Comparing to one of my refmac jobs, it is slightly different because of different system and options. However, I would guess that the missing labels are:
r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other But don't take my word for it - check it! The numbers should correlate with the "Restraint type" section in the log file. Look at the last instance of this, since non-bonded restraint counts get updated through the refinement. Cheers Martyn -----Original Message----- From: CCP4 bulletin board on behalf of Yu Wai Chen Sent: Wed 11/18/2009 11:43 PM To: [email protected] Subject: [ccp4bb] Data harvesting file corrupted in refmac Dear All, I was trying to upload a refmac-generated deposit file to PDB Autdep but it says the format is invalid. So I opened the file and have a look. In it I saw a number of lines with <nul><nul>... which I suspect was the cause of error. It looks like it is corrupted. Does anyone know why it happened? It seems the numeric values in these lines are all there and it is just the data labels that are corrupted/missing. Is there an easy way I can find out the missing data field names (and the correct order) that I can edit them into the deposit file without re-running refmac? The affected lines (section) are the following: +++++++++++++++++++++++++++++ loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target r_bond_refined_d 670 0.029 0.022 r_bond_other_d 467 0.001 0.020 r_angle_refined_deg 905 2.288 2.000 r_angle_other_deg 1158 3.113 3.000 r_dihedral_angle_1_deg 80 6.351 5.000 r_dihedral_angle_2_deg 27 33.598 24.815 r_dihedral_angle_3_deg 141 14.992 15.000 r_dihedral_angle_4_deg 4 22.156 15.000 r_chiral_restr 111 0.276 0.200 r_gen_planes_refined 688 0.010 0.021 r_gen_planes_other 120 0.002 0.020 115 0.299 0.200 411 0.189 0.200 292 0.168 0.200 306 0.095 0.200 67 0.269 0.200 7 0.218 0.200 r_symmetry_vdw_other 11 0.147 0.200 13 0.273 0.200 r_mcbond_it 402 2.576 1.500 r_mcbond_other 158 1.171 1.500 r_mcangle_it 670 3.553 2.000 r_mcangle_other 532 1.745 2.000 r_scbond_it 268 5.423 3.000 r_scbond_other 309 1.932 3.000 r_scangle_it 235 7.410 4.500 r_scangle_other 626 3.770 4.500 r_sphericity_free 108 20.126 5.000 r_sphericity_bonded 1130 5.566 5.000 r_rigid_bond_restr 1137 2.479 3.000 +++++++++++++++++++++++++++++++++++++ I am running refmac ver. 5.5.0072. Thanks in advance. Wai -- Scanned by iCritical.
