REMARKS Testing f' and f'' refinements remarks struct data_cns_mtf _cns_mtf.title ; FILENAME="/data/rwgk/test/tmp.mtf" FRAGMENT FOR COPROL121 FOR TESTING DATE:18-Nov-98 14:17:57 created by user: rwgk VERSION:0.4a ; loop_ _cns_mtf_atom.id _cns_mtf_atom.segment_id _cns_mtf_atom.residue_id _cns_mtf_atom.residue_name _cns_mtf_atom.atom_name _cns_mtf_atom.chemical_type _cns_mtf_atom.charge _cns_mtf_atom.atom_mass 1 'TEST' '1' 'VAL' 'HT1' 'HC' 0.350000 1.00800 2 'TEST' '1' 'VAL' 'HT2' 'HC' 0.350000 1.00800 3 'TEST' '1' 'VAL' 'N' 'NH3' -0.300000 14.0067 4 'TEST' '1' 'VAL' 'HT3' 'HC' 0.350000 1.00800 5 'TEST' '1' 'VAL' 'CA' 'CH1E' 0.250000 13.0190 6 'TEST' '1' 'VAL' 'CB' 'CH1E' 0.000000E+00 13.0190 7 'TEST' '1' 'VAL' 'CG1' 'CH3E' 0.000000E+00 15.0350 8 'TEST' '1' 'VAL' 'CG2' 'CH3E' 0.000000E+00 15.0350 9 'TEST' '1' 'VAL' 'C' 'C' 0.550000 12.0110 10 'TEST' '1' 'VAL' 'O' 'O' -0.550000 15.9994 11 'TEST' '2' 'LEU' 'N' 'NH1' -0.350000 14.0067 12 'TEST' '2' 'LEU' 'H' 'H' 0.250000 1.00800 13 'TEST' '2' 'LEU' 'CA' 'CH1E' 0.100000 13.0190 14 'TEST' '2' 'LEU' 'CB' 'CH2E' 0.000000E+00 14.0270 15 'TEST' '2' 'LEU' 'CG' 'CH1E' 0.000000E+00 13.0190 16 'TEST' '2' 'LEU' 'CD1' 'CH3E' 0.000000E+00 15.0350 17 'TEST' '2' 'LEU' 'CD2' 'CH3E' 0.000000E+00 15.0350 18 'TEST' '2' 'LEU' 'C' 'C' 0.550000 12.0110 19 'TEST' '2' 'LEU' 'O' 'O' -0.550000 15.9994 20 'TEST' '3' 'SER' 'N' 'NH1' -0.350000 14.0067 21 'TEST' '3' 'SER' 'H' 'H' 0.250000 1.00800 22 'TEST' '3' 'SER' 'CA' 'CH1E' 0.100000 13.0190 23 'TEST' '3' 'SER' 'CB' 'CH2E' 0.250000 14.0270 24 'TEST' '3' 'SER' 'OG' 'OH1' -0.650000 15.9994 25 'TEST' '3' 'SER' 'HG' 'H' 0.400000 1.00800 26 'TEST' '3' 'SER' 'C' 'C' 0.140000 12.0110 27 'TEST' '3' 'SER' 'OT1' 'OC' -0.570000 15.9994 28 'TEST' '3' 'SER' 'OT2' 'OC' -0.570000 15.9994 -1 ' ' ' ' ' ' ' ' ' ' -1.00000 -1.00000 loop_ _cns_mtf_bond.id[1] _cns_mtf_bond.id[2] 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 -1 -1 loop_ _cns_mtf_angle.id[1] _cns_mtf_angle.id[2] _cns_mtf_angle.id[3] 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 -1 -1 -1 loop_ _cns_mtf_dihedral.id[1] _cns_mtf_dihedral.id[2] _cns_mtf_dihedral.id[3] _cns_mtf_dihedral.id[4] 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 -1 -1 -1 -1 loop_ _cns_mtf_improper.id[1] _cns_mtf_improper.id[2] _cns_mtf_improper.id[3] _cns_mtf_improper.id[4] 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 -1 -1 -1 -1 loop_ _cns_mtf_explicit_nonbonded_exclusion.inb -1 loop_ _cns_mtf_explicit_nonbonded_exclusion.iblo 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 -1 loop_ _cns_mtf_group_linked_list.first_atom_id 0 5 8 10 13 17 19 22 25 -1 END param @CNS_TOPPAR:protein.param end coor REMARK FILENAME="" 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 do (q=0.8) ( resid 1 ) do (q=0.7) ( resid 2 ) do (q=0.9) ( resid 3 ) delete sele ( not known ) end flags excl * incl xray end {* read diffraction data *} xray declare name=fobs type=complex domain=reciprocal end declare name=fpart domain=reciprocal type=complex end declare name=fcalc domain=reciprocal type=complex end declare name=fom domain=reciprocal type=real end declare name=weight domain=reciprocal type=real end declare name=sigma domain=reciprocal type=real end declare name=test domain=reciprocal type=integer end 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 evaluate ($lr=10.) evaluate ($hr=3.) binresolution $lr $hr mapresolution $hr tselection=( $hr <= d <= $lr ) anomalous=true aselection=( not all ) generate 10. 3. predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end do (fobs=fcalc) ( all ) do (fpart=0) ( 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 predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target wa = 1000.0 end ! {* debug group B-factor and occupancy derivatives *} {* ============================================== *} xray evaluate ($lr=10.) evaluate ($hr=2.01) binresolution $lr $hr mapresolution $hr tselection=( $hr <= d <= $lr ) 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 ? predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target end xray 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* ) predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end 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 predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end statistics (rvalue(fobs,fcalc+fpart)) (rvalue[overall](fobs,fcalc+fpart)) selection=( $hr <= d <= $lr ) output=OUTPUT end evaluate ($lr=10.) evaluate ($hr=2.01) binresolution $lr $hr mapresolution $hr tselection=( $hr <= d <= $lr ) 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 show elem ( scatter_a1) ( all ) show elem ( scatter_a2) ( all ) show elem ( scatter_a3) ( all ) show elem ( scatter_a4) ( all ) show elem ( scatter_b1) ( all ) show elem ( scatter_b2) ( all ) show elem ( scatter_b3) ( all ) show elem ( scatter_b4) ( all ) show elem ( scatter_c) ( all ) show elem ( scatter_fp) ( all ) show elem ( scatter_fdp) ( all ) xray scatter ? end do (scatter_a1=11) ( chemical c* or chemical n* ) do (scatter_b1=21) ( chemical c* or chemical n* ) do (scatter_a2=12) ( chemical c* or chemical n* ) do (scatter_b2=22) ( chemical c* or chemical n* ) do (scatter_a3=13) ( chemical c* or chemical n* ) do (scatter_b3=23) ( chemical c* or chemical n* ) do (scatter_a4=14) ( chemical c* or chemical n* ) do (scatter_b4=24) ( chemical c* or chemical n* ) do (scatter_c=0) ( chemical c* or chemical n* ) do (scatter_fp=15) ( chemical c* or chemical n* ) do (scatter_fdp=25) ( chemical c* or chemical n* ) xray scatter ? end do (chemical=c) ( chemical c* ) do (chemical=n) ( chemical n* ) xray scatter ? end stop