Appendix F: Test output from CCP4 RESTRAIN
data_toxd[native]
_entry.id toxd
_diffrn.id native
_audit.creation_date 1997-10-30T12:51:56+00:00
_software.classification refinement
_software.contact_author 'Ian J. Tickle, etal'
_software.contact_author_email tickle@mail.cryst.bbk.ac.uk
_software.description 'Macromol. Refinement for Struct Amplitudes, Phases & Energy'
_software.name restrain_atomIsoB_FreeSet
_software.version ' 4.4.9 Sep 8 1997'
_cell.length_a 73.530
_cell.length_b 39.060
_cell.length_c 23.150
_cell.angle_alpha 90.000
_cell.angle_beta 90.000
_cell.angle_gamma 90.000
_Symmetry.Int_Tables_number 19
_Symmetry.space_group_name_H-M 'P 21 21 21'
loop_
_Symmetry_equiv.id
_Symmetry_equiv.pos_as_xyz
1 X,Y,Z
2 1/2-X,-Y,1/2+Z
3 -X,1/2+Y,1/2-Z
4 1/2+X,1/2-Y,-Z
_refine.details
;
The function minimised by RESTRAIN:
M = SUM [w(f) (|Fo| - G.|Fc|)^2] (=M(a))
+ SUM [w(p) (PHIo - PHIc)^2] (=M(b))
+ SUM [w(d) (d(t) - d(c))^2] + SUM [w(b) (b(o) -b(min))^2]
+ SUM [w(v) |V|^2] + SUM [w(c) (d(t) - d(c))^2] (=M(c))
+ SUM [w(U) delta-U^2] + SUM [w(Ua) delta-Ua^2]
The factors w(f), w(p), w(d) and w(c) are weighting factors,
the choice of which determines the relative influence of the
terms in the function M which is to be minimised.
where:-
w(f) = weight for structure amplitude,
Fo = observed structure amplitude,
G = scale factor,
Fc = calculated structure amplitude,
w(p) = weight for phase,
PHIo = estimated phase (from isomorphous and/or anomalous data),
PHIc = calculated phase,
w(d) = weight for restrained distance,
d(t) = target interatomic distance,
d(c) = calculated interatomic distance,
w(b) = weight for non-bonded interactions,
b(o) = observed distance between two non-bonded atoms,
b(min) = minimum distance allowed for such atoms,
w(U) = weight for isotropic thermal parameter difference,
delta-U = isotropic thermal parameter diff for restrained atoms,
w(Ua) = weight for anisotropic thermal parameter difference,
delta-Ua = along-bond component of anisotropic thermal parameter
difference for restrained atoms,
w(v) = weight for planarity restraints,
V = mean square deviation from best plane of a planar group
of atoms,
w(c) = weight for chirality restraints.
RESTRAIN uses energy weighting that involves the application
of geometric restraints to the structure during refinement.
Energy weighting uses a dictionary of target interatomic
distances and standard deviations which govern the allowed
deviations from the target values.
Weights Case Ideal r.m.s deviations
W(d) = WE(1)^2 if dt < 2.12 A 0.02A
W(d) = WE(2)^2 if 2.12 A < dt < 2.625 A 0.04A
W(d) = WE(3)^2 if d(t) > 2.625 A 0.05A
W(v) = WE(4)^2 for planar peptide groups 0.01A
W(c) = WE(5)^2 for all other planar groups 0.01A
W(c) = WE(6)^2 for edges of chiral tetrahedra 0.00A
Chiral restraints are applied as distance restraints along
the edges of chiral tetrahedra with d(t)<=2.12A. In all
cases WE(i)^2 is the weighting factor that decides the
relative weight of the particular energy restraint and the
other terms in the function minimised.
;
_refine.ls_weighting_scheme 'based on measured sigma F'
_refine.ls_weighting_details
;
Weighting applied used a modified form of one proposed
by Rees (1976) and involves the use of the standard deviations
of F(obs). The weights are given by the formula:
w(f) = WF(1).S^WF(2) / [WF(3).sigma(Fo)^2 + WF(4).Fo^2]
where S = sin(theta)/lambda
WF(1) = 1.0000
WF(2) = 3.2135
WF(3) = 0.0701
WF(4) = 6.1267E-05
;
_refine.ls_matrix_type diagonal+energy_off_diagonal
_refine.ls_d_res_low 36.765
_refine.ls_d_res_high 2.297
_refine.solvent_model_details
;
Disordered solvent's contribution to the Bragg scattering
at low angles was allowed for by applying Babinet's Principle.
Accordingly modified form factors (or scattering cross-sections)
f' are used in the structure factor calculations.
f' = f - SB1*exp(-1/2*SB2*q^2)
where q = 4.PI.sin(theta)/lamda.
and SB1= 5.6031 ; SB2= 1.6716
;
_refine.ls_number_parameters 2239
_refine.ls_number_restraints 2496
_refine.ls_number_reflns_R_work 3009
_refine.ls_number_reflns_R_free 152
_refine.ls_R_factor_R_work 0.202
_refine.ls_R_factor_R_free 0.314
_refine.ebi_ls_RG_work 0.190
_refine.ebi_ls_RG_free 0.281
_refine.ebi_ls_Correlation_coeff_Fo_to_Fc 0.885080
_refine.ebi_ls_Correlation_coeff_Fo_to_Fc_Free 0.748523
loop_
_EBI_refine_funct_minimised.type
_EBI_refine_funct_minimised.NumTerms
_EBI_refine_funct_minimised.Residual
sum(W*Delta(Amplitude)^2 3009 1621.3
sum(W*Delta(Plane+Rigid)^2 85 56.68
sum(W*Delta(Distance)^2 1219 163.59
sum(W*Delta(U-tempfactors)^2 1192 69.338
Total_Function 5505 1910.9
loop_
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.ebi_rmsdev_observed
_refine_ls_restr.ebi_rmsdev_dictionary
_refine_ls_restr.ebi_U_sigma_wghts
' Distances < 2.12' 509 0.005 0.022 ?
' Distances 2.12 < D < 2.625' 671 0.016 0.037 ?
' Distances > 2.625' 39 0.034 0.043 ?
' Peptide Planes' 59 0.002 0.010 ?
' Ring and other planes' 26 0.014 0.010 ?
'r.m.s. diffs for Uiso atoms at dist 1.2-1.4' 212 0.106 ? 1.800
'r.m.s. diffs for Uiso atoms at dist 1.4-1.6' 288 0.101 ? 1.800
'r.m.s. diffs for Uiso atoms at dist 1.8-2.0' 6 0.077 ? 1.800
'r.m.s. diffs for Uiso atoms at dist 2.0-2.2' 10 0.114 ? 1.800
'r.m.s. diffs for Uiso atoms at dist 2.2-2.4' 215 0.119 ? 1.800
'r.m.s. diffs for Uiso atoms at dist >2.4' 461 0.106 ? 1.800
loop_
_refine_ls_shell.d_res_high
_refine_ls_shell.d_res_low
_refine_ls_shell.number_reflns_all
_refine_ls_shell.number_reflns_R_work
_refine_ls_shell.R_factor_R_work
_refine_ls_shell.number_reflns_R_free
_refine_ls_shell.R_factor_R_free
4.17 36.76 590 559 0.274 31 0.563
3.31 4.17 535 511 0.160 24 0.144
2.89 3.31 531 505 0.155 26 0.245
2.63 2.89 530 506 0.182 24 0.253
2.44 2.63 517 494 0.200 23 0.322
2.30 2.44 458 434 0.225 24 0.315
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