Hello, I am having some trouble refining a structure with Nitric Oxide coordinated to the Heme Fe. I attempted to merge two Cif files. One for another ligand (CNL) and one for NO (NO.cif). I have saved the merged file as CinNO2.cif. In the defualt refinement I type the following into the command line: Mymodel.mtz mymodel.pdb CinNO2.cif Phenix refine runs fine without any errors but pushes the NO much further than the 1.9 angstrom specified by the links in the cif file. I have pasted the contents of the cif file below. The NO, Fe links are at the end of the file. Thank you for any help you can provide. -Yarrow # Files merged : Tue Oct 4 10:11:22 2011 # # CNL.cif # NO.cif # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level CNL CNL Unknown ligand 29 11 . NO NO Unknown ligand 2 2 . # data_comp_CNL # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z CNL C1 C CT . 55.3085 -9.1280 -43.0216 CNL C2 C CH2 . 55.6432 -10.5699 -43.1750 CNL C3 C CH2 . 54.6509 -11.3139 -43.9725 CNL C4 C CH1 . 53.4902 -10.4784 -44.3504 CNL C5 C CH2 . 53.9278 -9.3349 -45.0693 CNL C6 C CH2 . 54.8932 -8.4964 -44.3064 CNL C7 C CH3 . 56.3801 -8.3679 -42.3275 CNL C8 C CT . 52.9353 -9.9244 -43.0573 CNL C9 C CH3 . 52.3495 -11.0301 -42.2453 CNL C10 C CH3 . 51.8314 -8.9341 -43.2982 CNL O O O2 . 54.1049 -9.2461 -42.2221 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd CNL C1 C2 single 1.488 0.020 CNL C1 C6 single 1.491 0.020 CNL C1 C7 single 1.486 0.020 CNL C1 O single 1.450 0.020 CNL C2 C3 single 1.475 0.020 CNL C3 C4 single 1.479 0.020 CNL C4 C5 single 1.420 0.020 CNL C4 C8 single 1.512 0.020 CNL C5 C6 single 1.489 0.020 CNL C8 C9 single 1.492 0.020 CNL C8 C10 single 1.502 0.020 CNL C8 O single 1.589 0.020 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd CNL C3 C2 C1 113.16 3.000 CNL C5 C6 C1 112.56 3.000 CNL C8 O C1 110.85 3.000 CNL C6 C1 C2 112.60 3.000 CNL C7 C1 C2 112.43 3.000 CNL O C1 C2 99.48 3.000 CNL C4 C3 C2 112.41 3.000 CNL C5 C4 C3 110.02 3.000 CNL C8 C4 C3 106.05 3.000 CNL C6 C5 C4 113.20 3.000 CNL C9 C8 C4 109.75 3.000 CNL C10 C8 C4 111.96 3.000 CNL O C8 C4 109.61 3.000 CNL C8 C4 C5 104.53 3.000 CNL C7 C1 C6 112.76 3.000 CNL O C1 C6 106.18 3.000 CNL O C1 C7 112.51 3.000 CNL C10 C8 C9 106.70 3.000 CNL O C8 C9 108.62 3.000 CNL O C8 C10 110.10 3.000 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period CNL Var_01 C4 C8 O C1 10.40 30.0 3 CNL Var_02 C9 C8 O C1 130.31 30.0 3 CNL Var_03 C10 C8 O C1 -113.19 30.0 3 # loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign CNL chir_01 C1 C6 C7 O both CNL chir_02 C4 C3 C5 C8 both # data_comp__NO # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z NO N N N . -5.7690 4.3760 32.3600 NO O O O . -4.8990 5.2460 32.3600 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd NO N O double 1.150 0.02 # data_link_list loop_ _chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 _chem_link.name HEM-CYS HEM . . CYS . . bond_CYS-SG_=_HEM-FE NO -HEM HEM . . NO . . bond_HEM-FE_=_NO-N # data_link_HEM-CYS # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd HEM-CYS 1 FE 2 SG . 2.300000 0.020 # loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd HEM-CYS 2 SG 1 FE 1 NC 109.471221 3.000 HEM-CYS 1 FE 2 SG 2 CB 109.471221 3.000 # data_link_NO -HEM # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd NO -HEM 1 N 2 FE . 1.900000 0.020 # loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd NO -HEM 2 FE 1 N 1 O 140 3.000 NO -HEM 1 N 2 FE 2 NC 103 3.000 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697