REMARKS Testing b-factor and occupancy 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 delete sele ( not known ) end ! ! do ( store1 = b ) ( all ) !! these B-factors correspond to R-factor of 0.0 do ( store3 = b ) ( all ) ! modify the B-factors do ( b = b * 1.5 ) ( not ( name ca or name c or name o ) ) do ( b = b * 0.5 ) ( name ca or name c or name o ) show element ( b ) ( not name h* ) ! flags excl * incl xref 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 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= 1.204 180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 1.204 359.970 FPART= 0.000 0.000 INDE -2 0 0 FOBS= 28.876 180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 28.876 179.970 FPART= 0.000 0.000 INDE -1 0 0 FOBS= 18.437 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 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 18.437 359.970 FPART= 0.000 0.000 INDE 2 0 0 FOBS= 28.876 180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 28.876 179.970 FPART= 0.000 0.000 INDE 3 0 0 FOBS= 1.204 180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 1.204 359.970 FPART= 0.000 0.000 INDE -3 1 0 FOBS= 8.071 254.870 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.071 250.450 FPART= 0.000 0.000 INDE -2 1 0 FOBS= 16.475 270.750 FOM=-1.00 WEIGHT= 1.0 FCALC= 16.475 265.223 FPART= 0.000 0.000 INDE -1 1 0 FOBS= 16.832 3.959 FOM=-1.00 WEIGHT= 1.0 FCALC= 16.832 7.360 FPART= 0.000 0.000 INDE 1 1 0 FOBS= 16.833 183.959 FOM=-1.00 WEIGHT= 1.0 FCALC= 16.833 187.387 FPART= 0.000 0.000 INDE 2 1 0 FOBS= 16.478 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 74.870 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.066 70.468 FPART= 0.000 0.000 INDE -3 2 0 FOBS= 3.765 352.489 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.765 5.590 FPART= 0.000 0.000 INDE -2 2 0 FOBS= 12.829 150.719 FOM=-1.00 WEIGHT= 1.0 FCALC= 12.829 146.287 FPART= 0.000 0.000 INDE -1 2 0 FOBS= 4.732 262.008 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.732 235.745 FPART= 0.000 0.000 INDE 0 2 0 FOBS= 91.413 294.823 FOM=-1.00 WEIGHT= 1.0 FCALC= 91.413 295.716 FPART= 0.000 0.000 INDE 1 2 0 FOBS= 4.732 262.008 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.732 235.745 FPART= 0.000 0.000 INDE 2 2 0 FOBS= 12.829 150.719 FOM=-1.00 WEIGHT= 1.0 FCALC= 12.829 146.287 FPART= 0.000 0.000 INDE 3 2 0 FOBS= 3.765 352.489 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.765 5.590 FPART= 0.000 0.000 INDE -2 3 0 FOBS= 9.792 246.772 FOM=-1.00 WEIGHT= 1.0 FCALC= 9.792 235.459 FPART= 0.000 0.000 INDE -1 3 0 FOBS= 15.988 171.678 FOM=-1.00 WEIGHT= 1.0 FCALC= 15.988 175.160 FPART= 0.000 0.000 INDE 1 3 0 FOBS= 15.969 351.678 FOM=-1.00 WEIGHT= 1.0 FCALC= 15.969 355.142 FPART= 0.000 0.000 INDE 2 3 0 FOBS= 9.799 66.772 FOM=-1.00 WEIGHT= 1.0 FCALC= 9.799 55.454 FPART= 0.000 0.000 INDE -2 4 0 FOBS= 8.095 117.995 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.095 111.181 FPART= 0.000 0.000 INDE -1 4 0 FOBS= 12.838 165.927 FOM=-1.00 WEIGHT= 1.0 FCALC= 12.838 168.365 FPART= 0.000 0.000 INDE 0 4 0 FOBS= 9.832 230.370 FOM=-1.00 WEIGHT= 1.0 FCALC= 9.832 247.156 FPART= 0.000 0.000 INDE 1 4 0 FOBS= 12.838 165.927 FOM=-1.00 WEIGHT= 1.0 FCALC= 12.838 168.365 FPART= 0.000 0.000 INDE 2 4 0 FOBS= 8.095 117.995 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.095 111.181 FPART= 0.000 0.000 INDE -2 5 0 FOBS= 5.404 161.671 FOM=-1.00 WEIGHT= 1.0 FCALC= 5.404 152.488 FPART= 0.000 0.000 INDE -1 5 0 FOBS= 3.744 77.777 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.744 103.224 FPART= 0.000 0.000 INDE 1 5 0 FOBS= 3.747 257.777 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.747 283.207 FPART= 0.000 0.000 INDE 2 5 0 FOBS= 5.405 341.671 FOM=-1.00 WEIGHT= 1.0 FCALC= 5.405 332.490 FPART= 0.000 0.000 INDE -1 6 0 FOBS= 4.246 131.815 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.246 155.195 FPART= 0.000 0.000 INDE 0 6 0 FOBS= 2.777 179.726 FOM=-1.00 WEIGHT= 1.0 FCALC= 2.777 247.821 FPART= 0.000 0.000 INDE 1 6 0 FOBS= 4.246 131.815 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.246 155.195 FPART= 0.000 0.000 INDE -3 0 1 FOBS= 4.649 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 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 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 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 86.287 359.970 FPART= 0.000 0.000 INDE 1 0 1 FOBS= 16.298 180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 16.298 179.970 FPART= 0.000 0.000 INDE 2 0 1 FOBS= 9.157 180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 9.157 179.970 FPART= 0.000 0.000 INDE 3 0 1 FOBS= 6.784 180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.784 179.970 FPART= 0.000 0.000 INDE -3 1 1 FOBS= 4.071 270.596 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.071 270.210 FPART= 0.000 0.000 INDE -2 1 1 FOBS= 6.493 307.828 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.493 277.777 FPART= 0.000 0.000 INDE -1 1 1 FOBS= 6.559 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 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 70.243 FOM=-1.00 WEIGHT= 1.0 FCALC= 22.719 75.714 FPART= 0.000 0.000 INDE 2 1 1 FOBS= 1.817 296.681 FOM=-1.00 WEIGHT= 1.0 FCALC= 1.817 357.064 FPART= 0.000 0.000 INDE 3 1 1 FOBS= 3.134 225.419 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.134 252.496 FPART= 0.000 0.000 INDE -3 2 1 FOBS= 5.958 322.520 FOM=-1.00 WEIGHT= 1.0 FCALC= 5.958 324.013 FPART= 0.000 0.000 INDE -2 2 1 FOBS= 12.090 247.637 FOM=-1.00 WEIGHT= 1.0 FCALC= 12.090 244.049 FPART= 0.000 0.000 INDE -1 2 1 FOBS= 10.724 165.741 FOM=-1.00 WEIGHT= 1.0 FCALC= 10.724 161.056 FPART= 0.000 0.000 INDE 0 2 1 FOBS= 10.840 295.630 FOM=-1.00 WEIGHT= 1.0 FCALC= 10.840 306.988 FPART= 0.000 0.000 INDE 1 2 1 FOBS= 14.694 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 91.179 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.962 98.076 FPART= 0.000 0.000 INDE 3 2 1 FOBS= 6.065 104.899 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.065 94.272 FPART= 0.000 0.000 INDE -2 3 1 FOBS= 4.147 93.771 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.147 91.481 FPART= 0.000 0.000 INDE -1 3 1 FOBS= 4.981 119.372 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.981 129.676 FPART= 0.000 0.000 INDE 0 3 1 FOBS= 23.202 317.796 FOM=-1.00 WEIGHT= 1.0 FCALC= 23.202 318.582 FPART= 0.000 0.000 INDE 1 3 1 FOBS= 25.201 9.081 FOM=-1.00 WEIGHT= 1.0 FCALC= 25.201 19.585 FPART= 0.000 0.000 INDE 2 3 1 FOBS= 3.961 160.825 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.961 135.196 FPART= 0.000 0.000 INDE -2 4 1 FOBS= 6.815 166.430 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.815 162.376 FPART= 0.000 0.000 INDE -1 4 1 FOBS= 6.801 207.606 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.801 235.632 FPART= 0.000 0.000 INDE 0 4 1 FOBS= 3.412 138.013 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.412 85.578 FPART= 0.000 0.000 INDE 1 4 1 FOBS= 10.184 121.528 FOM=-1.00 WEIGHT= 1.0 FCALC= 10.184 125.920 FPART= 0.000 0.000 INDE 2 4 1 FOBS= 8.646 46.091 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.646 45.478 FPART= 0.000 0.000 INDE -1 5 1 FOBS= 4.754 295.285 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.754 291.308 FPART= 0.000 0.000 INDE 0 5 1 FOBS= 4.226 199.300 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.226 245.587 FPART= 0.000 0.000 INDE 1 5 1 FOBS= 8.489 327.083 FOM=-1.00 WEIGHT= 1.0 FCALC= 8.489 346.198 FPART= 0.000 0.000 INDE -1 6 1 FOBS= 5.863 143.212 FOM=-1.00 WEIGHT= 1.0 FCALC= 5.863 179.336 FPART= 0.000 0.000 INDE 0 6 1 FOBS= 2.031 168.004 FOM=-1.00 WEIGHT= 1.0 FCALC= 2.031 240.837 FPART= 0.000 0.000 INDE 1 6 1 FOBS= 2.021 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 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.302 359.970 FPART= 0.000 0.000 INDE -1 0 2 FOBS= 6.303 180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.303 179.970 FPART= 0.000 0.000 INDE 0 0 2 FOBS= 6.944 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 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 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.761 359.970 FPART= 0.000 0.000 INDE -2 1 2 FOBS= 3.810 351.971 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.810 338.726 FPART= 0.000 0.000 INDE -1 1 2 FOBS= 4.279 176.911 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.279 221.553 FPART= 0.000 0.000 INDE 0 1 2 FOBS= 3.077 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 49.086 FOM=-1.00 WEIGHT= 1.0 FCALC= 21.532 54.450 FPART= 0.000 0.000 INDE 2 1 2 FOBS= 7.134 266.096 FOM=-1.00 WEIGHT= 1.0 FCALC= 7.134 258.062 FPART= 0.000 0.000 INDE -2 2 2 FOBS= 2.856 250.303 FOM=-1.00 WEIGHT= 1.0 FCALC= 2.856 264.182 FPART= 0.000 0.000 INDE -1 2 2 FOBS= 14.597 100.709 FOM=-1.00 WEIGHT= 1.0 FCALC= 14.597 99.949 FPART= 0.000 0.000 INDE 0 2 2 FOBS= 7.042 105.969 FOM=-1.00 WEIGHT= 1.0 FCALC= 7.042 109.076 FPART= 0.000 0.000 INDE 1 2 2 FOBS= 0.421 60.147 FOM=-1.00 WEIGHT= 1.0 FCALC= 0.421 148.108 FPART= 0.000 0.000 INDE 2 2 2 FOBS= 4.378 198.882 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.378 194.834 FPART= 0.000 0.000 INDE -2 3 2 FOBS= 1.477 54.226 FOM=-1.00 WEIGHT= 1.0 FCALC= 1.477 105.140 FPART= 0.000 0.000 INDE -1 3 2 FOBS= 3.284 236.327 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.284 205.912 FPART= 0.000 0.000 INDE 0 3 2 FOBS= 9.549 279.789 FOM=-1.00 WEIGHT= 1.0 FCALC= 9.549 288.462 FPART= 0.000 0.000 INDE 1 3 2 FOBS= 7.598 7.618 FOM=-1.00 WEIGHT= 1.0 FCALC= 7.598 21.080 FPART= 0.000 0.000 INDE 2 3 2 FOBS= 5.166 178.557 FOM=-1.00 WEIGHT= 1.0 FCALC= 5.166 186.753 FPART= 0.000 0.000 INDE -1 4 2 FOBS= 4.172 348.466 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.172 357.490 FPART= 0.000 0.000 INDE 0 4 2 FOBS= 6.420 123.103 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.420 101.150 FPART= 0.000 0.000 INDE 1 4 2 FOBS= 7.892 132.394 FOM=-1.00 WEIGHT= 1.0 FCALC= 7.892 142.602 FPART= 0.000 0.000 INDE 0 5 2 FOBS= 3.160 122.410 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.160 108.399 FPART= 0.000 0.000 INDE -1 0 3 FOBS= 8.336 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 0.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 12.879 359.970 FPART= 0.000 0.000 INDE 1 0 3 FOBS= 0.178 180.000 FOM=-1.00 WEIGHT= 1.0 FCALC= 0.178 179.970 FPART= 0.000 0.000 INDE -1 1 3 FOBS= 1.919 79.278 FOM=-1.00 WEIGHT= 1.0 FCALC= 1.919 81.052 FPART= 0.000 0.000 INDE 0 1 3 FOBS= 6.643 250.716 FOM=-1.00 WEIGHT= 1.0 FCALC= 6.643 256.018 FPART= 0.000 0.000 INDE 1 1 3 FOBS= 3.182 47.493 FOM=-1.00 WEIGHT= 1.0 FCALC= 3.182 65.574 FPART= 0.000 0.000 INDE -1 2 3 FOBS= 4.483 357.004 FOM=-1.00 WEIGHT= 1.0 FCALC= 4.483 323.108 FPART= 0.000 0.000 INDE 0 2 3 FOBS= 5.826 313.546 FOM=-1.00 WEIGHT= 1.0 FCALC= 5.826 303.393 FPART= 0.000 0.000 INDE 1 2 3 FOBS= 1.619 75.798 FOM=-1.00 WEIGHT= 1.0 FCALC= 1.619 92.155 FPART= 0.000 0.000 end evaluate ($lr=10.) evaluate ($hr=3) binresolution $lr $hr tselection=( $hr <= d <= $lr ) mapresolution 2. predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target wa = 1000.0 declare name=deri1 type=complex domain=reciprocal end declare name=deri2 type=complex domain=reciprocal end end ! {* debug B-factor derivatives *} {* ========================== *} fix selection=( not ( id 18 or id 19 or id 20 ) ) end xray tolerance=0.0 evaluate ($lr=10.) evaluate ($hr=2.4) binresolution $lr $hr mapresolution $hr tselection=( $hr <= d <= $lr ) method=direct optimize b-factors rweight=0.5 step=0.001 ! step for debugger debug=true end method=fft fft grid=0.3 prime=5 avoid=2 end optimize b-factors rweight=0.5 step=0.01 ! step for debugger debug=true end end do (store2=b) ( all ) {* test B-factor cutoffs and dervatives *} show ( b ) ( ( id 18 or id 19 or id 20 ) ) xray method=direct optimize bfactors bmin=10 bmax=20 step=0.000001 rweight=0 debug=true end method=fft end do (b=store2) ( all ) {* now run some B-factor refinement *} fix selection=( not all ) end xray method=direct evaluate ($lr=10.) evaluate ($hr=1.51) binresolution $lr $hr mapresolution $hr tselection=( $hr <= d <= $lr ) 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 predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target end {* print and compare B-factors *} show elem ( b ) ( not hydro ) do ( bcomp = store1 - b ) ( all ) show elem ( bcomp ) ( not hydro ) xray method=direct evaluate ($lr=10.) evaluate ($hr=1.51) binresolution $lr $hr mapresolution $hr tselection=( $hr <= d <= $lr ) 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 predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target end do (store9=b) ( all ) do ( b=5. ) ( all ) xray 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 show element (b ) ( all ) do (b=store9) ( all ) set seed=123 end do (store9=b) ( all ) do ( b=5. ) ( all ) do (b=b + gauss(1.5)) ( name ca or name n or name c ) do (b=b + gauss(2.0)) ( not hydrogen and not ( name ca or name n or name c )) xray 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 show ( b ) ( all ) xray 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 bmin=-200 bmax=200 end end show element (b ) ( all ) do (b=store9) ( all ) {* print and compare B-factors *} show elem ( b ) ( not hydro ) do ( bcomp = store3 - b ) ( all ) show elem ( bcomp ) ( not hydro ) do ( b = 10.0 ) ( not hydro ) xray method=direct predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target {* test isotropic B with K refinement *} evaluate ($k2=1.0) target=( resi[k=$k2](amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi[k=$k2](amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall,k=$k2](fobs,fcalc+fpart)) optimize overall-bfactor name=fcalc kscale=true k=1.0 nstep=20 drop=0.4 b=0.0 tolerance=0.0 end target=( resi(amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi(amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall](fobs,fcalc+fpart)) do (deri1=fcalc) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 selection=( 10.0 >= d >= 1.513 ) end {* test anisotropic B with K refinement *} evaluate ($k2=1) target=( resi[k=$k2](amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi[k=$k2](amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall,k=$k2](fobs,fcalc+fpart)) optimize overall-bfactor name=fcalc anisotropic=true isotropic=true kscale=true k=1.0 nstep=20 drop=0.4 b=0.0 tolerance=0.0 end target=( resi(amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi(amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall](fobs,fcalc+fpart)) do (deri1=fcalc) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 selection=( 10.0 >= d >= 1.513 ) anisotropic=true end {* test isotropic B without K refinement *} evaluate ($k2=1) target=( resi[k=$k2](amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi[k=$k2](amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall,k=$k2](fobs,fcalc+fpart)) optimize overall-bfactor name=fcalc kscale=false k=1.0 bscale=true nstep=5 drop=0.4 b=0.0 tolerance=0.0 end optimize overall-bfactor method=lbfgs name=fcalc kscale=false k=1.0 bscale=true nstep=5 drop=0.4 b=0.0 tolerance=0.0 end do (deri1=fcalc) ( all ) multiscale ffk=1 bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 k2=1 selection=( 10.0 >= d >= 1.513 ) end {* test anisotropic B without K refinement and without isotropic refinement *} evaluate ($k2=1) target=( resi[k=$k2](amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi[k=$k2](amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall,k=$k2](fobs,fcalc+fpart)) optimize overall-bfactor name=fcalc anisotropic=true isotropic=false kscale=false k=1.0 bscale=true nstep=4 drop=0.4 b=0.0 tolerance=0.0 end optimize overall-bfactor name=fcalc anisotropic=true isotropic=false method=lbfgs kscale=false k=1.0 bscale=true nstep=4 drop=0.4 b=0.0 tolerance=0.0 end {* test anisotropic B with K refinement and without isotropic refinement *} evaluate ($k2=1) target=( resi[k=$k2](amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi[k=$k2](amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall,k=$k2](fobs,fcalc+fpart)) optimize overall-bfactor name=fcalc anisotropic=true isotropic=false kscale=true k=1.0 bscale=true nstep=30 drop=0.4 b=0.0 tolerance=0.0 end optimize overall-bfactor name=fcalc anisotropic=true isotropic=false kscale=true k=1.0 bscale=true nstep=30 drop=0.4 b=0.0 tolerance=0.0 debug=true end optimize overall-bfactor name=fcalc anisotropic=true isotropic=false method=lbfgs kscale=true k=1.0 bscale=true nstep=30 drop=0.4 b=0.0 tolerance=0.0 end {* test anisotropic B without K refinement *} evaluate ($k2=1) target=( resi[k=$k2](amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi[k=$k2](amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall,k=$k2](fobs,fcalc+fpart)) optimize overall-bfactor name=fcalc anisotropic=true isotropic=true kscale=false k=1.0 bscale=true nstep=10 drop=0.4 b=0.0 tolerance=0.0 end do (deri1=fcalc) ( all ) multiscale ffk=$k2 bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 k2=1 selection=( 10.0 >= d >= 1.513 ) anisotropic=true end do (deri1=fcalc) ( all ) multiscale ffk=$k2 bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 k2=1 selection=( 10.0 >= d >= 1.513 ) anisotropic=true isotropic=false end target=( resi(amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi(amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall](fobs,fcalc+fpart)) optimize overall-bfactor name=fcalc nstep=0 step=0.0001 b=10.0 debug=true end optimize overall-bfactor name=fcalc nstep=6 drop=0.4 b=0.0 tolerance=0.0 end print target predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target optimize overall-bfactor name=fcalc nstep=1 drop=0.4 b=0.0 tolerance=0.0 end {* test overall anisotropic b-factor optimization *} optimize overall-bfactor anisotropic=true isotropic=true name=fcalc debug=true step=0.0001 end optimize overall-bfactor anisotropic=true isotropic=true name=fcalc debug=true b11=2. b22=4. b33=3. b12=4. b13=3. b23=2. step=0.0001 end evaluate ($k2=1) target=( resi[k=$k2](amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi[k=$k2](amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall,k=$k2](fobs,fcalc+fpart)) optimize overall-bfactor kscale=true bscale=true anisotropic=true isotropic=true name=fcalc debug=true k=.9 b11=2. b22=4. b33=3. b12=4. b13=3. b23=2. step=0.0001 end target=( resi(amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi(amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall](fobs,fcalc+fpart)) optimize overall-bfactor kscale=false bscale=true anisotropic=true isotropic=true name=fcalc debug=true k=.9 b11=2. b22=4. b33=3. b12=4. b13=3. b23=2. step=0.0001 end optimize overall-bfactor kscale=false bscale=true anisotropic=true isotropic=false name=fcalc debug=true k=.9 b11=2. b22=4. b33=3. b12=4. b13=3. b23=2. step=0.0001 end optimize overall-bfactor kscale=false bscale=true anisotropic=false isotropic=true name=fcalc debug=true k=.9 b11=2. b22=4. b33=3. b12=4. b13=3. b23=2. step=0.0001 end optimize overall-bfactor kscale=false bscale=true anisotropic=false isotropic=false name=fcalc debug=true k=.9 b11=2. b22=4. b33=3. b12=4. b13=3. b23=2. step=0.0001 end evaluate ($k2=1) target=( resi[k=$k2](amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi[k=$k2](amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall,k=$k2](fobs,fcalc+fpart)) optimize overall-bfactor kscale=true bscale=false anisotropic=true isotropic=true name=fcalc debug=true k=.9 b11=2. b22=4. b33=3. b12=4. b13=3. b23=2. step=0.0001 end optimize overall-bfactor kscale=true bscale=false anisotropic=true isotropic=false name=fcalc debug=true k=.9 b11=2. b22=4. b33=3. b12=4. b13=3. b23=2. step=0.0001 end target=( resi(amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi(amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall](fobs,fcalc+fpart)) do (deri1=fcalc) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 selection=( 10.0 >= d >= 1.513 ) anisotropic=true isotropic=false end do (deri1=fcalc) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 selection=( 10.0 >= d >= 1.513 ) anisotropic=true end do (deri1=$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 isotropic=true name=fcalc nstep=8 drop=0.4 tolerance=0.0 end print target optimize overall-bfactor anisotropic=true isotropic=true name=fcalc nstep=1 drop=0.4 tolerance=0.0 end end do ( b=b+20. ) ( all ) xray predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target optimize overall-bfactor anisotropic=true isotropic=true name=fcalc nstep=10 drop=0.04 tolerance=0.0 end print target predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target optimize overall-bfactor name=fcalc nstep=1 drop=0.4 tolerance=0.0 end end {* make gaussian distributions, width 1.5 for backbone *} {* 2.0 for sidechains *} set seed=314159. end do ( b = b + gauss(1.5)) ( name ca or name n or name c ) do ( b = b + gauss(2.0)) ( not hydrogen and not ( name ca or name n or name c )) xray optimize b-factors nstep=10 end end show elem ( b )( not hydro ) ! modify the B-factors do ( b = b + 1.5 ) ( not ( name ca or name c or name o ) ) do ( b = b - 0.5 ) ( name ca or name c or name o ) do (store9=b) ( all ) {* debug group B-factor and occupancy derivatives *} {* ============================================== *} xray evaluate ($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 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 predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target end do (b=store9) ( all ) xray optimize group method=lbfgs 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 predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target end do (q=0.8) ( all ) xray evaluate ($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 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 do (q=1.) ( all ) do (q=1. ) ( ( name ca or name n or name c ) and resid 1 ) do (q=1. ) ( ( name ca or name n or name c ) and resid 2 ) do (q=1. ) ( ( name ca or name n or name c ) and resid 3 ) xray predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end do (fobs=combine(amplitude(fcalc),phase(fobs))) ( all ) end do (q=0.5 ) ( ( name ca or name n or name c ) and resid 1 ) do (q=0.7 ) ( ( name ca or name n or name c ) and resid 2 ) do (q=0.8 ) ( ( name ca or name n or name c ) and resid 3 ) do (store8=q) ( all ) xray 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 predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target end do (q=store8) ( all ) xray optimize group method=lbfgs 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 end show ( q ) ( name ca ) do (q=0.8 ) ( ( name ca or name n or name c ) and resid 1 ) do (b=10. ) ( ( name ca or name n or name c ) and resid 1 ) xray predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end do (fobs=combine(amplitude(fcalc),phase(fobs))) ( all ) end do (q=1.0 ) ( ( name ca or name n or name c ) and resid 1 ) do (b=12. ) ( ( name ca or name n or name c ) and resid 1 ) xray 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 predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target end show ( q ) ( name ca ) show ( b ) ( name ca ) do (q=1.0 ) ( ( name ca or name n or name c ) and resid 1 ) do (b=12. ) ( ( name ca or name n or name c ) and resid 1 ) xray optimize group method=lbfgs 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 predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target end show ( q ) ( name ca ) show ( b ) ( name ca ) do (store8=q) ( all ) do (store9=b) ( all ) do ( q=0.5 ) ( name all ) do ( b=10. ) ( name all ) xray 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 predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end print target end do ( q=0.5 ) ( name all ) do ( b=10. ) ( name all ) xray optimize group method=lbfgs drop=10. nstep=20 bmin=5. bmax=8 qmin=0.4 qmax=0.74 q=( ( name ca or name n or name c ) and resid 1 ) b=( ( name ca or name n or name c ) and resid 1 ) end end show (q) ( ( name ca or name n or name c ) and resid 1 ) show (b) ( ( name ca or name n or name c ) and resid 1 ) do (q=store8) ( all ) do (b=store9) ( all ) xray symmetry reset a=5.0 b=10.0 c=15. alpha=80.0 beta=100.0 gamma=120.0 evaluate ($lr=10.) evaluate ($hr=1.513) binresolution $lr $hr mapresolution $hr tselection=( $hr <= d <= $lr ) predict mode=reciprocal to=fcalc selection=( $hr <= d <= $lr ) atomselection=( not hydrogen ) end do (fobs=fcalc+gauss(3.0)) ( all ) do (deri1=fcalc) ( all ) multiscale bfmin=-200 bfmax=200. set1=fobs k1=-1 b1=0 set2=deri1 selection=( 10.0 >= d >= 1.513 ) anisotropic=true end do (deri1=$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 ) evaluate ($k2=1) target=( resi[k=$k2](amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi[k=$k2](amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall,k=$k2](fobs,fcalc+fpart)) do (deri1=fcalc) ( all ) optimize overall-bfactor kscale=true bscale=true anisotropic=true isotropic=true name=fcalc debug=true step=0.0001 end target=( resi(amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi(amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall](fobs,fcalc+fpart)) optimize overall-bfactor kscale=false bscale=true anisotropic=true isotropic=true name=fcalc debug=true step=0.0001 end optimize overall-bfactor kscale=false bscale=true anisotropic=true isotropic=true name=fcalc step=10 step=0.0001 nstep=60 end display 0.5 $B2_11 $B2_22 $B2_33 $B2_12 $B2_13 $B2_23 do (fcalc=0.5 *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 ) statistics (rvalue(fobs,fcalc+fpart)) (rvalue[overall](fobs,fcalc+fpart)) selection=( $hr <= d <= $lr ) output=OUTPUT end evaluate ($k2=1) target=( resi[k=$k2](amplitude(fobs),fcalc+fpart,1)) dtarget=( dresi[k=$k2](amplitude(fobs),fcalc+fpart,1)) monitor=( rvalue[overall,k=$k2](fobs,fcalc+fpart)) do (fcalc=deri1) ( all ) optimize overall-bfactor kscale=true bscale=true anisotropic=true isotropic=true name=fcalc step=10 step=0.0001 nstep=60 end do (fcalc=$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 ) statistics (rvalue[k=1](fobs,fcalc+fpart)) (rvalue[k=1,overall](fobs,fcalc+fpart)) selection=( $hr <= d <= $lr ) output=OUTPUT end multiscale ffk=$k2 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 ) statistics (rvalue[k=1](fobs,fcalc+fpart)) (rvalue[k=1,overall](fobs,fcalc+fpart)) selection=( $hr <= d <= $lr ) output=OUTPUT end do (fpart=fcalc) ( all ) associate fcalc ( not hydrogen ) target= ( resi(amplitude(fobs),fcalc,1)) dtarget(fcalc)=( dresi(amplitude(fobs),fcalc,1)) monitor=( rvalue[overall](fobs,fcalc)) optimize overall-bfactor kscale=false bscale=true anisotropic=true isotropic=true name=fcalc step=10 step=0.00001 nstep=60 end display 0.5 $B2_11 $B2_22 $B2_33 $B2_12 $B2_13 $B2_23 associate fpart ( not hydrogen ) target=( resi(amplitude(fobs),fpart,1)) dtarget(fpart)=( dresi(amplitude(fobs),fpart,1)) monitor=( rvalue[overall](fobs,fpart)) optimize overall-bfactor kscale=false bscale=true anisotropic=true isotropic=true name=fpart step=10 step=0.00001 nstep=60 end display 0.5 $B2_11 $B2_22 $B2_33 $B2_12 $B2_13 $B2_23 end ! test new group feature of "optimize Bfactor" do (b=20) ( all ) do (q=1) ( all ) xray associate reset associate fcalc ( not hydrogen ) target= ( resi(amplitude(fobs),fcalc,1)) dtarget(fcalc)=( dresi(amplitude(fobs),fcalc,1)) monitor=( rvalue[overall](fobs,fcalc)) method=direct optimize B-factors rweight=0 group=( resid 1 ) group=( resid 2 ) {*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 step=0.001 debug=true end optimize b-factors nstep=20 ! do 20 steps of conjugate gradient group=( resid 1 ) group=( resid 2 ) ! 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 bmin=-200 bmax=200 end end show element (b ) ( not hydrogen ) xray optimize B-factors rweight=0 bmin=10 bmax=15 group=( resid 1 ) group=( resid 2 ) {*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 step=0.001 debug=true end optimize b-factors nstep=20 ! do 20 steps of conjugate gradient group=( resid 1 ) group=( resid 2 ) bmin=10 bmax=15 ! 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 show element (b ) ( not hydrogen ) do (b=20) ( all ) do (q=1) ( all ) xray optimize b-factors nstep=20 ! do 20 steps of lbfgs method=lbfgs group=( resid 1 ) group=( resid 2 ) bmin=-200 bmax=200 ! 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 show element (b ) ( not hydrogen ) xray optimize b-factors nstep=20 ! do 20 steps of lbfgs method=lbfgs group=( resid 1 ) group=( resid 2 ) bmin=10 bmax=15 ! 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 show element (b ) ( not hydrogen ) stop