
  ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
  +  SHELXE  -  PHASING AND DENSITY MODIFICATION  -  Version 2006/3  +
  +  Copyright (C)  George M. Sheldrick 2001-6                       +
  +  Started at 16:55:58 on 19 May 2008                              +
  ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

 SHELXE has following modes of action (xx and yy are filename stems):

 shelxe xx [reads xx.hkl and xx.ins, phases from atoms]
 shelxe xx yy [normal mode: reads xx.hkl, yy.hkl, yy.res]
 shelxe xx.phi [reads xx.phi, xx.hkl, xx.ins]
 shelxe xx.fcf [reads only xx.fcf]
 shelxe xx.phi yy [reads xx.phi, xx.hkl, xx.ins, yy.hkl]
 shelxe xx.fcf yy [reads xx.fcf, yy.hkl, yy.res]

 xx.hkl contains native data, yy.hkl contains FA and alpha and should have
 been created using SHELXC or XPREP. xx.phi has .phs format but only the
 starting phases are read from it; if a .phi file is read, the cell and
 symmetry are read from xx.ins and the native F-values are read from xx.hkl.
 xx.fcf (from a SHELXL structure refinement) provides cell, symmetry and
 starting phases. The output phases are written to xx.phs, the log file is
 written to xx.lst and, if -b is set, improved substructure phases are
 output to xx.pha and revised heavy atoms to xx.hat.

 The first two modes provide density modification starting from atoms or
 phases, the third and fourth modes are for phase extension, the fifth is
 an inverse cross-Fourier for finding heavy atoms for a second derivative
 with the same origin as the first, and the last mode is useful to confirm
 the heavy atom substructure from the final refined phases. For these last
 two modes, the phases for the inverse Fourier are phi(nat)-alpha, where 
 phi(nat) may be refined (-m etc.) and alpha is taken from yy.hkl.

 SHELXE normally requires a few command line switches, e.g.

 shelxe xx yy -m20 -s0.45 -h8 -b

 would do 20 cycles density modification with a solvent content of 0.45,
 phasing from the first 8 heavy atoms in the yy.res file assuming that they
 are also present in the native structure (-h8) and then use the modified
 density to generate improved heavy atoms (-b). The switch -i may be added
 to invert the substructure (and if necessary the space group), this writes
 xx_i.phs instead of xx.phs etc., and so may be run in parallel. The new
 switch -e may be used to extrapolate the data to the specified resolution
 (the 'free lunch algorithm'); -e1.0 can produce spectacular results, but
 since a large number of cycles is required (-m400) and the 'contrast' and
 'connectivity' become unreliable, it is best to establish the substructure
 enantiomorph without -e first. The current values of all parameters are
 output at the start of the shelxe output, the default values will rarely
 need changing.

 Please cite: G.M. Sheldrick (2002), "Macromolecular phasing with SHELXE",
 Z. Kristallogr. 217, 644-650 whenever SHELXE proves useful.

 ==============================================================================

 Cell, symmetry and heavy atoms from:  vta1_br_sync_fa.res
 DelF from:  vta1_br_sync_fa.hkl
 Native data from:  vta1_br_sync.hkl
 Listing file:  vta1_br_sync.lst
 Phase output file: vta1_br_sync.phs
 Revised heavy atom sites: vta1_br_sync.hat
 Revised heavy atom phases: vta1_br_sync.pha

 Summary of parameters to be employed:

 -f NOT SET: read intensity not F from native .hkl file
 -i NOT SET: no structure inversion
 -n NOT SET: resolve 2-fold ambiguity if SAD or SIR
 -h heavy atoms present in native - use all
 -z NOT SET: sharpen density maps

 -d 0.000  high resolution limit to be applied to input data
 -e 1.000  high resolution limit for data extrapolation
 -m    20  cycles of density modification
 -j     5  output pseudo-free CC before every Nth cycle
 -s 0.500  solvent fraction
 -c 0.400  fraction of pixels in crossover region
 -g 1.100  solvent gamma flipping factor
 -v 1.500  low density reduction factor
 -w 0.200  weight for retained experimental phases
 -r  3.00  map resolution (multiplies maximum indices)
 -b   5.0  extra B for revised heavy atom sites
 -q   4.5  minimum height/sigma for revised heavy atom sites
 -l     2  space for  2000000 reflections

    13 heavy atoms read from .res file

     7601 reflections read from file vta1_br_sync_fa.hkl

    29156 reflections read from file vta1_br_sync.hkl

 Maximum resolution of native data =  1.250 Angstroms
    11 reflections with d > 1.450 and  27065 in range  1.450 > d > 1.000 added

 Fourier grid =   256 x  256 x   15     0.000 <= z <= 0.125

 92 point spherical net set up with radius 2.42A
  12 extra Fourier layers will be generated

 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 18.94%

 <wt> = 0.055 for initial phases
 <wt> = 0.076 after resolving 2-fold ambiguity
 <wt> = 0.232 after including heavy atoms
 <wt> = 0.241, Contrast = 0.277, Connect. = 0.830 for dens.mod. cycle 1
 <wt> = 0.265, Contrast = 0.377, Connect. = 0.848 for dens.mod. cycle 2
 <wt> = 0.300, Contrast = 0.474, Connect. = 0.825 for dens.mod. cycle 3
 <wt> = 0.300, Contrast = 0.601, Connect. = 0.862 for dens.mod. cycle 4
 Pseudo-free CC = 53.29 %
 <wt> = 0.300, Contrast = 0.650, Connect. = 0.867 for dens.mod. cycle 5
 <wt> = 0.300, Contrast = 0.679, Connect. = 0.876 for dens.mod. cycle 6
 <wt> = 0.300, Contrast = 0.692, Connect. = 0.878 for dens.mod. cycle 7
 <wt> = 0.300, Contrast = 0.693, Connect. = 0.882 for dens.mod. cycle 8
 <wt> = 0.300, Contrast = 0.691, Connect. = 0.885 for dens.mod. cycle 9
 Pseudo-free CC = 69.05 %
 <wt> = 0.300, Contrast = 0.682, Connect. = 0.887 for dens.mod. cycle 10
 <wt> = 0.300, Contrast = 0.674, Connect. = 0.889 for dens.mod. cycle 11
 <wt> = 0.300, Contrast = 0.661, Connect. = 0.891 for dens.mod. cycle 12
 <wt> = 0.300, Contrast = 0.651, Connect. = 0.892 for dens.mod. cycle 13
 <wt> = 0.300, Contrast = 0.638, Connect. = 0.894 for dens.mod. cycle 14
 Pseudo-free CC = 78.48 %
 <wt> = 0.300, Contrast = 0.628, Connect. = 0.894 for dens.mod. cycle 15
 <wt> = 0.300, Contrast = 0.616, Connect. = 0.894 for dens.mod. cycle 16
 <wt> = 0.300, Contrast = 0.607, Connect. = 0.893 for dens.mod. cycle 17
 <wt> = 0.300, Contrast = 0.598, Connect. = 0.893 for dens.mod. cycle 18
 <wt> = 0.300, Contrast = 0.591, Connect. = 0.892 for dens.mod. cycle 19
 <wt> = 0.300, Contrast = 0.584, Connect. = 0.892 for dens.mod. cycle 20

 Mean weight and estimated mapCC as a function of resolution
 d    inf - 2.76 - 2.17 - 1.89 - 1.71 - 1.59 - 1.49 - 1.42 - 1.35 - 1.30 - 1.26
 <wt>    0.707  0.808  0.835  0.848  0.852  0.847  0.841  0.791  0.746  0.725
 <mapCC> 0.850  0.921  0.957  0.976  0.977  0.976  0.976  0.974  0.974  0.967
 N        2941   2973   2930   3018   2809   3101   2700   3304   2790   2590

 Pseudo-free CC = 83.13 %

 Density (in map sigma units) at input heavy atom sites

  Site     x        y        z     occ*Z    density
    1   0.1736   0.5502   0.0106  16.0000    16.49
    2   0.2228   0.6236   0.1497  15.8880    16.20
    3   0.0737   0.6591   0.4167  14.5920    15.00
    4   0.1820   0.4074   0.0142  13.7760    17.09
    5  -0.0677   0.6781   0.4472  13.4560    13.10
    6   0.0861   0.6493   0.3842  13.4192    15.22
    7   0.1641   0.5599   0.0499  12.9808    14.15
    8   0.1509   0.7141   0.2996  12.8080    11.69
    9   0.1484   0.6912   0.2699  11.6720    10.77
   10   0.1638   0.4016  -0.0204  11.5328    14.42
   11  -0.0655   0.6990   0.4148  11.3136    12.68
   12   0.3177   0.6177  -0.0279   5.7168     2.89
   13   0.2383   0.6468  -0.0275   3.2928     1.19

 Site    x       y       z  h(sig) near old  near new
   1  0.1835  0.4084  0.0130  17.7  4/0.13  8/2.02 3/9.35 9/9.76 7/10.06
   2  0.2249  0.6240  0.1452  16.9  2/0.25  12/1.82 7/7.48 3/8.68 10/9.18
   3  0.1728  0.5502  0.0109  16.5  1/0.06  7/1.77 12/8.20 2/8.68 1/9.35
   4  0.0821  0.6524  0.3896  15.6  6/0.42  5/1.54 13/2.08 11/7.37 10/7.50
   5  0.0748  0.6593  0.4189  15.2  3/0.13  4/1.54 13/1.90 11/8.26 10/8.66
   6 -0.0609  0.6961  0.4202  15.0  11/0.44  9/2.10 5/9.24 13/9.61 8/9.83
   7  0.1655  0.5586  0.0451  14.7  7/0.26  3/1.77 12/7.29 2/7.48 1/10.06
   8  0.1639  0.4031 -0.0191  14.6  10/0.12  1/2.02 9/8.22 3/9.79 6/9.83
   9 -0.0695  0.6763  0.4530  13.9  5/0.32  6/2.10 8/8.22 5/9.68 1/9.76
  10  0.1520  0.6949  0.2786  13.9  9/0.53  11/2.03 13/7.30 4/7.50 5/8.66
  11  0.1461  0.7200  0.3022  13.3  8/0.52  10/2.03 13/6.62 4/7.37 5/8.26
  12  0.2446  0.6122  0.1237  11.8  2/2.03  2/1.82 7/7.29 3/8.20 10/10.95
  13  0.0840  0.6830  0.4000  -4.9  3/1.89  5/1.90 4/2.08 11/6.62 10/7.30

  ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
  +  SHELXE finished at 16:56:25      Total time:        26.38 secs  +
  ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
