000 12.0110 0 18 1 PHE HZ HA .140000 1.00800 0 19 1 PHE C C .480000 12.0110 0 20 1 PHE O O -.480000 15.9990 0 21 2 PRO N N -.360000 14.0070 0 22 2 PRO CA CT .000000 12.0110 0 23 2 PRO HA HA .100000 1.00800 0 24 2 PRO CB CT -.200000 12.0110 0 25 2 PRO HB1 HA .100000 1.00800 0 26 2 PRO HB2 HA .100000 1.00800 0 27 2 PRO CG CT -.200000 12.0110 0 28 2 PRO HG1 HA .100000 1.00800 0 29 2 PRO HG2 HA .100000 1.00800 0 30 2 PRO CD CT 0.600000E-01 12.0110 0 31 2 PRO HD1 HA .100000 1.00800 0 32 2 PRO HD2 HA .100000 1.00800 0 33 2 PRO C C .480000 12.0110 0 34 2 PRO O O -.480000 15.9990 0 35 3 THR N NH1 -.360000 14.0070 0 36 3 THR HN H .260000 1.00800 0 37 3 THR CA CT .000000 12.0110 0 38 3 THR HA HA .100000 1.00800 0 39 3 THR CB CT .180000 12.0110 0 40 3 THR HB HA .100000 1.00800 0 41 3 THR OG1 OH -.680000 15.9990 0 42 3 THR HG1 H .400000 1.00800 0 43 3 THR CG2 CT -.300000 12.0110 0 44 3 THR HG21 HA .100000 1.00800 0 45 3 THR HG22 HA .100000 1.00800 0 46 3 THR HG23 HA .100000 1.00800 0 47 3 THR C C .480000 12.0110 0 48 3 THR O O -.480000 15.9990 0 49 4 LYS N NH1 -.360000 14.0070 0 50 4 LYS HN H .260000 1.00800 0 51 4 LYS CA CT .000000 12.0110 0 52 4 LYS HA HA .100000 1.00800 0 53 4 LYS CB CT -.200000 12.0110 0 54 4 LYS HB1 HA .100000 1.00800 0 55 4 LYS HB2 HA .100000 1.00800 0 56 4 LYS CG CT -.200000 12.0110 0 57 4 LYS HG1 HA .100000 1.00800 0 58 4 LYS HG2 HA .100000 1.00800 0 59 4 LYS CD CT -.200000 12.0110 0 60 4 LYS HD1 HA .100000 1.00800 0 61 4 LYS HD2 HA .100000 1.00800 0 62 4 LYS CE CT .305000 12.0110 0 63 4 LYS HE1 HA .100000 1.00800 0 64 4 LYS HE2 HA .100000 1.00800 0 65 4 LYS NZ NH3 -.810000 14.0070 0 66 4 LYS HZ1 HC .435000 1.00800 0 67 4 LYS HZ2 HC .435000 1.00800 0 68 4 LYS HZ3 HC .435000 1.00800 0 69 4 LYS C C .480000 12.0110 0 70 4 LYS O O -.480000 15.9990 0 71 5 TRP N NH1 -.360000 14.0070 0 72 5 TRP HN H .260000 1.00800 0 73 5 TRP CA CT .000000 12.0110 0 74 5 TRP HA HA .100000 1.00800 0 75 5 TRP CB CT -.200000 12.0110 0 76 5 TRP HB1 HA .100000 1.00800 0 77 5 TRP HB2 HA .100000 1.00800 0 78 5 TRP CG CX -0.400000E-01 12.0110 0 79 5 TRP CD1 CW -0.100000E-01 12.0110 0 80 5 TRP HD1 HA .140000 1.00800 0 81 5 TRP CD2 CB -0.500000E-01 12.0110 0 82 5 TRP NE1 NA -.490000 14.0070 0 83 5 TRP HE1 H .400000 1.00800 0 84 5 TRP CE2 CN .130000 12.0110 0 85 5 TRP CE3 CA -.160000 12.0110 0 86 5 TRP HE3 HA .140000 1.00800 0 87 5 TRP CZ2 CA -.150000 12.0110 0 88 5 TRP HZ2 HA .140000 1.00800 0 89 5 TRP CZ3 CA -.150000 12.0110 0 90 5 TRP HZ3 HA .140000 1.00800 0 91 5 TRP CH2 CA -.180000 12.0110 0 92 5 TRP HH2 HA .140000 1.00800 0 93 5 TRP C C .480000 12.0110 0 94 5 TRP O O -.480000 15.9990 0 95 6 PHE N NH1 -.360000 14.0070 0 96 6 PHE HN H .260000 1.00800 0 97 6 PHE CA CT .000000 12.0110 0 98 6 PHE HA HA .100000 1.00800 0 99 6 PHE CB CT -.160000 12.0110 0 100 6 PHE HB1 HA .100000 1.00800 0 101 6 PHE HB2 HA .100000 1.00800 0 102 6 PHE CG CA 0.300000E-01 12.0110 0 103 6 PHE CD1 CA -.160000 12.0110 0 104 6 PHE HD1 HA .140000 1.00800 0 105 6 PHE CD2 CA -.160000 12.0110 0 106 6 PHE HD2 HA .140000 1.00800 0 107 6 PHE CE1 CA -.150000 12.0110 0 108 6 PHE HE1 HA .140000 1.00800 0 109 6 PHE CE2 CA -.150000 12.0110 0 110 6 PHE HE2 HA .140000 1.00800 0 111 6 PHE CZ CA -.150000 12.0110 0 112 6 PHE HZ HA .140000 1.00800 0 113 6 PHE C C .480000 12.0110 0 114 6 PHE O O -.480000 15.9990 0 119 !NBOND: bonds 1 2 1 3 3 4 3 5 5 6 5 7 5 8 8 9 9 10 8 11 11 12 9 13 13 14 11 15 15 16 13 17 17 18 15 17 3 19 19 20 21 22 22 23 22 24 24 25 24 26 24 27 27 28 27 29 27 30 30 31 30 32 30 21 22 33 33 34 19 21 35 36 35 37 37 38 37 39 39 40 39 41 41 42 39 43 43 44 43 45 43 46 37 47 47 48 33 35 49 50 49 51 51 52 51 53 53 54 53 55 53 56 56 57 56 58 56 59 59 60 59 61 59 62 62 63 62 64 62 65 65 66 65 67 65 68 51 69 69 70 47 49 71 72 71 73 73 74 73 75 75 76 75 77 75 78 78 79 79 80 78 81 79 82 82 83 82 84 81 84 81 85 85 86 84 87 87 88 85 89 89 90 87 91 91 92 89 91 73 93 93 94 69 71 95 96 95 97 97 98 97 99 99 100 99 101 99 102 102 103 103 104 102 105 105 106 103 107 107 108 105 109 109 110 107 111 111 112 109 111 97 113 113 114 93 95 113 1 214 !NTHETA: angles 2 1 3 1 3 4 1 3 5 1 3 19 4 3 5 4 3 19 3 5 6 3 5 7 3 5 8 5 3 19 6 5 7 6 5 8 7 5 8 5 8 9 5 8 11 8 9 10 9 8 11 8 9 13 10 9 13 8 11 12 8 11 15 12 11 15 9 13 14 9 13 17 14 13 17 11 15 16 11 15 17 16 15 17 13 17 18 13 17 15 18 17 15 3 19 20 21 22 23 21 22 24 22 21 30 21 22 33 23 22 24 23 22 33 22 24 25 22 24 26 22 24 27 24 22 33 25 24 26 25 24 27 26 24 27 24 27 28 24 27 29 24 27 30 28 27 29 28 27 30 29 27 30 27 30 31 27 30 32 27 30 21 31 30 32 31 30 21 32 30 21 22 33 34 3 19 21 20 19 21 19 21 22 19 21 30 36 35 37 35 37 38 35 37 39 35 37 47 38 37 39 38 37 47 37 39 40 37 39 41 37 39 43 39 37 47 40 39 41 40 39 43 39 41 42 41 39 43 39 43 44 39 43 45 39 43 46 44 43 45 44 43 46 45 43 46 37 47 48 22 33 35 34 33 35 33 35 37 33 35 36 50 49 51 49 51 52 49 51 53 49 51 69 52 51 53 52 51 69 51 53 54 51 53 55 51 53 56 53 51 69 54 53 55 54 53 56 55 53 56 53 56 57 53 56 58 53 56 59 57 56 58 57 56 59 58 56 59 56 59 60 56 59 61 56 59 62 60 59 61 60 59 62 61 59 62 59 62 63 59 62 64 59 62 65 63 62 64 63 62 65 64 62 65 62 65 66 62 65 67 62 65 68 66 65 67 66 65 68 67 65 68 51 69 70 37 47 49 48 47 49 47 49 51 47 49 50 72 71 73 71 73 74 71 73 75 71 73 93 74 73 75 74 73 93 73 75 76 73 75 77 73 75 78 75 73 93 76 75 77 76 75 78 77 75 78 75 78 79 75 78 81 78 79 80 79 78 81 78 79 82 80 79 82 78 81 84 78 81 85 79 82 83 79 82 84 83 82 84 82 84 81 82 84 87 84 81 85 81 84 87 81 85 86 81 85 89 86 85 89 84 87 88 84 87 91 88 87 91 85 89 90 85 89 91 90 89 91 87 91 92 87 91 89 92 91 89 73 93 94 51 69 71 70 69 71 69 71 73 69 71 72 96 95 97 95 97 98 95 97 99 95 97 113 98 97 99 98 97 113 97 99 100 97 99 101 97 99 102 99 97 113 100 99 101 100 99 102 101 99 102 99 102 103 99 102 105 102 103 104 103 102 105 102 103 107 104 103 107 102 105 106 102 105 109 106 105 109 103 107 108 103 107 111 108 107 111 105 109 110 105 109 111 110 109 111 107 111 112 107 111 109 112 111 109 97 113 114 73 93 95 94 93 95 93 95 97 93 95 96 97 113 1 114 113 1 113 1 3 113 1 2 11 !NPHI: dihedrals 8 5 3 1 9 8 5 3 41 39 37 35 56 53 51 49 59 56 53 51 62 59 56 53 65 62 59 56 78 75 73 71 79 78 75 73 102 99 97 95 103 102 99 97 68 !NIMPHI: impropers 4 1 19 5 12 11 15 17 16 15 17 13 18 17 13 9 14 13 9 8 10 9 8 11 5 8 11 15 8 9 13 17 9 13 17 15 13 17 15 11 17 15 11 8 15 11 8 9 11 8 9 13 23 21 33 24 22 21 19 30 38 35 47 39 40 37 41 43 34 33 35 37 36 35 33 22 22 33 35 37 52 49 69 53 48 47 49 51 50 49 47 37 37 47 49 51 74 71 93 75 81 84 87 91 84 87 91 89 87 91 89 85 91 89 85 81 89 85 81 84 85 81 84 87 79 82 84 87 79 78 81 85 82 84 87 91 82 84 81 85 78 81 85 89 78 81 84 87 88 87 91 89 92 91 89 85 90 89 91 87 86 85 89 91 83 82 84 81 80 79 82 84 75 78 81 84 70 69 71 73 72 71 69 51 51 69 71 73 98 95 113 99 106 105 109 111 110 109 111 107 112 111 107 103 108 107 103 102 104 103 102 105 99 102 105 109 102 103 107 111 103 107 111 109 107 111 109 105 111 109 105 102 109 105 102 103 105 102 103 107 94 93 95 97 96 95 93 73 73 93 95 97 114 113 1 3 2 1 113 97 97 113 1 3 19 3 21 22 19 20 21 22 0 !NDON: donors 0 !NACC: acceptors 18 !NNB 17 15 13 11 9 8 91 89 87 85 84 81 111 109 107 105 103 102 0 0 0 0 0 0 0 1 2 2 3 3 4 4 5 5 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 7 7 7 8 9 9 10 10 11 11 12 12 12 12 12 12 12 12 12 12 12 13 14 14 15 15 16 16 17 17 18 18 18 18 6 0 !NGRP 0 0 0 20 0 0 34 0 0 48 0 0 70 0 0 94 0 0 end { read structure file } coor REMARK FILENAME="USER:[NILGES.C2]C2_01.SAF;2" REMARK randoma01 final structure REMARK DATE: 3-JUN-89 18:50:57 created by user: NILGES ATOM 1 N PHE 1 2.099 -0.708 -0.487 1.00 0.00 ATOM 2 HN PHE 1 2.770 -0.387 -1.118 1.00 0.00 ATOM 3 CA PHE 1 1.159 -1.850 -0.935 1.00 0.00 ATOM 4 HA PHE 1 0.416 -1.441 -1.597 1.00 0.00 ATOM 5 CB PHE 1 2.056 -2.837 -1.684 1.00 0.00 ATOM 6 HB1 PHE 1 2.506 -2.337 -2.531 1.00 0.00 ATOM 7 HB2 PHE 1 2.835 -3.176 -1.027 1.00 0.00 ATOM 8 CG PHE 1 1.249 -4.032 -2.191 1.00 0.00 ATOM 9 CD1 PHE 1 0.734 -4.034 -3.499 1.00 0.00 ATOM 10 HD1 PHE 1 0.910 -3.186 -4.146 1.00 0.00 ATOM 11 CD2 PHE 1 1.014 -5.143 -1.364 1.00 0.00 ATOM 12 HD2 PHE 1 1.406 -5.155 -0.356 1.00 0.00 ATOM 13 CE1 PHE 1 -0.001 -5.127 -3.970 1.00 0.00 ATOM 14 HE1 PHE 1 -0.394 -5.120 -4.977 1.00 0.00 ATOM 15 CE2 PHE 1 0.278 -6.236 -1.839 1.00 0.00 ATOM 16 HE2 PHE 1 0.101 -7.087 -1.197 1.00 0.00 ATOM 17 CZ PHE 1 -0.228 -6.227 -3.141 1.00 0.00 ATOM 18 HZ PHE 1 -0.792 -7.072 -3.508 1.00 0.00 ATOM 19 C PHE 1 0.438 -2.578 0.240 1.00 0.00 ATOM 20 O PHE 1 1.032 -2.783 1.279 1.00 0.00 ATOM 21 N PRO 2 -0.873 -3.033 0.048 1.00 0.00 ATOM 22 CA PRO 2 -1.722 -2.887 -1.213 1.00 0.00 ATOM 23 HA PRO 2 -1.099 -2.871 -2.066 1.00 0.00 ATOM 24 CB PRO 2 -2.553 -4.222 -1.204 1.00 0.00 ATOM 25 HB1 PRO 2 -3.619 -4.020 -1.254 1.00 0.00 ATOM 26 HB2 PRO 2 -2.269 -4.845 -2.049 1.00 0.00 ATOM 27 CG PRO 2 -2.216 -4.943 0.131 1.00 0.00 ATOM 28 HG1 PRO 2 -3.120 -5.308 0.613 1.00 0.00 ATOM 29 HG2 PRO 2 -1.553 -5.767 -0.086 1.00 0.00 ATOM 30 CD PRO 2 -1.486 -3.900 1.026 1.00 0.00 ATOM 31 HD1 PRO 2 -2.191 -3.335 1.634 1.00 0.00 ATOM 32 HD2 PRO 2 -0.734 -4.367 1.655 1.00 0.00 ATOM 33 C PRO 2 -2.817 -1.666 -1.181 1.00 0.00 ATOM 34 O PRO 2 -3.466 -1.484 -0.173 1.00 0.00 ATOM 35 N THR 3 -2.970 -0.880 -2.310 1.00 0.00 ATOM 36 HN THR 3 -2.364 -0.953 -2.986 1.00 0.00 ATOM 37 CA THR 3 -4.044 0.243 -2.398 1.00 0.00 ATOM 38 HA THR 3 -3.835 0.867 -3.272 1.00 0.00 ATOM 39 CB THR 3 -5.443 -0.389 -2.479 1.00 0.00 ATOM 40 HB THR 3 -6.204 0.343 -2.740 1.00 0.00 ATOM 41 OG1 THR 3 -5.675 -0.922 -1.212 1.00 0.00 ATOM 42 HG1 THR 3 -4.891 -0.767 -0.696 1.00 0.00 ATOM 43 CG2 THR 3 -5.441 -1.605 -3.409 1.00 0.00 ATOM 44 HG21 THR 3 -6.443 -1.997 -3.495 1.00 0.00 ATOM 45 HG22 THR 3 -5.085 -1.317 -4.386 1.00 0.00 ATOM 46 HG23 THR 3 -4.793 -2.371 -3.005 1.00 0.00 ATOM 47 C THR 3 -3.922 1.058 -1.191 1.00 0.00 ATOM 48 O THR 3 -4.720 0.983 -0.278 1.00 0.00 ATOM 49 N LYS 4 -2.911 1.863 -1.194 1.00 0.00 ATOM 50 HN LYS 4 -2.395 1.965 -1.948 1.00 0.00 ATOM 51 CA LYS 4 -2.541 2.542 0.001 1.00 0.00 ATOM 52 HA LYS 4 -3.386 2.904 0.542 1.00 0.00 ATOM 53 CB LYS 4 -1.882 1.336 0.690 1.00 0.00 ATOM 54 HB1 LYS 4 -1.679 1.558 1.670 1.00 0.00 ATOM 55 HB2 LYS 4 -2.565 0.468 0.665 1.00 0.00 ATOM 56 CG LYS 4 -0.531 0.920 -0.067 1.00 0.00 ATOM 57 HG1 LYS 4 0.245 1.368 0.408 1.00 0.00 ATOM 58 HG2 LYS 4 -0.419 -0.126 0.041 1.00 0.00 ATOM 59 CD LYS 4 -0.464 1.290 -1.657 1.00 0.00 ATOM 60 HD1 LYS 4 -1.100 0.624 -2.204 1.00 0.00 ATOM 61 HD2 LYS 4 -0.775 2.271 -1.837 1.00 0.00 ATOM 62 CE LYS 4 0.978 1.199 -2.212 1.00 0.00 ATOM 63 HE1 LYS 4 1.124 0.277 -2.740 1.00 0.00 ATOM 64 HE2 LYS 4 1.675 1.266 -1.423 1.00 0.00 ATOM 65 NZ LYS 4 1.228 2.325 -3.157 1.00 0.00 ATOM 66 HZ1 LYS 4 0.361 2.523 -3.695 1.00 0.00 ATOM 67 HZ2 LYS 4 1.992 2.063 -3.812 1.00 0.00 ATOM 68 HZ3 LYS 4 1.505 3.173 -2.621 1.00 0.00 ATOM 69 C LYS 4 -1.420 3.649 -0.216 1.00 0.00 ATOM 70 O LYS 4 -1.540 4.544 -1.030 1.00 0.00 ATOM 71 N TRP 5 -0.375 3.491 0.579 1.00 0.00 ATOM 72 HN TRP 5 -0.431 2.843 1.239 1.00 0.00 ATOM 73 CA TRP 5 0.883 4.275 0.488 1.00 0.00 ATOM 74 HA TRP 5 0.825 4.958 -0.353 1.00 0.00 ATOM 75 CB TRP 5 1.156 4.995 1.825 1.00 0.00 ATOM 76 HB1 TRP 5 1.586 4.313 2.534 1.00 0.00 ATOM 77 HB2 TRP 5 1.846 5.811 1.659 1.00 0.00 ATOM 78 CG TRP 5 -0.160 5.557 2.375 1.00 0.00 ATOM 79 CD1 TRP 5 -0.699 6.699 1.966 1.00 0.00 ATOM 80 HD1 TRP 5 -0.322 7.381 1.215 1.00 0.00 ATOM 81 CD2 TRP 5 -0.903 4.985 3.310 1.00 0.00 ATOM 82 NE1 TRP 5 -1.821 6.811 2.697 1.00 0.00 ATOM 83 HE1 TRP 5 -2.437 7.567 2.610 1.00 0.00 ATOM 84 CE2 TRP 5 -2.035 5.770 3.579 1.00 0.00 ATOM 85 CE3 TRP 5 -0.718 3.780 4.024 1.00 0.00 ATOM 86 HE3 TRP 5 0.134 3.155 3.823 1.00 0.00 ATOM 87 CZ2 TRP 5 -2.967 5.365 4.542 1.00 0.00 ATOM 88 HZ2 TRP 5 -3.836 5.974 4.740 1.00 0.00 ATOM 89 CZ3 TRP 5 -1.654 3.382 4.987 1.00 0.00 ATOM 90 HZ3 TRP 5 -1.506 2.464 5.535 1.00 0.00 ATOM 91 CH2 TRP 5 -2.775 4.173 5.244 1.00 0.00 ATOM 92 HH2 TRP 5 -3.493 3.864 5.990 1.00 0.00 ATOM 93 C TRP 5 1.981 3.202 0.226 1.00 0.00 ATOM 94 O TRP 5 2.671 3.235 -0.774 1.00 0.00 ATOM 95 N PHE 6 2.121 2.278 1.208 1.00 0.00 ATOM 96 HN PHE 6 1.658 2.408 2.058 1.00 0.00 ATOM 97 CA PHE 6 3.006 1.060 1.039 1.00 0.00 ATOM 98 HA PHE 6 3.685 1.211 0.195 1.00 0.00 ATOM 99 CB PHE 6 3.766 0.815 2.361 1.00 0.00 ATOM 100 HB1 PHE 6 4.092 1.757 2.774 1.00 0.00 ATOM 101 HB2 PHE 6 3.118 0.320 3.073 1.00 0.00 ATOM 102 CG PHE 6 4.987 -0.068 2.090 1.00 0.00 ATOM 103 CD1 PHE 6 6.273 0.498 2.008 1.00 0.00 ATOM 104 HD1 PHE 6 6.400 1.563 2.139 1.00 0.00 ATOM 105 CD2 PHE 6 4.840 -1.454 1.919 1.00 0.00 ATOM 106 HD2 PHE 6 3.858 -1.901 1.980 1.00 0.00 ATOM 107 CE1 PHE 6 7.388 -0.312 1.759 1.00 0.00 ATOM 108 HE1 PHE 6 8.374 0.130 1.695 1.00 0.00 ATOM 109 CE2 PHE 6 5.958 -2.261 1.670 1.00 0.00 ATOM 110 HE2 PHE 6 5.835 -3.325 1.537 1.00 0.00 ATOM 111 CZ PHE 6 7.230 -1.689 1.591 1.00 0.00 ATOM 112 HZ PHE 6 8.092 -2.313 1.398 1.00 0.00 ATOM 113 C PHE 6 2.057 -0.172 0.745 1.00 0.00 ATOM 114 O PHE 6 1.314 -0.568 1.614 1.00 0.00 END parameter { set energy parameters } @TOPPAR:parallhdg.pro nbonds atom nbxmod -3 tolerance 0.5 repel 0.75 rcon 4.0 rexp 2 cutnb 4.5 end end flags include relaxation end { include the relaxation energy term } vector ident (store1) { non-exchangable protons } (name h* and not (name hn or name ht3 or (resn lys and name hz#) or (resn arg and (name he or name hh#)) or (resn asn and name hd2#) or (resn gln and name he2#) or (resn ser and name hg) or (resn thr and name hg1) or (resn tyr and name hh) or (resn trp and name he1) or (resn his and name hd1))) vector ident (store2) { exchangable protons } (name hn or name ht3 or (resn lys and name hz#) or (resn arg and (name he or name hh#)) or (resn asn and name hd2#) or (resn gln and name he2#) or (resn ser and name hg) or (resn thr and name hg1) or (resn tyr and name hh) or (resn trp and name he1) or (resn his and name hd1)) relaxation nrestraints 200 { expected number of restraints } { ============================= specify the physical parameters of the system } group H2O { a group of spectra, DMSO, is defined } select H2O (name h*) { all protons relax } unresolved H2O methyl { methyl protons are unresolved } end omega H2O 500.0e6 { spectrometer frequency in Hz } taucorrel H2O { correlation times ( in s) } model lipari { and order parameters } vector (name hn or name ha) (name hn or name ha) 0.75e-9 0.85 vector (name hn or name ha) (name h* and not (name hn or name ha)) 0.75e-9 0.80 vector (name h* and not (name hn or name ha)) (name h* and not (name hn or name ha)) 0.75e-9 0.65 end occupancy H2O (store2) 0.9 group D2O { a group of spectra, D2O, is defined } select D2O (store1) unresolved D2O methyl { methyl protons are unresolved } end omega D2O 500.0e6 { spectrometer frequency in Hz } taucorrel D2O { correlation times ( in s) } model lipari { and order parameters } vector (store1 and (name hn or name ha)) (store1 and (name hn or name ha)) 0.75e-9 0.85 vector (store1 and (name hn or name ha)) (store1 and not (name hn or name ha)) 0.75e-9 0.80 vector (store1 and not (name hn or name ha)) (store1 and not (name hn or name ha)) 0.75e-9 0.65 end average 3 { r-3 average to methyl groups } { ========================================================== read in the data } classification H300 { define a classification, D300 } remarks intensities for c2 from NOESY, 300 ms error_format input uniform value 0.05 mode absolute end set echo off message off end assign (resid 1 and name hn) (resid 1 and name hb2) 1.6 assign (resid 1 and name hn) (resid 1 and name hb1) 1.4 assign (resid 1 and name ha) (resid 2 and name ha) 5.1 assign (resid 1 and name ha) (resid 3 and name hn) 0.41 assign (resid 1 and name hn) (resid 6 and name ha) 2.4 assign (resid 2 and name ha) (resid 2 and name hb1) 0.36 assign (resid 2 and name ha) (resid 2 and name hg2) 0.47 assign (resid 2 and name ha) (resid 3 and name hn) 0.15 assign (resid 2 and name hg1) (resid 2 and name hd#) 0.44 assign (resid 2 and name hg2) (resid 2 and name hd#) 0.20 assign (resid 3 and name hn) (resid 3 and name hg1) 0.26 assign (resid 3 and name hn) (resid 3 and name hg2#) 0.23 assign (resid 3 and name hn) (resid 4 and name hb#) 0.23 assign (resid 3 and name hn) (resid 4 and name hd#) 0.12 assign (resid 3 and name hg1) (resid 3 and name hg2#) 0.37 assign (resid 3 and name hg1) (resid 4 and name hn) 0.09 assign (resid 4 and name hn) (resid 4 and name ha) 1.15 assign (resid 4 and name hn) (resid 4 and name hb#) 0.73 assign (resid 4 and name hn) (resid 4 and name hg#) 0.18 assign (resid 4 and name ha) (resid 4 and name hb#) 1.18 assign (resid 4 and name ha) (resid 5 and name hn) 0.40 assign (resid 4 and name hb#) (resid 4 and name hg#) 2.31 assign (resid 4 and name hb#) (resid 5 and name hn) 0.14 assign (resid 5 and name hn) (resid 5 and name ha) 0.93 assign (resid 5 and name hn) (resid 6 and name hn) 0.51 assign (resid 6 and name hn) (resid 6 and name ha) 0.45 assign (resid 6 and name ha) (resid 6 and name hb#) 0.40 set echo on message on end clgroup H300 H2O { which belongs to group D2O } taumix H300 0.30 { mixing time, in s } minint H300 0.05 { minimum measurable intensity } classification D200 { define a classification, D300 } remarks noe intensity table for mixing time 200 ms in D2O error_format input uniform value 0.05 mode absolute end set echo off message off end assign (resid 1 and name ha) (resid 2 and name ha) 3.7 assign (resid 2 and name ha) (resid 2 and name hb1) 0.31 assign (resid 2 and name ha) (resid 2 and name hg2) 0.35 assign (resid 2 and name hg1) (resid 2 and name hd#) 0.32 assign (resid 2 and name hg2) (resid 2 and name hd#) 0.16 assign (resid 3 and name hg1) (resid 3 and name hg2#) 0.24 assign (resid 4 and name ha) (resid 4 and name hb#) 0.87 assign (resid 4 and name hb#) (resid 4 and name hg#) 1.64 assign (resid 6 and name ha) (resid 6 and name hb#) 0.12 set echo on message on end clgroup D200 D2O { which belongs to group D2O } taumix D200 0.20 { mixing time, in s } minint D200 0.05 { minimum measurable intensity } classification D300 { define a classification, D300 } remarks noe intensity table for mixing time 300 ms in D2O error_format input uniform value 0.05 mode absolute end set echo off message off end assign (resid 1 and name ha) (resid 2 and name ha) 5.1 assign (resid 2 and name ha) (resid 2 and name hb1) 0.36 assign (resid 2 and name ha) (resid 2 and name hg2) 0.47 assign (resid 2 and name hg1) (resid 2 and name hd#) 0.44 assign (resid 2 and name hg2) (resid 2 and name hd#) 0.20 assign (resid 3 and name hg1) (resid 3 and name hg2#) 0.37 assign (resid 4 and name ha) (resid 4 and name hb#) 1.18 assign (resid 4 and name hb#) (resid 4 and name hg#) 2.31 assign (resid 6 and name ha) (resid 6 and name hb#) 0.40 set echo on message on end clgroup D300 D2O { which belongs to group D2O } taumix D300 0.30 { mixing time, in s } minint D300 0.05 { minimum measurable intensity } sort { sort the intensities wrt spin pair } cutoff { cutoff used for gradient and relaxation matrix } mode all value 4.5 end potential parabola { error estimates are not used } iexp 0.1666666667 { Dev = I_calc^iexp - I_obs^iexp } eexp 2 { E = Dev^eexp } calibrate { calculate spectrum and calibration factor } quality 0.33 automatic off reference all group class end weight D300 2000 { set the relaxation weight } tolerance 0.00 { relaxation energy has to be calculated every step } print threshold 9999 end { print R-factor of initial structure } end minimize powell nstep 25 end { minimize with NOESY intensity restraints } write coor end stop