[phenixbb] Nitric Oxide ligand keeps getting pushed far away from specified links in CIF
Yarrow Madrona
amadrona at uci.edu
Tue Nov 29 11:45:35 PST 2011
Hi Pavel,
The .geo file indicated a longer bond than I had specified. I had copied a
lot of that from others doing refinement in Refmac. So I have tried to
redo everything by generating a new cif file in elbow and phenix.metal
coordination to generate the bond angles and distances. I then adjusted
the distances and angles. However when I run:
Phenix.refine mymodel.mtz mymodel.pdb model.cif model.edits
I get an error saying that it does not recognize NO. I am not sure how to
do enter the "apply CIF modifications". Is this necessary?
I'm sorry about all this trouble. I am new to generating ligands and so
forth.
Number of atoms with unknown nonbonded energy type symbols: 4
"ATOM 3204 N NO A 700 .*.A N "
"ATOM 3205 O NO A 700 .*.A O "
"ATOM 6410 N NO B 600 .*.B N "
"ATOM 6411 O NO B 600 .*.B O "
Time building chain proxies: 4.87, per 1000 atoms: 0.73
Number of scatterers: 6698
At special positions: 0
Unit cell: (64.176, 68.437, 104.047, 90, 95.79, 90)
Space group: P 1 21 1 (No. 4)
Number of sites at special positions: 0
Number of scattering types: 5
Type Number sf(0)
Fe 2 26.01
S 22 16.00
O 1464 8.00
N 1108 7.00
C 4102 6.00
sf(0) = scattering factor at diffraction angle 0.
Sorry: Fatal problems interpreting PDB file:
Number of atoms with unknown nonbonded energy type symbols: 4
Please edit the PDB file to resolve the problems and/or supply a
CIF file with matching restraint definitions, along with
apply_cif_modification and apply_cif_link parameter definitions
if necessary.
Also note that phenix.ready_set and phenix.elbow are available
for creating restraint definitions (CIF files).
> 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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>
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
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