<xsd:complexType name="pdbx_refine_componentType">
<xsd:annotation>
<xsd:documentation xml:lang="en">Data items in the PDBX_REFINE_COMPONENT category record statistics of the final model relative to the density map. Example 1 -</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element name="pdbx_refine_component" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:all>
<xsd:element name="B_iso" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The average isotropic B factors for the group of atoms (e.g. residue or ligand, side chain, main chain). The B factors for each atom is given by attribute B_iso_or_equiv in category atom_site</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="B_iso_main_chain" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The average isotropic B factors for the group of atoms (e.g. residue or ligand, side chain, main chain). The B factors for each atom is given by attribute B_iso_or_equiv in category atom_site</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="B_iso_side_chain" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The average isotropic B factors for the group of atoms (e.g. residue or ligand, side chain, main chain). The B factors for each atom is given by attribute B_iso_or_equiv in category atom_site</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="PDB_ins_code" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">A component of the identifier for the component. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site ATOM_SITE category.</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="auth_asym_id" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">A component of the identifier for the component. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="auth_comp_id" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">A component of the identifier for the component. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="auth_seq_id" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">A component of the identifier for the component. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="connect" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The index of connectivity is the product of the (2Fobs-Fcal) electron density values for the backbone atoms (N, CA and C) divided by the average value for the structure. Low values (less than 1.0) of this index indicate breaks in the backbone electron density which may be due to flexibility of the chain or incorrect tracing. connect = [(D(xi)...D(xi))^(1/N)] /<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="correlation" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">Correlation coefficient of electron density for each residue or ligand, side chain, main chain The density correlation coefficient is calculated for each component from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model map (Fcalc) - "Rcalc" : D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>) where <Robs> is the mean of "observed" densities of atoms of the component (backbone or side chain). <Rcalc> is the mean of "calculated" densities of component atoms. The value of density for some atom from map R(x) is: sum_i ( R(xi) * Ratom(xi - xa) ) Dens = ---------------------------------- sum_i ( Ratom(xi - xa) ) where Ratom(x) is atomic electron density for the x-th grid point. xa - vector of the centre of atom. xi - vector of the i-th point of grid. Sum is taken over all grid points which have distance from the center of the atom less than the Radius_limit. For all atoms Radius_limit = 2.5 A. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="correlation_main_chain" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">Correlation coefficient of electron density for each residue or ligand, side chain, main chain The density correlation coefficient is calculated for each component from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model map (Fcalc) - "Rcalc" : D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>) where <Robs> is the mean of "observed" densities of atoms of the component (backbone or side chain). <Rcalc> is the mean of "calculated" densities of component atoms. The value of density for some atom from map R(x) is: sum_i ( R(xi) * Ratom(xi - xa) ) Dens = ---------------------------------- sum_i ( Ratom(xi - xa) ) where Ratom(x) is atomic electron density for the x-th grid point. xa - vector of the centre of atom. xi - vector of the i-th point of grid. Sum is taken over all grid points which have distance from the center of the atom less than the Radius_limit. For all atoms Radius_limit = 2.5 A. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="correlation_side_chain" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">Correlation coefficient of electron density for each residue or ligand, side chain, main chain The density correlation coefficient is calculated for each component from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model map (Fcalc) - "Rcalc" : D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>) where <Robs> is the mean of "observed" densities of atoms of the component (backbone or side chain). <Rcalc> is the mean of "calculated" densities of component atoms. The value of density for some atom from map R(x) is: sum_i ( R(xi) * Ratom(xi - xa) ) Dens = ---------------------------------- sum_i ( Ratom(xi - xa) ) where Ratom(x) is atomic electron density for the x-th grid point. xa - vector of the centre of atom. xi - vector of the i-th point of grid. Sum is taken over all grid points which have distance from the center of the atom less than the Radius_limit. For all atoms Radius_limit = 2.5 A. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="density_index" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The index of density is the product of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 1.0) may be problematic for model fitting. index = [(D(xi)...D(xi))^(1/N)] /<D>_all Where : D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="density_index_main_chain" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The index of density is the product of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 1.0) may be problematic for model fitting. index = [(D(xi)...D(xi))^(1/N)] /<D>_all Where : D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="density_index_side_chain" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The index of density is the product of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 1.0) may be problematic for model fitting. index = [(D(xi)...D(xi))^(1/N)] /<D>_all Where : D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="density_ratio" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The density ratio is similar to the density index, but summation of the density for the group is used for calculation. The ratio of density is the summation of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 0.4) of this ratio may be problematic for the group. index = [Sum~i D(xi)]/<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the average value of density for the structure. The summation is for all the atoms of group.</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="density_ratio_main_chain" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The density ratio is similar to the density index, but summation of the density for the group is used for calculation. The ratio of density is the summation of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 0.4) of this ratio may be problematic for the group. index = [Sum~i D(xi)]/<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the average value of density for the structure. The summation is for all the atoms of group.</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="density_ratio_side_chain" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The density ratio is similar to the density index, but summation of the density for the group is used for calculation. The ratio of density is the summation of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 0.4) of this ratio may be problematic for the group. index = [Sum~i D(xi)]/<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the average value of density for the structure. The summation is for all the atoms of group.</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="real_space_R" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">Real space R factor of electron density for each component, residue side chain, or main chain. The real space R factor is calculated by the equation R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)] Where: Dobs is the observed electron density, Dcal is the calculated electron density, summation is for all the grid points Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="real_space_R_main_chain" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">Real space R factor of electron density for each component, residue side chain, or main chain. The real space R factor is calculated by the equation R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)] Where: Dobs is the observed electron density, Dcal is the calculated electron density, summation is for all the grid points Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="real_space_R_side_chain" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">Real space R factor of electron density for each component, residue side chain, or main chain. The real space R factor is calculated by the equation R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)] Where: Dobs is the observed electron density, Dcal is the calculated electron density, summation is for all the grid points Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="shift" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The tendency of the group of atoms (e.g. residue or ligand, side chain, main chain) to move away from its current position. Displacement of atoms from electron density is estimated from the difference (Fobs - Fcal) map. The displacement vector is the ratio of the gradient of difference density to the curvature. The amplitude of the displacement vector is an indicator of the positional error. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="shift_main_chain" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The tendency of the group of atoms (e.g. residue or ligand, side chain, main chain) to move away from its current position. Displacement of atoms from electron density is estimated from the difference (Fobs - Fcal) map. The displacement vector is the ratio of the gradient of difference density to the curvature. The amplitude of the displacement vector is an indicator of the positional error. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="shift_side_chain" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:decimal">
<xsd:annotation>
<xsd:documentation xml:lang="en">The tendency of the group of atoms (e.g. residue or ligand, side chain, main chain) to move away from its current position. Displacement of atoms from electron density is estimated from the difference (Fobs - Fcal) map. The displacement vector is the ratio of the gradient of difference density to the curvature. The amplitude of the displacement vector is an indicator of the positional error. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:all>
<xsd:attribute name="label_alt_id" use="required" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">A component of the identifier for the component. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="label_asym_id" use="required" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">A component of the identifier for the component. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="label_comp_id" use="required" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">A component of the identifier for the component. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="label_seq_id" use="required" type="xsd:integer">
<xsd:annotation>
<xsd:documentation xml:lang="en">A component of the identifier for the component. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:complexType> |