REMARKS Testing b-factor and occupancy refinements remarks struct PSF 4 !NTITLE REMARKS FILENAME="$9$DRB2:[KURIYAN.EXPLORER.TEST1]TEST.PSF;1" REMARKS FRAGMENT FOR COPROL121 FOR TESTING REMARKS REMARKS DATE: 1-APR-87 10:29:58 created by user: KURIYAN 28 !NATOM 1 TEST 1 VAL HT1 HC 0.350000 1.00800 0 2 TEST 1 VAL HT2 HC 0.350000 1.00800 0 3 TEST 1 VAL N NH3 -0.300000 14.0067 0 4 TEST 1 VAL HT3 HC 0.350000 1.00800 0 5 TEST 1 VAL CA CH1E 0.250000 13.0190 0 6 TEST 1 VAL CB CH1E 0.000000E+00 13.0190 0 7 TEST 1 VAL CG1 CH3E 0.000000E+00 15.0350 0 8 TEST 1 VAL CG2 CH3E 0.000000E+00 15.0350 0 9 TEST 1 VAL C C 0.550000 12.0110 0 10 TEST 1 VAL O O -0.550000 15.9994 0 11 TEST 2 LEU N NH1 -0.350000 14.0067 0 12 TEST 2 LEU H H 0.250000 1.00800 0 13 TEST 2 LEU CA CH1E 0.100000 13.0190 0 14 TEST 2 LEU CB CH2E 0.000000E+00 14.0270 0 15 TEST 2 LEU CG CH1E 0.000000E+00 13.0190 0 16 TEST 2 LEU CD1 CH3E 0.000000E+00 15.0350 0 17 TEST 2 LEU CD2 CH3E 0.000000E+00 15.0350 0 18 TEST 2 LEU C C 0.550000 12.0110 0 19 TEST 2 LEU O O -0.550000 15.9994 0 20 TEST 3 SER N NH1 -0.350000 14.0067 0 21 TEST 3 SER H H 0.250000 1.00800 0 22 TEST 3 SER CA CH1E 0.100000 13.0190 0 23 TEST 3 SER CB CH2E 0.250000 14.0270 0 24 TEST 3 SER OG OH1 -0.650000 15.9994 0 25 TEST 3 SER HG H 0.400000 1.00800 0 26 TEST 3 SER C C 0.140000 12.0110 0 27 TEST 3 SER OT1 OC -0.570000 15.9994 0 28 TEST 3 SER OT2 OC -0.570000 15.9994 0 27 !NBOND: bonds 3 5 5 9 9 10 5 6 6 7 6 8 1 3 2 3 4 3 11 13 13 18 18 19 11 12 13 14 14 15 15 16 15 17 9 11 20 22 22 26 20 21 22 23 23 24 24 25 18 20 26 27 26 28 39 !NTHETA: angles 3 5 9 3 5 6 5 9 10 9 5 6 5 6 7 5 6 8 7 6 8 1 3 2 2 3 4 2 3 5 1 3 4 1 3 5 4 3 5 11 13 18 13 11 12 11 13 14 13 18 19 18 13 14 13 14 15 14 15 16 14 15 17 16 15 17 5 9 11 10 9 11 9 11 13 9 11 12 20 22 26 22 20 21 20 22 23 26 22 23 22 23 24 23 24 25 13 18 20 19 18 20 18 20 22 18 20 21 22 26 27 22 26 28 27 26 28 15 !NPHI: dihedrals 3 5 6 7 2 3 5 9 1 3 5 9 4 3 5 9 11 13 14 15 13 14 15 17 9 11 13 18 3 5 9 11 5 9 11 13 20 22 23 24 22 23 24 25 18 20 22 26 11 13 18 20 13 18 20 22 20 22 26 28 10 !NIMPHI: impropers 5 3 9 6 6 8 7 5 13 11 18 14 15 17 16 14 9 5 11 10 11 9 13 12 22 20 26 23 18 13 20 19 20 18 22 21 26 22 28 27 6 !NDON: donors 3 1 3 2 3 4 11 12 20 21 24 25 5 !NACC: acceptors 10 9 19 18 24 0 27 26 28 26 0 !NNB 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 !NGRP 0 2 0 5 0 0 8 1 0 10 1 0 13 0 0 17 1 0 19 1 0 22 1 0 25 2 0 END param @TOPPAR:param19.pro end coor REMARK FILENAME="TH:[KURIYAN.EXPLORER.TEST1]TEST1.PDB;1" REMARK - parameter file PARAM19 - REMARK PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) REMARK TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) REMARK JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 REMARK DATE: 1-APR-87 14:48:04 created by user: KURIYAN ATOM 1 HT1 VAL 1 -3.950 -0.677 -2.142 1.00 0.00 TEST ATOM 2 HT2 VAL 1 -4.064 0.998 -1.881 1.00 0.00 TEST ATOM 3 N VAL 1 -4.207 0.060 -1.454 1.00 25.01 TEST ATOM 4 HT3 VAL 1 -5.206 -0.049 -1.186 1.00 0.00 TEST ATOM 5 CA VAL 1 -3.353 -0.070 -0.245 1.00 10.21 TEST ATOM 6 CB VAL 1 -3.658 -1.409 0.478 1.00 26.78 TEST ATOM 7 CG1 VAL 1 -3.667 -1.256 2.018 1.00 25.94 TEST ATOM 8 CG2 VAL 1 -4.972 -2.085 0.140 1.00 28.48 TEST ATOM 9 C VAL 1 -1.899 0.093 -0.656 1.00 10.47 TEST ATOM 10 O VAL 1 -1.503 -0.499 -1.673 1.00 14.11 TEST ATOM 11 N LEU 2 -1.104 0.902 0.074 1.00 17.15 TEST ATOM 12 H LEU 2 -1.490 1.500 0.747 1.00 0.00 TEST ATOM 13 CA LEU 2 0.340 0.876 -0.150 1.00 9.88 TEST ATOM 14 CB LEU 2 1.098 2.086 0.497 1.00 13.33 TEST ATOM 15 CG LEU 2 0.790 3.394 -0.296 1.00 13.63 TEST ATOM 16 CD1 LEU 2 -0.578 3.799 -0.189 1.00 13.95 TEST ATOM 17 CD2 LEU 2 1.732 4.405 0.290 1.00 14.84 TEST ATOM 18 C LEU 2 0.873 -0.476 0.385 1.00 6.06 TEST ATOM 19 O LEU 2 0.434 -0.879 1.428 1.00 8.72 TEST ATOM 20 N SER 3 1.811 -0.923 -0.413 1.00 13.05 TEST ATOM 21 H SER 3 1.940 -0.537 -1.304 1.00 0.00 TEST ATOM 22 CA SER 3 2.652 -2.004 0.059 1.00 9.81 TEST ATOM 23 CB SER 3 3.463 -2.643 -1.064 1.00 15.39 TEST ATOM 24 OG SER 3 4.388 -1.619 -1.668 1.00 16.37 TEST ATOM 25 HG SER 3 3.872 -0.891 -2.023 1.00 0.00 TEST ATOM 26 C SER 3 3.590 -1.457 1.157 1.00 7.20 TEST ATOM 27 OT1 SER 3 3.770 -0.296 1.284 1.00 14.37 TEST END delete sele ( not known ) end ! ! vector do ( store1 = b ) ( all ) !! these B-factors correspond to R-factor of 0.0 vector do ( store3 = b ) ( all ) ! modify the B-factors vector do ( b = b * 1.5 ) ( not ( name ca or name c or name o ) ) vector do ( b = b * 0.5 ) ( name ca or name c or name o ) vector show element ( b ) ( not name h* ) ! flags excl * incl xrefin end {* read diffraction data *} xrefin a=5.0 b=10.0 c=5.0 alpha=90.0 beta=90.0 gamma=90.0 symmetry=(x,y,z) symmetry=(-X,Y+1/2,-Z) SCATter ( chemical C* ) 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600 SCATter ( chemical N* ) 12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -11.529 SCATter ( chemical O* ) 3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 .250800 SCATter ( chemical S* ) 6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 .866900 nreflections=1000 reflections INDE -3 0 0 FOBS= 1.204 PHASE=180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 1.204 359.970 FPART= 0.000 0.000 INDE -2 0 0 FOBS= 28.876 PHASE=180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 28.876 179.970 FPART= 0.000 0.000 INDE -1 0 0 FOBS= 18.437 PHASE= 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 18.437 359.970 FPART= 0.000 0.000 INDE 1 0 0 FOBS= 18.437 PHASE= 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 18.437 359.970 FPART= 0.000 0.000 INDE 2 0 0 FOBS= 28.876 PHASE=180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 28.876 179.970 FPART= 0.000 0.000 INDE 3 0 0 FOBS= 1.204 PHASE=180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 1.204 359.970 FPART= 0.000 0.000 INDE -3 1 0 FOBS= 8.071 PHASE=254.870 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.071 250.450 FPART= 0.000 0.000 INDE -2 1 0 FOBS= 16.475 PHASE=270.750 FOM=-1.00 WEIGHT= 1.0 FCALC= 16.475 265.223 FPART= 0.000 0.000 INDE -1 1 0 FOBS= 16.832 PHASE= 3.959 FOM=-1.00 WEIGHT= 1.0 FCALC= 16.832 7.360 FPART= 0.000 0.000 INDE 1 1 0 FOBS= 16.833 PHASE=183.959 FOM=-1.00 WEIGHT= 1.0 FCALC= 16.833 187.387 FPART= 0.000 0.000 INDE 2 1 0 FOBS= 16.478 PHASE= 90.750 FOM=-1.00 WEIGHT= 1.0 FCALC= 16.478 85.221 FPART= 0.000 0.000 INDE 3 1 0 FOBS= 8.066 PHASE= 74.870 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.066 70.468 FPART= 0.000 0.000 INDE -3 2 0 FOBS= 3.765 PHASE=352.489 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.765 5.590 FPART= 0.000 0.000 INDE -2 2 0 FOBS= 12.829 PHASE=150.719 FOM=-1.00 WEIGHT= 1.0 FCALC= 12.829 146.287 FPART= 0.000 0.000 INDE -1 2 0 FOBS= 4.732 PHASE=262.008 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.732 235.745 FPART= 0.000 0.000 INDE 0 2 0 FOBS= 91.413 PHASE=294.823 FOM=-1.00 WEIGHT= 1.0 FCALC= 91.413 295.716 FPART= 0.000 0.000 INDE 1 2 0 FOBS= 4.732 PHASE=262.008 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.732 235.745 FPART= 0.000 0.000 INDE 2 2 0 FOBS= 12.829 PHASE=150.719 FOM=-1.00 WEIGHT= 1.0 FCALC= 12.829 146.287 FPART= 0.000 0.000 INDE 3 2 0 FOBS= 3.765 PHASE=352.489 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.765 5.590 FPART= 0.000 0.000 INDE -2 3 0 FOBS= 9.792 PHASE=246.772 FOM=-1.00 WEIGHT= 1.0 FCALC= 9.792 235.459 FPART= 0.000 0.000 INDE -1 3 0 FOBS= 15.988 PHASE=171.678 FOM=-1.00 WEIGHT= 1.0 FCALC= 15.988 175.160 FPART= 0.000 0.000 INDE 1 3 0 FOBS= 15.969 PHASE=351.678 FOM=-1.00 WEIGHT= 1.0 FCALC= 15.969 355.142 FPART= 0.000 0.000 INDE 2 3 0 FOBS= 9.799 PHASE= 66.772 FOM=-1.00 WEIGHT= 1.0 FCALC= 9.799 55.454 FPART= 0.000 0.000 INDE -2 4 0 FOBS= 8.095 PHASE=117.995 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.095 111.181 FPART= 0.000 0.000 INDE -1 4 0 FOBS= 12.838 PHASE=165.927 FOM=-1.00 WEIGHT= 1.0 FCALC= 12.838 168.365 FPART= 0.000 0.000 INDE 0 4 0 FOBS= 9.832 PHASE=230.370 FOM=-1.00 WEIGHT= 1.0 FCALC= 9.832 247.156 FPART= 0.000 0.000 INDE 1 4 0 FOBS= 12.838 PHASE=165.927 FOM=-1.00 WEIGHT= 1.0 FCALC= 12.838 168.365 FPART= 0.000 0.000 INDE 2 4 0 FOBS= 8.095 PHASE=117.995 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.095 111.181 FPART= 0.000 0.000 INDE -2 5 0 FOBS= 5.404 PHASE=161.671 FOM=-1.00 WEIGHT= 1.0 FCALC= 5.404 152.488 FPART= 0.000 0.000 INDE -1 5 0 FOBS= 3.744 PHASE= 77.777 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.744 103.224 FPART= 0.000 0.000 INDE 1 5 0 FOBS= 3.747 PHASE=257.777 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.747 283.207 FPART= 0.000 0.000 INDE 2 5 0 FOBS= 5.405 PHASE=341.671 FOM=-1.00 WEIGHT= 1.0 FCALC= 5.405 332.490 FPART= 0.000 0.000 INDE -1 6 0 FOBS= 4.246 PHASE=131.815 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.246 155.195 FPART= 0.000 0.000 INDE 0 6 0 FOBS= 2.777 PHASE=179.726 FOM=-1.00 WEIGHT= 1.0 FCALC= 2.777 247.821 FPART= 0.000 0.000 INDE 1 6 0 FOBS= 4.246 PHASE=131.815 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.246 155.195 FPART= 0.000 0.000 INDE -3 0 1 FOBS= 4.649 PHASE= 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.649 359.970 FPART= 0.000 0.000 INDE -2 0 1 FOBS= 1.141 PHASE= 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 1.141 359.970 FPART= 0.000 0.000 INDE -1 0 1 FOBS= 11.255 PHASE= 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 11.255 359.970 FPART= 0.000 0.000 INDE 0 0 1 FOBS= 86.287 PHASE= 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 86.287 359.970 FPART= 0.000 0.000 INDE 1 0 1 FOBS= 16.298 PHASE=180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 16.298 179.970 FPART= 0.000 0.000 INDE 2 0 1 FOBS= 9.157 PHASE=180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 9.157 179.970 FPART= 0.000 0.000 INDE 3 0 1 FOBS= 6.784 PHASE=180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.784 179.970 FPART= 0.000 0.000 INDE -3 1 1 FOBS= 4.071 PHASE=270.596 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.071 270.210 FPART= 0.000 0.000 INDE -2 1 1 FOBS= 6.493 PHASE=307.828 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.493 277.777 FPART= 0.000 0.000 INDE -1 1 1 FOBS= 6.559 PHASE= 46.882 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.559 34.399 FPART= 0.000 0.000 INDE 0 1 1 FOBS= 2.951 PHASE= 63.122 FOM=-1.00 WEIGHT= 1.0 FCALC= 2.951 58.758 FPART= 0.000 0.000 INDE 1 1 1 FOBS= 22.719 PHASE= 70.243 FOM=-1.00 WEIGHT= 1.0 FCALC= 22.719 75.714 FPART= 0.000 0.000 INDE 2 1 1 FOBS= 1.817 PHASE=296.681 FOM=-1.00 WEIGHT= 1.0 FCALC= 1.817 357.064 FPART= 0.000 0.000 INDE 3 1 1 FOBS= 3.134 PHASE=225.419 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.134 252.496 FPART= 0.000 0.000 INDE -3 2 1 FOBS= 5.958 PHASE=322.520 FOM=-1.00 WEIGHT= 1.0 FCALC= 5.958 324.013 FPART= 0.000 0.000 INDE -2 2 1 FOBS= 12.090 PHASE=247.637 FOM=-1.00 WEIGHT= 1.0 FCALC= 12.090 244.049 FPART= 0.000 0.000 INDE -1 2 1 FOBS= 10.724 PHASE=165.741 FOM=-1.00 WEIGHT= 1.0 FCALC= 10.724 161.056 FPART= 0.000 0.000 INDE 0 2 1 FOBS= 10.840 PHASE=295.630 FOM=-1.00 WEIGHT= 1.0 FCALC= 10.840 306.988 FPART= 0.000 0.000 INDE 1 2 1 FOBS= 14.694 PHASE= 58.885 FOM=-1.00 WEIGHT= 1.0 FCALC= 14.694 69.329 FPART= 0.000 0.000 INDE 2 2 1 FOBS= 8.962 PHASE= 91.179 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.962 98.076 FPART= 0.000 0.000 INDE 3 2 1 FOBS= 6.065 PHASE=104.899 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.065 94.272 FPART= 0.000 0.000 INDE -2 3 1 FOBS= 4.147 PHASE= 93.771 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.147 91.481 FPART= 0.000 0.000 INDE -1 3 1 FOBS= 4.981 PHASE=119.372 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.981 129.676 FPART= 0.000 0.000 INDE 0 3 1 FOBS= 23.202 PHASE=317.796 FOM=-1.00 WEIGHT= 1.0 FCALC= 23.202 318.582 FPART= 0.000 0.000 INDE 1 3 1 FOBS= 25.201 PHASE= 9.081 FOM=-1.00 WEIGHT= 1.0 FCALC= 25.201 19.585 FPART= 0.000 0.000 INDE 2 3 1 FOBS= 3.961 PHASE=160.825 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.961 135.196 FPART= 0.000 0.000 INDE -2 4 1 FOBS= 6.815 PHASE=166.430 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.815 162.376 FPART= 0.000 0.000 INDE -1 4 1 FOBS= 6.801 PHASE=207.606 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.801 235.632 FPART= 0.000 0.000 INDE 0 4 1 FOBS= 3.412 PHASE=138.013 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.412 85.578 FPART= 0.000 0.000 INDE 1 4 1 FOBS= 10.184 PHASE=121.528 FOM=-1.00 WEIGHT= 1.0 FCALC= 10.184 125.920 FPART= 0.000 0.000 INDE 2 4 1 FOBS= 8.646 PHASE= 46.091 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.646 45.478 FPART= 0.000 0.000 INDE -1 5 1 FOBS= 4.754 PHASE=295.285 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.754 291.308 FPART= 0.000 0.000 INDE 0 5 1 FOBS= 4.226 PHASE=199.300 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.226 245.587 FPART= 0.000 0.000 INDE 1 5 1 FOBS= 8.489 PHASE=327.083 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.489 346.198 FPART= 0.000 0.000 INDE -1 6 1 FOBS= 5.863 PHASE=143.212 FOM=-1.00 WEIGHT= 1.0 FCALC= 5.863 179.336 FPART= 0.000 0.000 INDE 0 6 1 FOBS= 2.031 PHASE=168.004 FOM=-1.00 WEIGHT= 1.0 FCALC= 2.031 240.837 FPART= 0.000 0.000 INDE 1 6 1 FOBS= 2.021 PHASE= 29.207 FOM=-1.00 WEIGHT= 1.0 FCALC= 2.021 35.011 FPART= 0.000 0.000 INDE -2 0 2 FOBS= 4.302 PHASE= 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.302 359.970 FPART= 0.000 0.000 INDE -1 0 2 FOBS= 6.303 PHASE=180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.303 179.970 FPART= 0.000 0.000 INDE 0 0 2 FOBS= 6.944 PHASE= 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.944 359.970 FPART= 0.000 0.000 INDE 1 0 2 FOBS= 0.078 PHASE= 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 0.078 179.970 FPART= 0.000 0.000 INDE 2 0 2 FOBS= 4.761 PHASE= 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.761 359.970 FPART= 0.000 0.000 INDE -2 1 2 FOBS= 3.810 PHASE=351.971 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.810 338.726 FPART= 0.000 0.000 INDE -1 1 2 FOBS= 4.279 PHASE=176.911 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.279 221.553 FPART= 0.000 0.000 INDE 0 1 2 FOBS= 3.077 PHASE= 46.054 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.077 16.942 FPART= 0.000 0.000 INDE 1 1 2 FOBS= 21.532 PHASE= 49.086 FOM=-1.00 WEIGHT= 1.0 FCALC= 21.532 54.450 FPART= 0.000 0.000 INDE 2 1 2 FOBS= 7.134 PHASE=266.096 FOM=-1.00 WEIGHT= 1.0 FCALC= 7.134 258.062 FPART= 0.000 0.000 INDE -2 2 2 FOBS= 2.856 PHASE=250.303 FOM=-1.00 WEIGHT= 1.0 FCALC= 2.856 264.182 FPART= 0.000 0.000 INDE -1 2 2 FOBS= 14.597 PHASE=100.709 FOM=-1.00 WEIGHT= 1.0 FCALC= 14.597 99.949 FPART= 0.000 0.000 INDE 0 2 2 FOBS= 7.042 PHASE=105.969 FOM=-1.00 WEIGHT= 1.0 FCALC= 7.042 109.076 FPART= 0.000 0.000 INDE 1 2 2 FOBS= 0.421 PHASE= 60.147 FOM=-1.00 WEIGHT= 1.0 FCALC= 0.421 148.108 FPART= 0.000 0.000 INDE 2 2 2 FOBS= 4.378 PHASE=198.882 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.378 194.834 FPART= 0.000 0.000 INDE -2 3 2 FOBS= 1.477 PHASE= 54.226 FOM=-1.00 WEIGHT= 1.0 FCALC= 1.477 105.140 FPART= 0.000 0.000 INDE -1 3 2 FOBS= 3.284 PHASE=236.327 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.284 205.912 FPART= 0.000 0.000 INDE 0 3 2 FOBS= 9.549 PHASE=279.789 FOM=-1.00 WEIGHT= 1.0 FCALC= 9.549 288.462 FPART= 0.000 0.000 INDE 1 3 2 FOBS= 7.598 PHASE= 7.618 FOM=-1.00 WEIGHT= 1.0 FCALC= 7.598 21.080 FPART= 0.000 0.000 INDE 2 3 2 FOBS= 5.166 PHASE=178.557 FOM=-1.00 WEIGHT= 1.0 FCALC= 5.166 186.753 FPART= 0.000 0.000 INDE -1 4 2 FOBS= 4.172 PHASE=348.466 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.172 357.490 FPART= 0.000 0.000 INDE 0 4 2 FOBS= 6.420 PHASE=123.103 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.420 101.150 FPART= 0.000 0.000 INDE 1 4 2 FOBS= 7.892 PHASE=132.394 FOM=-1.00 WEIGHT= 1.0 FCALC= 7.892 142.602 FPART= 0.000 0.000 INDE 0 5 2 FOBS= 3.160 PHASE=122.410 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.160 108.399 FPART= 0.000 0.000 INDE -1 0 3 FOBS= 8.336 PHASE= 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.336 359.970 FPART= 0.000 0.000 INDE 0 0 3 FOBS= 12.879 PHASE= 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 12.879 359.970 FPART= 0.000 0.000 INDE 1 0 3 FOBS= 0.178 PHASE=180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 0.178 179.970 FPART= 0.000 0.000 INDE -1 1 3 FOBS= 1.919 PHASE= 79.278 FOM=-1.00 WEIGHT= 1.0 FCALC= 1.919 81.052 FPART= 0.000 0.000 INDE 0 1 3 FOBS= 6.643 PHASE=250.716 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.643 256.018 FPART= 0.000 0.000 INDE 1 1 3 FOBS= 3.182 PHASE= 47.493 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.182 65.574 FPART= 0.000 0.000 INDE -1 2 3 FOBS= 4.483 PHASE=357.004 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.483 323.108 FPART= 0.000 0.000 INDE 0 2 3 FOBS= 5.826 PHASE=313.546 FOM=-1.00 WEIGHT= 1.0 FCALC= 5.826 303.393 FPART= 0.000 0.000 INDE 1 2 3 FOBS= 1.619 PHASE= 75.798 FOM=-1.00 WEIGHT= 1.0 FCALC= 1.619 92.155 FPART= 0.000 0.000 end update print target wa = 1000.0 end ! {* debug B-factor derivatives *} {* ========================== *} cons fix=( not ( id 18 or id 19 or id 20 ) ) end xrefin tolerance=0.0 resol 10.0 2.4 method=direct optimize b-factors rweight=0.5 step=0.001 ! step for debugger debug=true end method=fft fft grid=0.3 prime=5 avoid=2 end optimize b-factors rweight=0.5 step=0.01 ! step for debugger debug=true end end {* now run some B-factor refinement *} cons fix=( not all ) end xrefin method=direct resolution 10.0 1.51 optimize b-factors nstep=20 ! do 20 steps of conjugate gradient step_size=10.0 ! expected initial drop in energy tolerance=0.0 ! gradient that terminates minimization rweight=-0.2 ! set weight on bfactor restraints by comparing gradient ! set the target standard deviations for 1-2 and 1-3 pair B-factors ! These are set to be very loose in the test case because ! the Fcalcs are from a structure with loosely restrained B's. ! Normally set these to 2.0 or 3.0 bsigma=( all ) = 7.0 asigma=( all ) = 8.0 end update print target end {* print and compare B-factors *} vector show elem ( b ) ( not hydro ) vector do ( bcomp = store1 - b ) ( all ) vector show elem ( bcomp ) ( not hydro ) xrefin method=direct resolution 10.0 1.51 optimize b-factors nstep=20 ! do 20 steps of conjugate gradient step_size=10.0 ! expected initial drop in energy tolerance=0.0 ! gradient that terminates minimization rweight=0.0 ! no restraints ! set the target standard deviations for 1-2 and 1-3 pair B-factors ! These are set to be very loose in the test case because ! the Fcalcs are from a structure with loosely restrained B's. ! Normally set these to 2.0 or 3.0 bsigma=( all ) = 7.0 asigma=( all ) = 8.0 end update print target end vector do (store9=b) ( all ) vector do ( b=5. ) ( all ) xrefin optimize b-factors nstep=20 ! do 20 steps of conjugate gradient step_size=10.0 ! expected initial drop in energy tolerance=0.0 ! gradient that terminates minimization rweight=0.0 ! no restraints bmin=4. bmax=6. ! set the target standard deviations for 1-2 and 1-3 pair B-factors ! These are set to be very loose in the test case because ! the Fcalcs are from a structure with loosely restrained B's. ! Normally set these to 2.0 or 3.0 bsigma=( all ) = 7.0 asigma=( all ) = 8.0 end end vector show element (b ) ( all ) vector do (b=store9) ( all ) vector do (store9=b) ( all ) vector do ( b=5. ) ( all ) vector do (b=b + gauss(1.5)) ( name ca or name n or name c ) vector do (b=b + gauss(2.0)) ( not hydrogen and not ( name ca or name n or name c )) xrefin optimize bfactors nstep=-1 { analysis only: check initial rms B values } {* for main-chain atoms *} bsigma=( name ca or name n or name c or name o )=1.0 asigma=( name ca or name n or name c or name o )=1.0 {* for side-chain atoms *} bsigma=( not( name ca or name n or name c or name o or name hydr ))=1.0 asigma=( not( name ca or name n or name c or name o or name hydr ))=1.0 end display $BRMS_BOND $BN_BOND $NGROUP_BOND $BRMS_BOND_1 $BN_BOND_1 $BRMS_BOND_2 $BN_BOND_2 display $NGROUP_ANGL $BRMS_ANGL $BN_ANGL $BRMS_ANGL_1 $BN_ANGL_1 $BRMS_ANGL_2 $BN_ANGL_2 display $NGROUP_NCS end xrefin optimize b-factors nstep=20 ! do 20 steps of conjugate gradient ! set the target standard deviations for 1-2 and 1-3 pair B-factors ! These are set to be very loose in the test case because ! the Fcalcs are from a structure with loosely restrained B's. ! Normally set these to 2.0 or 3.0 {*Target sigma for 1-2 B-factor pairs*} {*(for backbone and side chain). *} bsigma=( name ca or name n or name c or name o )=1.5 bsigma=( not( name ca or name n or name c or name o ))=2.0 {*Target sigma for 1-3 (angle)*} {*B-factor pairs. *} asigma=( name ca or name n or name c or name o )=2.0 asigma=( not( name ca or name n or name c or name o ))=2.5 end end vector show element (b ) ( all ) vector do (b=store9) ( all ) {* print and compare B-factors *} vector show elem ( b ) ( not hydro ) vector do ( bcomp = store3 - b ) ( all ) vector show elem ( bcomp ) ( not hydro ) vector do ( b = 10.0 ) ( not hydro ) xrefin method=direct update print target {* test isotropic B with K refinement *} ffk=1.0 optimize overall-bfactor kscale=true k=1.0 apply=false nstep=20 drop=0.4 b=0.0 tolerance=0.0 end ffk=0.0 do (deri1=fcalc) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 selection=( 10.0 >= d >= 1.513 ) end {* test anisotropic B with K refinement *} ffk=1.0 optimize overall-bfactor anisotropic=true kscale=true k=1.0 apply=false nstep=20 drop=0.4 b=0.0 tolerance=0.0 end ffk=0.0 do (deri1=fcalc) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 selection=( 10.0 >= d >= 1.513 ) anisotropic=true end {* test isotropic B without K refinement *} ffk=1.0 optimize overall-bfactor kscale=false k=1.0 bscale=true apply=false nstep=5 drop=0.4 b=0.0 tolerance=0.0 end do (deri1=fcalc) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 k2=1 selection=( 10.0 >= d >= 1.513 ) end ffk=0.0 {* test anisotropic B without K refinement *} ffk=1.0 optimize overall-bfactor anisotropic=true kscale=false k=1.0 bscale=true apply=false nstep=10 drop=0.4 b=0.0 tolerance=0.0 end do (deri1=fcalc) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 k2=1 selection=( 10.0 >= d >= 1.513 ) anisotropic=true end ffk=0.0 optimize overall-bfactor nstep=0 step=0.0001 b=10.0 debug=true end optimize overall-bfactor nstep=6 drop=0.4 b=0.0 tolerance=0.0 end print target update print target print target optimize overall-bfactor nstep=1 drop=0.4 b=0.0 tolerance=0.0 end {* test overall anisotropic b-factor optimization *} optimize overall-bfactor anisotropic=true debug=true step=0.0001 end optimize overall-bfactor anisotropic=true debug=true b11=2. b22=4. b33=3. b12=4. b13=3. b23=2. step=0.0001 end ffk=1 optimize overall-bfactor kscale=true bscale=true anisotropic=true debug=true k=.9 b11=2. b22=4. b33=3. b12=4. b13=3. b23=2. step=0.0001 end ffk=0 optimize overall-bfactor kscale=false bscale=true anisotropic=true debug=true k=.9 b11=2. b22=4. b33=3. b12=4. b13=3. b23=2. step=0.0001 end optimize overall-bfactor kscale=false bscale=true anisotropic=false debug=true k=.9 b11=2. b22=4. b33=3. b12=4. b13=3. b23=2. step=0.0001 end ffk=1 optimize overall-bfactor kscale=true bscale=false anisotropic=true debug=true k=.9 b11=2. b22=4. b33=3. b12=4. b13=3. b23=2. step=0.0001 end ffk=0 do (deri1=fcalc) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 selection=( 10.0 >= d >= 1.513 ) anisotropic=true end do (deri1=$K2*exp(-( $B2_11*h*h*$astar*$astar +$B2_22*k*k*$bstar*$bstar +$B2_33*l*l*$cstar*$cstar +2.0*$B2_12*h*k*$astar*$bstar +2.0*$B2_13*h*l*$astar*$cstar +2.0*$B2_23*k*l*$bstar*$cstar )/4.0)*deri1) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 selection=( 10.0 >= d >= 1.513 ) anisotropic=true end do (deri2=exp(-( 2. *h*h*$astar*$astar +4. *k*k*$bstar*$bstar +2. *l*l*$cstar*$cstar)/4.0)*deri1) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri2 selection=( 10.0 >= d >= 1.513 ) anisotropic=true end do (deri1=$K2*exp(-( $B2_11*h*h*$astar*$astar +$B2_22*k*k*$bstar*$bstar +$B2_33*l*l*$cstar*$cstar +2.0*$B2_12*h*k*$astar*$bstar +2.0*$B2_13*h*l*$astar*$cstar +2.0*$B2_23*k*l*$bstar*$cstar )/4.0)*deri2) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 selection=( 10.0 >= d >= 1.513 ) anisotropic=true end optimize overall-bfactor anisotropic=true nstep=8 drop=0.4 tolerance=0.0 end print target optimize overall-bfactor anisotropic=true nstep=1 drop=0.4 tolerance=0.0 end end vector do ( b=b+20. ) ( all ) xrefin update print target optimize overall-bfactor anisotropic=true nstep=10 drop=0.04 tolerance=0.0 end print target update optimize overall-bfactor nstep=1 drop=0.4 tolerance=0.0 end end {* make gaussian distributions, width 1.5 for backbone *} {* 2.0 for sidechains *} set seed=314159. end vector do ( b = b + gauss(1.5)) ( name ca or name n or name c ) vector do ( b = b + gauss(2.0)) ( not hydrogen and not ( name ca or name n or name c )) xrefin optimize b-factors nstep=10 end end vector show elem ( b )( not hydro ) ! modify the B-factors vector do ( b = b + 1.5 ) ( not ( name ca or name c or name o ) ) vector do ( b = b - 0.5 ) ( name ca or name c or name o ) {* debug group B-factor and occupancy derivatives *} {* ============================================== *} xrefin resol 10.0 2.01 method=fft lookup=true optimize group drop=0.01 ! step for debugger b=( ( name ca or name n or name c ) and resid 1 ) b=( ( name ca or name n or name c ) and resid 2 ) b=( ( name ca or name n or name c ) and resid 3 ) debug=true end method=fft lookup=false optimize group drop=0.00001 ! step for debugger b=( ( name ca or name n or name c ) and resid 1 ) b=( ( name ca or name n or name c ) and resid 2 ) b=( ( name ca or name n or name c ) and resid 3 ) debug=true end method=direct optimize group drop=0.00001 ! step for debugger b=( ( name ca or name n or name c ) and resid 1 ) b=( ( name ca or name n or name c ) and resid 2 ) b=( ( name ca or name n or name c ) and resid 3 ) debug=true end optimize group drop=10. nstep=8 b=( not ( hydro or name ca or name c or name o ) ) b=( name ca or name c or name o ) tolerance=0.0 end update print target end vector do (q=0.8) ( all ) xrefin resol 10.0 2.01 method=fft lookup=true optimize group drop=0.01 ! step for debugger q=( ( name ca or name n or name c ) and resid 1 ) q=( ( name ca or name n or name c ) and resid 2 ) q=( ( name ca or name n or name c ) and resid 3 ) debug=true end method=fft lookup=false optimize group drop=0.00001 ! step for debugger q=( ( name ca or name n or name c ) and resid 1 ) q=( ( name ca or name n or name c ) and resid 2 ) q=( ( name ca or name n or name c ) and resid 3 ) debug=true end method=direct optimize group drop=0.00001 ! step for debugger q=( ( name ca or name n or name c ) and resid 1 ) q=( ( name ca or name n or name c ) and resid 2 ) q=( ( name ca or name n or name c ) and resid 3 ) debug=true end end vector do (q=1.) ( all ) vector do (q=1. ) ( ( name ca or name n or name c ) and resid 1 ) vector do (q=1. ) ( ( name ca or name n or name c ) and resid 2 ) vector do (q=1. ) ( ( name ca or name n or name c ) and resid 3 ) xrefin update do amplitude (fobs=fcalc) end vector do (q=0.5 ) ( ( name ca or name n or name c ) and resid 1 ) vector do (q=0.7 ) ( ( name ca or name n or name c ) and resid 2 ) vector do (q=0.8 ) ( ( name ca or name n or name c ) and resid 3 ) xrefin optimize group drop=100. nstep=16 q=( ( name ca or name n or name c ) and resid 1 ) q=( ( name ca or name n or name c ) and resid 2 ) q=( ( name ca or name n or name c ) and resid 3 ) end update print target end vector show ( q ) ( name ca ) vector do (q=0.8 ) ( ( name ca or name n or name c ) and resid 1 ) vector do (b=10. ) ( ( name ca or name n or name c ) and resid 1 ) xrefin update do amplitude (fobs=fcalc) end vector do (q=1.0 ) ( ( name ca or name n or name c ) and resid 1 ) vector do (b=12. ) ( ( name ca or name n or name c ) and resid 1 ) xrefin optimize group drop=10. nstep=20 q=( ( name ca or name n or name c ) and resid 1 ) b=( ( name ca or name n or name c ) and resid 1 ) end update print target end vector show ( q ) ( name ca ) vector show ( b ) ( name ca ) vector do (store8=q) ( all ) vector do (store9=b) ( all ) vector do ( q=0.5 ) ( name all ) vector do ( b=10. ) ( name all ) xrefin optimize group drop=10. nstep=20 bmin=5. bmax=8 qmin=0.4 qmax=0.74 q=( ( name ca or name n or name c ) and resid 1 ) b=( ( name ca or name n or name c ) and resid 1 ) end update print target end vector show (q) ( ( name ca or name n or name c ) and resid 1 ) vector show (b) ( ( name ca or name n or name c ) and resid 1 ) vector do (q=store8) ( all ) vector do (b=store9) ( all ) xrefin symmetry reset a=5.0 b=10.0 c=15. alpha=80.0 beta=100.0 gamma=120.0 resolution 10.0 1.513 update do (fobs=fcalc+gauss(3.0)) ( all ) do (deri1=fcalc) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 selection=( 10.0 >= d >= 1.513 ) anisotropic=true end do (deri1=$K2*exp(-( $B2_11*h*h*$astar*$astar +$B2_22*k*k*$bstar*$bstar +$B2_33*l*l*$cstar*$cstar +2.0*$B2_12*h*k*$astar*$bstar +2.0*$B2_13*h*l*$astar*$cstar +2.0*$B2_23*k*l*$bstar*$cstar )/4.0)*deri1) ( all ) do (deri2=$K2*exp(-( 1.*h*h*$astar*$astar +2.*k*k*$bstar*$bstar +3.*l*l*$cstar*$cstar +2.0*4.*h*k*$astar*$bstar +2.0*5.*h*l*$astar*$cstar +2.0*6.*k*l*$bstar*$cstar )/4.0)*deri1) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri2 selection=( 10.0 >= d >= 1.513 ) anisotropic=true end do (deri1=$K2*exp(-( $B2_11*h*h*$astar*$astar +$B2_22*k*k*$bstar*$bstar +$B2_33*l*l*$cstar*$cstar +2.0*$B2_12*h*k*$astar*$bstar +2.0*$B2_13*h*l*$astar*$cstar +2.0*$B2_23*k*l*$bstar*$cstar )/4.0)*deri2) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 selection=( 10.0 >= d >= 1.513 ) anisotropic=true end do (fobs=fcalc) ( all ) do (fcalc=2.*exp(-( 1.2*h*h*$astar*$astar +3.2*k*k*$bstar*$bstar +1.2*l*l*$cstar*$cstar +2.0*3.4*h*k*$astar*$bstar +2.0*4.4*h*l*$astar*$cstar +2.0*5.5*k*l*$bstar*$cstar )/4.0)*fcalc) ( all ) ffk=1. do (deri1=fcalc) ( all ) optimize overall-bfactor kscale=true bscale=true anisotropic=true debug=true step=0.0001 end ffk=0 optimize overall-bfactor kscale=false bscale=true anisotropic=true debug=true step=0.0001 end optimize overall-bfactor kscale=false bscale=true anisotropic=true step=10 step=0.0001 apply=false nstep=60 end display $ffk $B2_11 $B2_22 $B2_33 $B2_12 $B2_13 $B2_23 do (fcalc=$ffk*exp(-( $B_11*h*h*$astar*$astar +$B_22*k*k*$bstar*$bstar +$B_33*l*l*$cstar*$cstar +2.0*$B_12*h*k*$astar*$bstar +2.0*$B_13*h*l*$astar*$cstar +2.0*$B_23*k*l*$bstar*$cstar )/4.0)*fcalc) ( all ) print r ffk=1 do (fcalc=deri1) ( all ) optimize overall-bfactor kscale=true bscale=true anisotropic=true step=10 step=0.0001 apply=false nstep=60 end do (fcalc=$kscale*exp(-( $B_11*h*h*$astar*$astar +$B_22*k*k*$bstar*$bstar +$B_33*l*l*$cstar*$cstar +2.0*$B_12*h*k*$astar*$bstar +2.0*$B_13*h*l*$astar*$cstar +2.0*$B_23*k*l*$bstar*$cstar )/4.0)*fcalc) ( all ) print r multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 selection=( 10.0 >= d >= 1.513 ) anisotropic=true end do (fcalc=$K2*exp(-( $B2_11*h*h*$astar*$astar +$B2_22*k*k*$bstar*$bstar +$B2_33*l*l*$cstar*$cstar +2.0*$B2_12*h*k*$astar*$bstar +2.0*$B2_13*h*l*$astar*$cstar +2.0*$B2_23*k*l*$bstar*$cstar )/4.0)*deri1) ( all ) print r end stop