REMARKS Testing f' and f'' 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 vector do (q=0.8) ( resid 1 ) vector do (q=0.7) ( resid 2 ) vector do (q=0.9) ( resid 3 ) delete sele ( not known ) end 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 imag 4. 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 resolution 10. 3 anomalous=true aselection=( not all ) generate update do (fobs=fcalc) ( all ) scatter reset SCATter ( chemical C* ) 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .4 SCATter ( chemical N* ) 12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -13. imag 4. SCATter ( chemical O* ) 3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 -.1 SCATter ( chemical S* ) 6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 -1.0 update print target wa = 1000.0 end ! {* 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 fp=( chemical c* ) fp=( chemical n* ) fp=( chemical o* ) debug=true end method=fft lookup=false optimize group drop=0.00001 ! step for debugger fp=( chemical c* ) fp=( chemical n* ) fp=( chemical o* ) debug=true end method=direct optimize group drop=0.00001 ! step for debugger fp=( chemical c* ) fp=( chemical n* ) fp=( chemical o* ) debug=true end scatter ? optimize group drop=10. nstep=5 fp=( chemical c* ) fp=( chemical n* ) fp=( chemical o* ) tolerance=0.0 end scatter ? update print target end xrefin scatter reset SCATter ( chemical C* ) 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .4 SCATter ( chemical N* ) 12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -13. imag 4. SCATter ( chemical O* ) 3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 -.1 SCATter ( chemical S* ) 6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 -1.0 aselection=( chemical N* ) update do (fobs=fcalc) ( all ) scatter reset SCATter ( chemical C* ) 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .4 SCATter ( chemical N* ) 12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -13. imag 10. SCATter ( chemical O* ) 3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 -.1 SCATter ( chemical S* ) 6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 -1.0 update print r resol 10.0 2.01 method=fft lookup=true optimize group drop=0.01 ! step for debugger fdp=( chemical c* ) fdp=( chemical n* ) fdp=( chemical o* ) debug=true end method=fft lookup=false optimize group drop=0.00001 ! step for debugger fdp=( chemical c* ) fdp=( chemical n* ) fdp=( chemical o* ) debug=true end method=direct optimize group drop=0.00001 ! step for debugger fdp=( chemical c* ) fdp=( chemical n* ) fdp=( chemical o* ) debug=true end optimize group drop=10. nstep=5 fdp=( chemical c* ) fdp=( chemical n* ) fdp=( chemical o* ) tolerance=0.0 end scatter ? end vector show elem ( scatter_a1) ( all ) vector show elem ( scatter_a2) ( all ) vector show elem ( scatter_a3) ( all ) vector show elem ( scatter_a4) ( all ) vector show elem ( scatter_b1) ( all ) vector show elem ( scatter_b2) ( all ) vector show elem ( scatter_b3) ( all ) vector show elem ( scatter_b4) ( all ) vector show elem ( scatter_fp) ( all ) vector show elem ( scatter_fdp) ( all ) xrefin scatter ? end vector do (scatter_a1=11) ( chemical c* or chemical n* ) vector do (scatter_b1=21) ( chemical c* or chemical n* ) vector do (scatter_a2=12) ( chemical c* or chemical n* ) vector do (scatter_b2=22) ( chemical c* or chemical n* ) vector do (scatter_a3=13) ( chemical c* or chemical n* ) vector do (scatter_b3=23) ( chemical c* or chemical n* ) vector do (scatter_a4=14) ( chemical c* or chemical n* ) vector do (scatter_b4=24) ( chemical c* or chemical n* ) vector do (scatter_fp=15) ( chemical c* or chemical n* ) vector do (scatter_fdp=25) ( chemical c* or chemical n* ) xrefin scatter ? end vector do (chemical=c) ( chemical c* ) vector do (chemical=n) ( chemical n* ) xrefin scatter ? end stop