archiv specify items to be placed in reflection records

uov overall isotropic thermal parameter

dampsh shift damping factors to control refinement

print print control line

reflim limits on reflections to be included in refinement

rtest set up survey of R values to assess refinement

scale scale factors

scanis anisotropic scale factor

solmod solvent model parameters

stats number and limits of d shells for R value survey

wgtb set thermal restraint weighting

wgtchi set chiral centre restraint weighting

wgtcon set contact distance restraint weighting

wgtdis set distance restraint weighting

wgtpla set plane restraint weighting

wgtref set structure factor restraint weighting

wgtshf set excessive shift restraint weighting

wgtsym set noncrystallographic symmetry restraint weighting

wgttor set torsion angle restraint weighting

noref control atoms included in refinement

PROLSQ Option Code

congugent gradient cycles ncy n 50

Lagrange multiplier scale lag n 10

refinement to fit diffraction data¹ xrfapply

nxr skip

refinement to fit idealized geometry ¹ geoapply

nge skip

set individ, tf's to overall value tfs set tf's to overall

refine populations if input <1.0 pop refine populations

anomolous dispersion noa do not apply

ano apply dispersion

thermal parameters ova overall isotropic

iso individual isotropic

data set number dsn n 1

constrain origin orx along x no

ory along y no

orz along z no

punch atoms in PDB format pch yes no

1 The default is to use both types of information in the refinement. If both types are set to skip the result will be a simple copying of the bdf from one file to another, i.e. a null refinement.

archiv 1- ID numbers of data items to be added to or deleted from the bdf

Positive ID numbers signal addition, negative deletion.

uov 1 B overall or U overall depending on magnitude U from input bdf

If value is 0 < U < 0.2 the quantity is stored as U. If the quantity is 0.2 < B < 40.0 it is multiplied by 78.9568 and stored as U. This line is ignored unless in overall t.f. mode.

dampsh 1-3 damping factor for x, y , z parameter shifts 0.5

4 damping factor for B parameter shifts 0.5

5 damping factor for population parameter shifts 0.5

6-11 damping factor for B11 to B23 parameter shifts 0.5

These damping factors are to be applied to parameter shifts determined by the least-squares process. These factors will be used to establish the new parameters written to the output bdf and, optionally on unitpch:. Factors between 0 & 4 allowed.

N.B. Unequal damping factors will distort the geometry.

print Option Code

list first m reflections lfir m 10

list reflection data flis m every mth refln 0

list first n input atoms ilis n 99999

list updated atoms alis m 0/1/2 no/all/>shift limit

atom shifts on x, y, z parc d only shifts > d 0.1

temperature factor shifts bcut d 0.25

population param. shifts popc d 0.25

torsion angle printing ntor statistics only

stor all standards and statistics

ctor d single angle contacts 0.1

mtor d multiple 0.1

chiral centres printing nchi statistics only

wchi worst case chiral centres

achi all chiral centres

hydrogen bond printing nhbo statistics only

hbon all possible H bonds

restrained distances¹ disc d dists of type code "J" 5

restrained planes plan d all planes with RMS 2

deviation > d*sigp

1 Print only if |DIDEAL-DMODEL| >= d*SIGD(J) If d=0.0, print all.

reflim Option Code

discard reflections fmin x < x 0

smin x sinθ/λ < x 0

smax x sinθ/λ > x 1.5

dmax x d maximum 1000

dmin x d minimum 0.35

sigm x < σ 0

Note: Use either d or sinθ/λ specs but not both.

rtest 1 sampling frequency for included reflections¹ 10000

2 sampling frequency for excluded reflections² 0

3 sampling offset of included reflection subset 0

4 sampling offset of excluded reflection subset 0

5 number of coordinate, x, y, z, shift steps to be tested 1

6 number of B steps to be tested 1

7-n factors to multiply shifts for testing³ 0.5

Set up R testing for reflection subsets. The subsets are defined by the reflection count plus a constant modulo the frequency being zero. After the least-squares refinement structure factors are recalculated for the subsets in order to evaluate the efficacy of the shift damping and progress of the refinement.

1Time consuming if this is set too low and fields 5 & 6 too large.

2 Excluded from the refinement but used in subsequent structure factor R value estimate. This gives a stringent test of convergence, but caution is required or the number of reflections eliminated may be too great.

3 These are the same kind of factors as those in the dampsh line, e.g. x(test) = x(start) +factor*x(shift) The sum of fields 5 & 6 determines the value of n.

scale 1 scale factor input bdf

2 scale group number 1

scanis 1 component of overall anisotropic scaling of 0

2-6 components

solmod 1 linear scale K for partial 1

2 exponential scale U for partial 0

3 linear scale UK for analytic solvent attenuation function 1

4 exp. scale UB for analytic solvent attenuation function 0

5 electron density plateau level for unoccupied model space 0

stats 1-7 resolution limits for reciprocal space shells used for R-factors

Maximum of seven shells; default one. Values supplied must be descending order of d-spacings in Å.

wgtb 1 weight for temperature factor restraints 1

2 σ of type 1 main-chain bond distances 1

3 σ of type 2 main-chain angle distance 1.5

4 σ of type 3 side-chain bond distance 1

5 σ of type 4 side-chain angle distance 1

6 σ of type 5 X-H bond 0.5

7 σ of type 6 X-H angle 1

8 σ of type 7 hydrogen-bond, metal, etc 0

wgtchi 1 weight for chiral centre restraints WC 1

2 σ(χ) 0.15

wgtcon 1 weight for van der Waals contacts WV 0.5

2 σ(vdW) 0.5

3 type 1 distance factor in Ź -0.3

4 type 2 distance factor in Ź 0

5 type 3 distance factor in Ź -0.2

6 type 4 distance factor in Ź 0

1 These fields may be used to supply parameters to modify the minimum "theoretical" van der Waals contact distance of four possible types which are defined and calculated in PROTIN. There are four parameters corresponding to:

1) Atoms in which the relative position is determined by only one torsion angle.

2) Two atoms in which >two torsion angles are involved, multiple torsion contact.

3) A possible (X....Y) hydrogen bond pair involving contacts between nitrogen-oxygen pairs, but not N main - N main or O main - O main.

4) A possible (X-H....Y) hydrogen bond.

Note: The distance factors must be negative amounts. They are used to adjust the ideal contact distances supplied from PROTIN in order to establish when a contact should be restrained.

wgtdis 1 weight for distance restraints WD 1

2 σ of type¹ 1 bonded distances (e.g. Cα - C) 0.03

3 σ of type¹ 2 angle distances (e.g. N - C) 0.04

4 σ of type¹ 3 planar 1-4 distances (e.g. O i-1 - Cα1) 0.05

5 σ of type¹ 4 bond distances involving H (e.g. Cα- H) 0.1

6 σ of type¹ 5 angle distance involving H (e.g. Hα- C) 0.08

7 σ of type¹ 6 hydrogen bond, metal 0

8 σ of type¹ 7 coordination, etc 0

wgtpla 1 weight for plane restraints, WP 1

2 σ of a plane 0.02

The weight applied to the derivative is: (WP/(σ(p))².

wgtref 1 weighting scheme as 1 through 5 1

2 A term for weights 4

3 B term for weights 0

wgtshf 1 shifts magnitude restraint positional PDEL 0.2

2 shifts magnitude restraint thermal BDEL 3

3 shifts magnitude restraint population QDEL 0.1

4 σ for tight positional restraints 0.05

5 σ for medium positional restraints 0.5

6 σ for loose positional restraints 2.0

7 σ for tight thermal restraints 0.5

8 σ for medium thermal restraints 1

9 σ for loose thermal restraints 0

wgtsym 1 weight scale non-crystallographic symmetry restraints WS 1

wgttor 1 weight scale torsion angle restraints 1

2 σ(T) secondary structure angle φ or ψ 15

3 σ(T) planar angle such as ω 3

4 σ(T) staggered angle such as χ1 15

5 σ(T) orthonormal angle such as χ2 of aromatics 20

noref 1- atom labels for atoms which are not refined

More than one noref line may be entered.