1st file

IF F01 =F0 THEN PRINT CHR (7) "Would Overwrite 1st file " .GOTO 1190... 

If the command BOND appears in the header of the. ins file, SHELXL writes into the. 1st file a table of all bond lengths and angles in the connectivity table. BOND H expands this table to include all distances and angles involving hydrogen atoms as well. 

If the crystallographer or chemist wishes certain torsion angles to appear in a separate table in the. 1st file, each of these torsion angles can be specified in a CONF command ... 

SHELXL calculates a least-squares plane through the first na atoms of the named atoms. The equation of this plane, together with the deviations of all named atoms from the plane and the angle to the previous least-squares plane (if present) are written into the. 1st file. If na is not specified, the program fits the plane through all named atoms. 

This calculates the best plane through the first five atoms (the Cp ligand) and the distance of all atoms mentioned (including the Ti) from that plane. All distances, together with standard uncertainties, are written into the. 1st file. 

If the command htab (without extensions) appears in the header of the. ins file, SHELXL performs a search over all polar hydrogen atoms present in the structure and examines hydrogen bonding. The bonds listed in the. 1st file are those for which the distance between acceptor and hydrogen atom are smaller than the radius of the acceptor atom plus 2.0 A, and the angle between the donor atom, the hydrogen and the acceptor atom is larger than 110°. 

The command MORE m sets the amount of output into the. 1st file. MORE 0 gives the least and MORE 3 the most verbose output. The default value for m is 1. 

If the command ACTA appears in the header of an. ins file, SHELXL generates such a. cif file. ACTA automatically sets the BOND, fmap 2, plan and LIST 4 instructions and ACTA cannot be combined with other fmap or LIST commands. Torsion angles defined by CONF and hydrogen bonds defined by HTAB are also written into the. cif file, while quantities defined by RTAB and MPLA are only tabulated in the. 1st file. 

These lines have to be typed manually and generate informative output about the hydrogen bonds (htab) and the planarity of the four membered rings (MPLA) in the file in-03.1st. You can find this information towards the end of the. 1st file, directly after the table with bond lengths and angles. The EQIV command is explained in detail in Chapter 3, htab is described in Chapters 2 and 3, and MPLA is explained in Chapter 2. 

Note that the refined value of any free variable has a calculated standard uncertainty, which is listed in the. 1st file. The value of this standard uncertainty is supposed to be much smaller than the value for the free variable, or the disorder represented by the free variable would not be very meaningful. ... 

The next. 1st file will contain all the information you need to check whether the restraints are used properly. If MORE 3 is given in the. ins file fhe. 1st file contains a list of all distances treated as equivalent by SHELXL. After ten cycles of SHELXL, the files ga-03.res and ga-03.1sf contain the results of the disorder refinement (see Figure 5.6). 

These distances are sensible at this temperature (- 140°C). A list of X-H distances at the temperature defined by the TEMP instruction in the. ins file, can be found in the 1st file. See also Chapter 3. 

Sometimes SHH XS finds two groups of potential solutions, where one corresponds only to a pseudo-solution. If this pseudo-solution has the lower combined figure of merit of the two, the program will chose it over the correct solution. In such a case it is common practice to examine the SHELXS. 1st file, identify the odier possible solution and run the program a second time specifying die seminvariants in the TREF command. This book is about structure refinement, not die solution of die phase problem and for furdier details die reader is referred to the SHELX manual or the original publication (Sheldrick, 1990). 

Whenever extinction is refined, it is important to check in the. 1st file whether the extinction coefficient refines to sensible values with a reasonably small standard uncertainty. This is the case here, so we will keep EXTI in. Unfortunately, removing the E AD P constraint causes the carbon atom C(6) to be NPD again. This is not unusual for global pseudo-symmetry, as the abovementioned correlation among symmetry-related but not equivalent atoms can lead to problems with anisotropic refinement. Therefore, we decide to live with this constraint and finalize the refinement by adjusting the weighting scheme. The final model in P2 ln is in the file s-05a.res. 

For all of the most disagreeable reflections in the. 1st file, Fo is much greater thanFc. 

In acentric space groups and in the presence of heavy atoms such as osmium it should be possible to determine the absolute stmcture and the absolute structure parameter needs to be checked (.1st file). The Flack parameter x (Flack, 1983) is refined to 0.54(2). This could mean that the absolute structure is wrong and space group P3 is the correct one instead of P32 and/or that there is some additional racemic twinning. This can be tested by changing the TWIN and BASF command lines ... 

A closer look into the. 1st file can help all the most disagreeable reflections are observed much stronger than calculated (F F ) and for all of them I = 3n ... 

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