[phenixbb] Nitric Oxide ligand keeps getting pushed far away from specified links in CIF

Pavel Afonine pafonine at lbl.gov
Mon Nov 28 14:32:45 PST 2011


Hi Yarrow,

phenix.refine always creates a .geo file that lists all the geometry 
restraints used in refinement. Looking in this file you can always tell 
which atoms is involved in which restraints, as well as ideal and actual 
restraint parameter values (bond length, for example).

As a very first step I would check .geo file to make sure the restraints 
are correctly set up for atoms in question.

Pavel


On 11/28/11 2:19 PM, Yarrow Madrona wrote:
> 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
>
>



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