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Methods, Problems and Solutions

Restrained Rietveld Structure Refinement of Organics

Using Crystals to optimise an organic model and graphically generate bond/angle and planar restraints for Rietveld programs

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The following will go through modelling a molecule in Crystals with the option of DLS (Distance Least Squares); generating all the restraint commands that can then be transformed into the format for your favourite Rietveld software.

WinCRYSTALS 2000 (Crystals for Windows Single Crystal Suite) - David Watkin

A trick to make things happy when passing the restraint commands to the Rietveld software - is to match the Atom Labelling/Atom Numbering system.

For Fullprof, it is important to match the Atom Labels which are used to define restraints. But it GSAS it is important to match the Atom Numbering system which are used to define restraints (not the Atom Labels).

Also refer to Randomly Perturbing Atomic Positions in Crystals. This can be relevant for successfully performing DLS and refinement involving pseudo-symmetry.

For extra information on using these features in Crystals, also refer to:

The Laboratory Powder X-ray Diffraction Data

The Data we are hoping to perform a restrained Rietveld refinement with is standard laboratory Bragg-Brentano X-ray data collecting using Cu X-ray radiation of Tetracycline Hydrochloride (one of the structures of the Structure Determination from Powder Diffractometery Round Robin).

Screen dump of a Rietveld plot

(For comparison with single crystal results of tetracycline refer: "Tetracycline hydrochloride: a synchrotron micro-crystal study" Clegg W. & Teat S.J. Acta Cryst., C56 , 1343-1345 (2000))

Molecular Structure for Inputting into Crystals

The easiest method to input the structure into Crystals is to create a Shelx file and use a "dummy" HKL file so you can perform the DLS if required. Noting again what was mentioned above that the atom numbers match up with what will be inserted into the Rietveld program you are using (for GSAS, this is not the atom "name" but the atom "number - *") (for Fullprof, this is the "atom name/atom label")

If you already have a starting file in Fullprof, GSAS or LHPM-Rietica format, Ortep-3 by Louis Farrugia can be used to read in the file, then export into Shelx format. 

TITL    tetracycline in space group P2(1)2(1)2(1)
CELL    1.54056  10.9300  12.7162  15.7085   90.000   90.000   90.000
ZERR    4         0.0009   0.0011   0.0013    0.001    0.001    0.001
LATT   -1
SYMM     1/2 - X, - Y, 1/2 + Z
SYMM     - X, 1/2 + Y, 1/2 - Z
SYMM     1/2 + X, 1/2 - Y, - Z
SFAC     C    H    Cl   N    O
UNIT      88  100    4    8   32
FVAR    1.0
Cl1     3   0.92963   0.41939  -0.00197  11.00000   0.025
O2      5   0.00860   0.36560   0.43967  11.00000   0.025
O3      5   0.14530   0.46012   0.12979  11.00000   0.025
O4      5   0.75140   0.64335   0.07408  11.00000   0.025
O5      5   0.36340   0.71743   0.18883  11.00000   0.025
O6      5   0.58000   0.60174   0.29547  11.00000   0.025
O7      5   0.35060   0.60822   0.35612  11.00000   0.025
O8      5   0.16470   0.50211   0.38835  11.00000   0.025
O9      5   0.66230   0.81863   0.04211  11.00000   0.025
N10     4   0.74650   0.44880   0.14281  11.00000   0.025
N11     4   0.46940   0.85510   0.08138  11.00000   0.025
C12     1   0.02070   0.32040   0.36224  11.00000   0.025
C13     1  -0.05250   0.23450   0.34350  11.00000   0.025
C14     1  -0.04360   0.18880   0.26570  11.00000   0.025
C15     1   0.03780   0.22530   0.20360  11.00000   0.025
C16     1   0.11130   0.31050   0.22057  11.00000   0.025
C17     1   0.19620   0.36090   0.15436  11.00000   0.025
C18     1   0.31780   0.38720   0.19906  11.00000   0.025
C19     1   0.41480   0.43140   0.13903  11.00000   0.025
C20     1   0.52410   0.47660   0.18811  11.00000   0.025
C21     1   0.62830   0.50410   0.12622  11.00000   0.025
C22     1   0.65260   0.62040   0.11090  11.00000   0.025
C23     1   0.55790   0.69230   0.12673  11.00000   0.025
C24     1   0.45880   0.66630   0.18199  11.00000   0.025
C25     1   0.48280   0.57050   0.24083  11.00000   0.025
C26     1   0.36900   0.54390   0.29061  11.00000   0.025
C27     1   0.29400   0.46240   0.27178  11.00000   0.025
C28     1   0.18670   0.44460   0.32353  11.00000   0.025
C29     1   0.10600   0.35780   0.30253  11.00000   0.025
C30     1   0.56220   0.79110   0.08265  11.00000   0.025
C31     1   0.21610   0.29190   0.07690  11.00000   0.025
C32     1   0.73180   0.33240   0.13840  11.00000   0.025
C33     1   0.80960   0.48110   0.22280  11.00000   0.025
HKLF    4
END

Importing the structure into Crystals

As described in Setting up Crystals to perform DLS (Distance Least Squares) on an Organic Structure (Cimetidine) to generate an idealised structure from powder diffraction data solved co-ordinates, use X-ray Data, Shelx (INS, RES) menu to import the structure file, then X-ray Data, Reflection Data to import a dummy HKL file in Shelx format.

In the latest GUI version of Crystals, you can use the Refinement, F or F2 and advanced options GUI to instruct Crystals not to use reflections. Just declick the Use Reflections checkbox but make sure the Use Restraints checkbox is "on".

Turning of refinement of HKLs in Crystals via the GUI

You can also use the following command line method to tell Crystals that you "do not want" to refine on any HKLs (answer the questions this script queries you on). 

#script inlist23

When prompted with:

Do you wish to use LIST 6 reflections? (keyword [YES])

Type NO and continue on to finish the script.

Using the mouse, delete the Chlorine atom as this is independent of the molecule we wish to optimise (click right mouse button when the mouse cursor is over the Chlorine atom).

(NOTE: If your are not intending to do any DLS, there is no need to import the dummy HKL file)

This should lead to the following type of screen in Crystals:

Screen dump of Crystals

Generating the default list of bond-length/bond-angle restraints

(You may have to play a bit here to make sure the limits encompass the range of bond lengths joining the atoms. The following are safe defaults for tetracycline but may not be good defaults for other molecules).

In the bottom left hand "script input" command line type (or cut/paste): 


#rele punch dls.txt
#DISTANCE
OUTPUT PUNCH=RESTRAIN
SELECT TYPE=INTRA RANGE=LIMITS  (supresses bonds and angles to atoms in nearby symmetry
                                 generated molecules)
LIM 0 1.9 0 1.9                     (set the limits in Angstrom on how far the bonds and angles should search.
                                    LIMITS DMINIMUM= DMAXIMUM= AMINIMUM= AMAXIMUM= )  
end

#rele punch dummy.txt           (Releases and unlocks the previous dls.txt file from Crystals)

If you only want to generate bond lengths (no bond angles) 


#rele punch dls.txt
#DISTANCE
OUTPUT PUNCH=RESTRAIN
SELECT TYPE=INTRA RANGE=LIMITS  (supresses bonds and angles to atoms in nearby symmetry
                                 generated molecules)
LIM 0 1.9 0 0                     (set the limits in Angstrom on how far the bonds and angles should search.
                                    LIMITS DMINIMUM= DMAXIMUM= AMINIMUM= AMAXIMUM= )  
end

#rele punch dummy.txt           (Releases and unlocks the previous dls.txt file from Crystals)

Possibly stating the obvious: if you want to separate the bond lengths and bond angles lists into two separate files: 


#rele punch lengths.txt
#DISTANCE
OUTPUT PUNCH=RESTRAIN
SELECT TYPE=INTRA RANGE=LIMITS  
LIM 0 1.9 0 0
end

#rele punch dummy.txt           (Releases and unlocks the previous dls.txt file from Crystals)



#rele punch angles.txt
#DISTANCE
OUTPUT PUNCH=RESTRAIN
SELECT TYPE=INTRA RANGE=LIMITS  
LIM 0 0 0 1.9
end

#rele punch dummy.txt           (Releases and unlocks the previous dls.txt file from Crystals)

The resulting default lengths and angles list

#
# Punched on 10/25/00 at 20:24:12
#
#LIST     16                                                                    
DIST   1.352,.01= O(2) to C(12)
DIST   1.432,.01= O(3) to C(17)
DIST   1.259,.01= O(4) to C(22)
DIST   1.234,.01= O(5) to C(24)
DIST   1.422,.01= O(6) to C(25)
DIST   1.330,.01= O(7) to C(26)
DIST   1.276,.01= O(8) to C(28)
DIST   1.313,.01= O(9) to C(30)
DIST   1.494,.01= N(10) to C(21)
DIST   1.490,.01= N(10) to C(32)
DIST   1.491,.01= N(10) to C(33)
ANGL 111,1= C(21) to N(10) to C(32)
ANGL 115,1= C(21) to N(10) to C(33)
ANGL 111,1= C(32) to N(10) to C(33)
DIST   1.301,.01= N(11) to C(30)
DIST   1.386,.01= C(12) to C(13)
DIST   1.405,.01= C(12) to C(29)
ANGL 118,1= O(2) to C(12) to C(13)
ANGL 121,1= O(2) to C(12) to C(29)
ANGL 121,1= C(13) to C(12) to C(29)
DIST   1.357,.01= C(13) to C(14)
ANGL 119,1= C(12) to C(13) to C(14)
DIST   1.399,.01= C(14) to C(15)
ANGL 122,1= C(13) to C(14) to C(15)
DIST   1.375,.01= C(15) to C(16)
ANGL 120,1= C(14) to C(15) to C(16)
DIST   1.534,.01= C(16) to C(17)
DIST   1.422,.01= C(16) to C(29)
ANGL 123,1= C(15) to C(16) to C(17)
ANGL 119,1= C(15) to C(16) to C(29)
ANGL 117,1= C(17) to C(16) to C(29)
DIST   1.540,.01= C(17) to C(18)
DIST   1.516,.01= C(17) to C(31)
ANGL 108,1= O(3) to C(17) to C(16)
ANGL 105,1= O(3) to C(17) to C(18)
ANGL 108,1= C(16) to C(17) to C(18)
ANGL 110,1= O(3) to C(17) to C(31)
ANGL 113,1= C(16) to C(17) to C(31)
ANGL 112,1= C(18) to C(17) to C(31)
DIST   1.526,.01= C(18) to C(19)
DIST   1.512,.01= C(18) to C(27)
ANGL 113,1= C(17) to C(18) to C(19)
ANGL 109,1= C(17) to C(18) to C(27)
ANGL 111,1= C(19) to C(18) to C(27)
DIST   1.534,.01= C(19) to C(20)
ANGL 112,1= C(18) to C(19) to C(20)
DIST   1.538,.01= C(20) to C(21)
DIST   1.522,.01= C(20) to C(25)
ANGL 110,1= C(19) to C(20) to C(21)
ANGL 110,1= C(19) to C(20) to C(25)
ANGL 113,1= C(21) to C(20) to C(25)
DIST   1.522,.01= C(21) to C(22)
ANGL 115,1= N(10) to C(21) to C(20)
ANGL 110,1= N(10) to C(21) to C(22)
ANGL 117,1= C(20) to C(21) to C(22)
DIST   1.403,.01= C(22) to C(23)
ANGL 117,1= O(4) to C(22) to C(21)
ANGL 124,1= O(4) to C(22) to C(23)
ANGL 118,1= C(21) to C(22) to C(23)
DIST   1.427,.01= C(23) to C(24)
DIST   1.435,.01= C(23) to C(30)
ANGL 121,1= C(22) to C(23) to C(24)
ANGL 117,1= C(22) to C(23) to C(30)
ANGL 121,1= C(24) to C(23) to C(30)
DIST   1.552,.01= C(24) to C(25)
ANGL 125,1= O(5) to C(24) to C(23)
ANGL 120,1= O(5) to C(24) to C(25)
ANGL 115,1= C(23) to C(24) to C(25)
DIST   1.508,.01= C(25) to C(26)
ANGL 109,1= O(6) to C(25) to C(20)
ANGL 105,1= O(6) to C(25) to C(24)
ANGL 110,1= C(20) to C(25) to C(24)
ANGL 111,1= O(6) to C(25) to C(26)
ANGL 111,1= C(20) to C(25) to C(26)
ANGL 110,1= C(24) to C(25) to C(26)
DIST   1.354,.01= C(26) to C(27)
ANGL 113,1= O(7) to C(26) to C(25)
ANGL 123,1= O(7) to C(26) to C(27)
ANGL 124,1= C(25) to C(26) to C(27)
DIST   1.445,.01= C(27) to C(28)
ANGL 123,1= C(18) to C(27) to C(26)
ANGL 118,1= C(18) to C(27) to C(28)
ANGL 119,1= C(26) to C(27) to C(28)
DIST   1.451,.01= C(28) to C(29)
ANGL 121,1= O(8) to C(28) to C(27)
ANGL 120,1= O(8) to C(28) to C(29)
ANGL 119,1= C(27) to C(28) to C(29)
ANGL 119,1= C(12) to C(29) to C(16)
ANGL 121,1= C(12) to C(29) to C(28)
ANGL 120,1= C(16) to C(29) to C(28)
ANGL 118,1= O(9) to C(30) to N(11)
ANGL 120,1= O(9) to C(30) to C(23)
ANGL 122,1= N(11) to C(30) to C(23)
# Remove space after hash to activate next line
# USE LAST

Modifying the restraints file ready for possible DLS

Edit the dls.txt (or whatever you have called this file) and change the distances/angle restraints and ESD you consider appropriate to what you wish to use.

Also fix the origin and use limits to stop the DLS refinement sending the co-ordinates to outer-space. Thus edit the dls.txt file in your favourite text editor and add the following to the top before the first restraint: 

orig x
orig y
orig z
limit 0.01 x
limit 0.01 y
limit 0.01 z

Modifying the restraints file ready for possible DLS

Edit the dls.txt (or whatever you have called this file) and change the distances/angle restraints and ESD you consider appropriate to what you wish to use.

Also fix the origin and use limits to stop the DLS refinement sending the co-ordinates to outer-space. Thus edit the dls.txt file in your favourite text editor and add the following after the "#list 16" command but before the first restraint: 

orig x
orig y
orig z
limit 0.01 x
limit 0.01 y
limit 0.01 z

Importing the "restraints list" back into Crystals for graphical modification

If you are happy with the restraints file at this point, you can transform this into a Rietveld program format - or you can import this into Crystals so you can graphically add/delete restraints - as well as perform DLS if you wish.

In this case, the text file with the restraints list was called dls.txt. Thus in the Crystals command line type: 

#use  dls.txt

Screen dump of Crystals having imported the restraints list

Importing the "restraints list" back into Crystals for graphical modification

If you are happy with the restraints file at this point, you can transform this into a Rietveld program format - or you can import this into Crystals so you can graphically add/delete restraints - as well as perform DLS if you wish.

In this case, the text file with the restraints list was called dls.txt. Thus in the Crystals command line type: 

#use  dls.txt
end

Screen dump of Crystals having imported the restraints list

Adding Extra Restraints via the Crystals point and click graphical interface

To easily add and delete extra restraints, you can use the Crystals point and click graphical interface.

For instance click on the Benzene atoms as well as the Oxygen. Click right mouse button and add a Planar restraint (with an esd of 0.01).

This would have been the equivalent of typing the following in the Crystals script command line: 

PLANAR 0.010000  O(2) C(12) C(13) C(14) C(15) C(16) C(29)

Defining a Planar Restraint

Performing DLS or outputting the Restraints

You can now perform DLS (Distance Least Squares) by selecting the Refinement, Least Squares option in the Crystals menu. You may need to do this if your starting model was not well determined and modified the starting bond lengths and angles to idealised bond lengths. In this case, the starting molecule was obtained from single crystal data so should have accurate bond lengths and angles. You can add calculated hydrogens using Crystals (Structure, Add Hydrogens). If the bond lengths are set properly, the correct numbers of hydrogens should be added to the different Carbons.

DLS will change the structural co-ordinates such that you will need to reinput them into the Rietveld software (Structure, Edit Co-ordinates will allow you to copy the list of co-ordinates). Converting this atom list into a set of GSAS Macro commands could be a major time saver (don't forget to add in the Chlorine that was deleted as the first atom as per the inputted structure file).

And/or otherwise you can output the Restraints list (there are a number of ways of doing this - one is using Refinement, Edit Restraints - that can then be transformed into your favourite Rietveld format. The list we have so far: 

#
# Punched on 10/25/00 at 21:11:08
#
#LIST     16 
orig x
orig y
orig z
limit 0.01 x
limit 0.01 y
limit 0.01 z                                                                   
DIST   1.352,.01= O(2) TO C(12) 
DIST   1.432,.01= O(3) TO C(17) 
DIST   1.259,.01= O(4) TO C(22) 
DIST   1.234,.01= O(5) TO C(24) 
DIST   1.422,.01= O(6) TO C(25) 
DIST   1.330,.01= O(7) TO C(26) 
DIST   1.276,.01= O(8) TO C(28) 
DIST   1.313,.01= O(9) TO C(30) 
DIST   1.494,.01= N(10) TO C(21) 
DIST   1.490,.01= N(10) TO C(32) 
DIST   1.491,.01= N(10) TO C(33) 
ANGL 111,1= C(21) TO N(10) TO C(32) 
ANGL 115,1= C(21) TO N(10) TO C(33) 
ANGL 111,1= C(32) TO N(10) TO C(33) 
DIST   1.301,.01= N(11) TO C(30) 
DIST   1.386,.01= C(12) TO C(13) 
DIST   1.405,.01= C(12) TO C(29) 
ANGL 118,1= O(2) TO C(12) TO C(13) 
ANGL 121,1= O(2) TO C(12) TO C(29) 
ANGL 121,1= C(13) TO C(12) TO C(29) 
DIST   1.357,.01= C(13) TO C(14) 
ANGL 119,1= C(12) TO C(13) TO C(14) 
DIST   1.399,.01= C(14) TO C(15) 
ANGL 122,1= C(13) TO C(14) TO C(15) 
DIST   1.375,.01= C(15) TO C(16) 
ANGL 120,1= C(14) TO C(15) TO C(16) 
DIST   1.534,.01= C(16) TO C(17) 
DIST   1.422,.01= C(16) TO C(29) 
ANGL 123,1= C(15) TO C(16) TO C(17) 
ANGL 119,1= C(15) TO C(16) TO C(29) 
ANGL 117,1= C(17) TO C(16) TO C(29) 
DIST   1.540,.01= C(17) TO C(18) 
DIST   1.516,.01= C(17) TO C(31) 
ANGL 108,1= O(3) TO C(17) TO C(16) 
ANGL 105,1= O(3) TO C(17) TO C(18) 
ANGL 108,1= C(16) TO C(17) TO C(18) 
ANGL 110,1= O(3) TO C(17) TO C(31) 
ANGL 113,1= C(16) TO C(17) TO C(31) 
ANGL 112,1= C(18) TO C(17) TO C(31) 
DIST   1.526,.01= C(18) TO C(19) 
DIST   1.512,.01= C(18) TO C(27) 
ANGL 113,1= C(17) TO C(18) TO C(19) 
ANGL 109,1= C(17) TO C(18) TO C(27) 
ANGL 111,1= C(19) TO C(18) TO C(27) 
DIST   1.534,.01= C(19) TO C(20) 
ANGL 112,1= C(18) TO C(19) TO C(20) 
DIST   1.538,.01= C(20) TO C(21) 
DIST   1.522,.01= C(20) TO C(25) 
ANGL 110,1= C(19) TO C(20) TO C(21) 
ANGL 110,1= C(19) TO C(20) TO C(25) 
ANGL 113,1= C(21) TO C(20) TO C(25) 
DIST   1.522,.01= C(21) TO C(22) 
ANGL 115,1= N(10) TO C(21) TO C(20) 
ANGL 110,1= N(10) TO C(21) TO C(22) 
ANGL 117,1= C(20) TO C(21) TO C(22) 
DIST   1.403,.01= C(22) TO C(23) 
ANGL 117,1= O(4) TO C(22) TO C(21) 
ANGL 124,1= O(4) TO C(22) TO C(23) 
ANGL 118,1= C(21) TO C(22) TO C(23) 
DIST   1.427,.01= C(23) TO C(24) 
DIST   1.435,.01= C(23) TO C(30) 
ANGL 121,1= C(22) TO C(23) TO C(24) 
ANGL 117,1= C(22) TO C(23) TO C(30) 
ANGL 121,1= C(24) TO C(23) TO C(30) 
DIST   1.552,.01= C(24) TO C(25) 
ANGL 125,1= O(5) TO C(24) TO C(23) 
ANGL 120,1= O(5) TO C(24) TO C(25) 
ANGL 115,1= C(23) TO C(24) TO C(25) 
DIST   1.508,.01= C(25) TO C(26) 
ANGL 109,1= O(6) TO C(25) TO C(20) 
ANGL 105,1= O(6) TO C(25) TO C(24) 
ANGL 110,1= C(20) TO C(25) TO C(24) 
ANGL 111,1= O(6) TO C(25) TO C(26) 
ANGL 111,1= C(20) TO C(25) TO C(26) 
ANGL 110,1= C(24) TO C(25) TO C(26) 
DIST   1.354,.01= C(26) TO C(27) 
ANGL 113,1= O(7) TO C(26) TO C(25) 
ANGL 123,1= O(7) TO C(26) TO C(27) 
ANGL 124,1= C(25) TO C(26) TO C(27) 
DIST   1.445,.01= C(27) TO C(28) 
ANGL 123,1= C(18) TO C(27) TO C(26) 
ANGL 118,1= C(18) TO C(27) TO C(28) 
ANGL 119,1= C(26) TO C(27) TO C(28) 
DIST   1.451,.01= C(28) TO C(29) 
ANGL 121,1= O(8) TO C(28) TO C(27) 
ANGL 120,1= O(8) TO C(28) TO C(29) 
ANGL 119,1= C(27) TO C(28) TO C(29) 
ANGL 119,1= C(12) TO C(29) TO C(16) 
ANGL 121,1= C(12) TO C(29) TO C(28) 
ANGL 120,1= C(16) TO C(29) TO C(28) 
ANGL 118,1= O(9) TO C(30) TO N(11) 
ANGL 120,1= O(9) TO C(30) TO C(23) 
ANGL 122,1= N(11) TO C(30) TO C(23) 
PLANAR 0.010000  O(2) C(12) C(13) C(14) C(15) C(16) C(29) 
END                                                                             
# Remove space after hash to activate next line
# USE LAST

Manually Re-Sorted Restrains List Ready for Rietvelding

(Also, you may like to make the ESD's on the bond angles quite large as it is more difficult to determine these from theory) 

                                                             
DIST   1.352,.01= O(2) TO C(12) 
DIST   1.432,.01= O(3) TO C(17) 
DIST   1.259,.01= O(4) TO C(22) 
DIST   1.234,.01= O(5) TO C(24) 
DIST   1.422,.01= O(6) TO C(25) 
DIST   1.330,.01= O(7) TO C(26) 
DIST   1.276,.01= O(8) TO C(28) 
DIST   1.313,.01= O(9) TO C(30) 
DIST   1.494,.01= N(10) TO C(21) 
DIST   1.490,.01= N(10) TO C(32) 
DIST   1.491,.01= N(10) TO C(33) 
DIST   1.301,.01= N(11) TO C(30) 
DIST   1.386,.01= C(12) TO C(13) 
DIST   1.405,.01= C(12) TO C(29) 
DIST   1.357,.01= C(13) TO C(14) 
DIST   1.399,.01= C(14) TO C(15) 
DIST   1.375,.01= C(15) TO C(16) 
DIST   1.534,.01= C(16) TO C(17) 
DIST   1.422,.01= C(16) TO C(29) 
DIST   1.540,.01= C(17) TO C(18) 
DIST   1.516,.01= C(17) TO C(31) 
DIST   1.526,.01= C(18) TO C(19) 
DIST   1.512,.01= C(18) TO C(27) 
DIST   1.534,.01= C(19) TO C(20) 
DIST   1.538,.01= C(20) TO C(21) 
DIST   1.522,.01= C(20) TO C(25) 
DIST   1.522,.01= C(21) TO C(22) 
DIST   1.403,.01= C(22) TO C(23) 
DIST   1.427,.01= C(23) TO C(24) 
DIST   1.435,.01= C(23) TO C(30) 
DIST   1.552,.01= C(24) TO C(25) 
DIST   1.508,.01= C(25) TO C(26) 
DIST   1.354,.01= C(26) TO C(27) 
DIST   1.445,.01= C(27) TO C(28) 
DIST   1.451,.01= C(28) TO C(29) 
ANGL 111,1= C(21) TO N(10) TO C(32) 
ANGL 115,1= C(21) TO N(10) TO C(33) 
ANGL 111,1= C(32) TO N(10) TO C(33) 
ANGL 118,1= O(2) TO C(12) TO C(13) 
ANGL 121,1= O(2) TO C(12) TO C(29) 
ANGL 121,1= C(13) TO C(12) TO C(29) 
ANGL 119,1= C(12) TO C(13) TO C(14) 
ANGL 122,1= C(13) TO C(14) TO C(15) 
ANGL 120,1= C(14) TO C(15) TO C(16) 
ANGL 123,1= C(15) TO C(16) TO C(17) 
ANGL 119,1= C(15) TO C(16) TO C(29) 
ANGL 117,1= C(17) TO C(16) TO C(29) 
ANGL 108,1= O(3) TO C(17) TO C(16) 
ANGL 105,1= O(3) TO C(17) TO C(18) 
ANGL 108,1= C(16) TO C(17) TO C(18) 
ANGL 110,1= O(3) TO C(17) TO C(31) 
ANGL 113,1= C(16) TO C(17) TO C(31) 
ANGL 112,1= C(18) TO C(17) TO C(31) 
ANGL 113,1= C(17) TO C(18) TO C(19) 
ANGL 109,1= C(17) TO C(18) TO C(27) 
ANGL 111,1= C(19) TO C(18) TO C(27) 
ANGL 112,1= C(18) TO C(19) TO C(20) 
ANGL 110,1= C(19) TO C(20) TO C(21) 
ANGL 110,1= C(19) TO C(20) TO C(25) 
ANGL 113,1= C(21) TO C(20) TO C(25) 
ANGL 115,1= N(10) TO C(21) TO C(20) 
ANGL 110,1= N(10) TO C(21) TO C(22) 
ANGL 117,1= C(20) TO C(21) TO C(22) 
ANGL 117,1= O(4) TO C(22) TO C(21) 
ANGL 124,1= O(4) TO C(22) TO C(23) 
ANGL 118,1= C(21) TO C(22) TO C(23) 
ANGL 121,1= C(22) TO C(23) TO C(24) 
ANGL 117,1= C(22) TO C(23) TO C(30) 
ANGL 121,1= C(24) TO C(23) TO C(30) 
ANGL 125,1= O(5) TO C(24) TO C(23) 
ANGL 120,1= O(5) TO C(24) TO C(25) 
ANGL 115,1= C(23) TO C(24) TO C(25) 
ANGL 109,1= O(6) TO C(25) TO C(20) 
ANGL 105,1= O(6) TO C(25) TO C(24) 
ANGL 110,1= C(20) TO C(25) TO C(24) 
ANGL 111,1= O(6) TO C(25) TO C(26) 
ANGL 111,1= C(20) TO C(25) TO C(26) 
ANGL 110,1= C(24) TO C(25) TO C(26) 
ANGL 113,1= O(7) TO C(26) TO C(25) 
ANGL 123,1= O(7) TO C(26) TO C(27) 
ANGL 124,1= C(25) TO C(26) TO C(27) 
ANGL 123,1= C(18) TO C(27) TO C(26) 
ANGL 118,1= C(18) TO C(27) TO C(28) 
ANGL 119,1= C(26) TO C(27) TO C(28) 
ANGL 121,1= O(8) TO C(28) TO C(27) 
ANGL 120,1= O(8) TO C(28) TO C(29) 
ANGL 119,1= C(27) TO C(28) TO C(29) 
ANGL 119,1= C(12) TO C(29) TO C(16) 
ANGL 121,1= C(12) TO C(29) TO C(28) 
ANGL 120,1= C(16) TO C(29) TO C(28) 
ANGL 118,1= O(9) TO C(30) TO N(11) 
ANGL 120,1= O(9) TO C(30) TO C(23) 
ANGL 122,1= N(11) TO C(30) TO C(23) 
PLANAR 0.010000  O(2) C(12) C(13) C(14) C(15) C(16) C(29)

To go back one refinement step you can refer to Multiple UNDO in Crystals - restoring old structure models in Crystals or use: 

#disk
reset 5 0 -1
end

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