<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
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<a name="dmdm"><h1>dm 2.1</h1></a>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 5.99: dm                 version 5.99      :         ##
 ###############################################################
 User: sness  Run date:  8/10/2005 Run time: 03:25:16 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.

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</pre>

<a href="http://www.yorvic.york.ac.uk/~cowtan/dm/refs.html">dm reference:</a>
<blockquote>
K. Cowtan (1994),
  dm: An automated procedure for phase improvement by density modification.
  Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, p34-38.
</blockquote><p>


<a name="tocdm"><h2>Contents</h2></a>
<ul>
<li><a href="#commanddm">Command input</a>
<li><a href="#commentsdm">Comments</a>
<li><a href="#mtzindm">MTZ input</a>
<li><a href="#datachkdm">Data Checking</a>
<li><a href="#datascldm">Data Scaling</a>
<li><a href="#solmskdm">Solvent Mask</a>
<li><a href="#cyc0001dm">First Cycle</a>
<li><a href="#dataoutdm">Output</a>
</ul>

<a name="commanddm"><h2>Command Input</h2></a>
<pre>
 Data line--- <a href="/home/sness/crystal/ccp4-5.99.3/html/dm.html#mode">MODE    </a> SOLV
 Data line--- <a href="/home/sness/crystal/ccp4-5.99.3/html/dm.html#combine">COMBINE </a> PERT
 Data line--- <a href="/home/sness/crystal/ccp4-5.99.3/html/dm.html#scheme">SCHEME  </a> ALL
 Data line--- <a href="/home/sness/crystal/ccp4-5.99.3/html/dm.html#ncycle">NCYCLE  </a> AUTO
 Data line--- <a href="/home/sness/crystal/ccp4-5.99.3/html/dm.html#solc">SOLCONT </a> 0.622
 Data line--- <a href="/home/sness/crystal/ccp4-5.99.3/html/dm.html#ncsmask">NCSMASK </a> 
 Data line--- <a href="/home/sness/crystal/ccp4-5.99.3/html/dm.html#labin">LABIN   </a> FP=1_SCALEIT_X1_D2_F SIGFP=1_SCALEIT_X1_D2_SIGF PHIO=5_BP3_PHIB FOMO=5_BP3_FOM HLA=5_BP3_HLA HLB=5_BP3_HLB HLC=5_BP3_HLC
 Data line--- <a href="/home/sness/crystal/ccp4-5.99.3/html/dm.html#labout">LABOUT  </a> FDM=FDM PHIDM=PHIDM FOMDM=FOMDM HLADM=HLADM HLBDM=HLBDM HLCDM=HLCDM HLDDM=HLDDM
</pre>

<a name="commentsdm"><h2>Comments</h2></a>
Density modifications selected:<ul>
<li> Solvent flattening
<li> Histogram matching
</ul>

<h3>Number of cycles</h3>

You have chosen NCYCLE AUTO. This is a cautious mode which
runs few cycles of density modification and terminates at
the first indication of phase bias and FOM overestimation.
This is a good choice when you have weak data and no
averaging. However you must use SCHEME ALL (selected by
default).<p>


<h3>OK, continuing</h3></b>
<pre>

<a name="mtzindm"><h3>MTZ Input</h3></a>

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /home/sness/ccp4-sness/9_crank/workdb/crank.in.6_DM.mtz 

 * Title:

 Automatically extracted with extract-xml-columns.tcl test convert scal

 * Base dataset:

        0 HKL_base
          HKL_base
          HKL_base

 * Number of Datasets = 4

 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:

        1 dummy
          PEAK
          PEAK
             96.0000  120.0000  166.1300   90.0000   90.0000   90.0000
             1.10000
        2 dummy
          INFL
          INFL
             96.0000  120.0000  166.1300   90.0000   90.0000   90.0000
             1.20000
        3 AFRO
          AFRO
          AFRO
             96.0000  120.0000  166.1300   90.0000   90.0000   90.0000
             0.00000
        4 BP3-PHASED
          BP3-PHASED
          BP3-PHASED
             96.0000  120.0000  166.1300   90.0000   90.0000   90.0000
             0.00000

 * Number of Columns = 75

 * Number of Reflections = 19448

 * Missing value set to NaN in input mtz file

 * Column Labels :

 H K L INPUT_X1_D1_F INPUT_X1_D1_SIGF INPUT_X1_D1_F_PLUS INPUT_X1_D1_SIGF_PLUS INPUT_X1_D1_F_MINUS INPUT_X1_D1_SIGF_MINUS INPUT_X1_D1_DANO INPUT_X1_D1_SIGDANO INPUT_X1_D1_ISYM INPUT_X1_D1_I INPUT_X1_D1_SIGI INPUT_X1_D1_I_PLUS INPUT_X1_D1_SIGI_PLUS INPUT_X1_D1_I_MINUS INPUT_X1_D1_SIGI_MINUS 1_SCALEIT_X1_D1_F 1_SCALEIT_X1_D1_SIGF 1_SCALEIT_X1_D1_F_PLUS 1_SCALEIT_X1_D1_SIGF_PLUS 1_SCALEIT_X1_D1_F_MINUS 1_SCALEIT_X1_D1_SIGF_MINUS 1_SCALEIT_X1_D1_DANO 1_SCALEIT_X1_D1_SIGDANO 1_SCALEIT_X1_D1_ISYM 1_SCALEIT_X1_D1_I 1_SCALEIT_X1_D1_SIGI 1_SCALEIT_X1_D1_I_PLUS 1_SCALEIT_X1_D1_SIGI_PLUS 1_SCALEIT_X1_D1_I_MINUS 1_SCALEIT_X1_D1_SIGI_MINUS INPUT_X1_D2_F INPUT_X1_D2_SIGF INPUT_X1_D2_F_PLUS INPUT_X1_D2_SIGF_PLUS INPUT_X1_D2_F_MINUS INPUT_X1_D2_SIGF_MINUS INPUT_X1_D2_DANO INPUT_X1_D2_SIGDANO INPUT_X1_D2_ISYM INPUT_X1_D2_I INPUT_X1_D2_SIGI INPUT_X1_D2_I_PLUS INPUT_X1_D2_SIGI_PLUS INPUT_X1_D2_I_MINUS INPUT_X1_D2_SIGI_MINUS 1_SCALEIT_X1_D2_F 1_SCALEIT_X1_D2_SIGF 1_SCALEIT_X1_D2_F_PLUS 1_SCALEIT_X1_D2_SIGF_PLUS 1_SCALEIT_X1_D2_F_MINUS 1_SCALEIT_X1_D2_SIGF_MINUS 1_SCALEIT_X1_D2_DANO 1_SCALEIT_X1_D2_SIGDANO 1_SCALEIT_X1_D2_ISYM 1_SCALEIT_X1_D2_I 1_SCALEIT_X1_D2_SIGI 1_SCALEIT_X1_D2_I_PLUS 1_SCALEIT_X1_D2_SIGI_PLUS 1_SCALEIT_X1_D2_I_MINUS 1_SCALEIT_X1_D2_SIGI_MINUS 2_AFRO_E 2_AFRO_SIGE 2_AFRO_FA 2_AFRO_SIGFA 5_BP3_FB 5_BP3_PHIB 5_BP3_FOM 5_BP3_PHIBOH 5_BP3_HLA 5_BP3_HLB 5_BP3_HLC 5_BP3_HLD

 * Column Types :

 H H H F Q G L G L D Q Y R R K M K M F Q G L G L D Q Y R R K M K M F Q G L G L D Q Y R R K M K M F Q G L G L D Q Y R R K M K M R Q F Q F P W P A A A A

 * Associated datasets :

 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 4 4 4 4 4 4 4 4

 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above)

   96.0000  120.0000  166.1300   90.0000   90.0000   90.0000 

 *  Resolution Range :

    0.00254    0.15968     (     19.858 -      2.503 A )

 * Sort Order :

      1     2     3     0     0

 * Space group = 'C 2 2 21' (number     20)


 --- CIF Dictionary loaded ---
Logical name: "MMCIFDIC", full name "/home/sness/crystal/ccp4-5.99.3/lib/cif_mmdic.lib"
Information from DICTIONARY category:
Title: cif_mm.dic                       Version: 2.0.03       Datablock id: cif_mm.dic     




 --- Opening CIF ---
Logical name: "DEPOSITFILE", full name "/home/sness/DepositFiles/dummy/INFL.dm"

 --- CIF opened for output ---
The file has been initialised with no data blocks.



New data block "data_dummy[INFL]" created for logical unit "DEPOSITFILE"


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /home/sness/crystal/ccp4-5.99.3/lib/data/syminfo.lib

 Unit cell volume: 1913817.5
 Orthogonalisation matrices:
   96.000   0.000   0.000           0.010   0.000   0.000
    0.000 120.000   0.000           0.000   0.008   0.000
    0.000   0.000 166.130           0.000   0.000   0.006
 Real space metric tensor:      
    9216.0  14400.0  27599.2      0.0      0.0      0.0
 Reciprocal space metric tensor:
  0.000109 0.000069 0.000036 0.000000 0.000000 0.000000

 Grid dimensions   80  96 144  must contain the following prime
 factors for agreement with symmetry restrictions-    2   2   2


 Grid dimensions  120 144 200  must contain the following prime
 factors for agreement with symmetry restrictions-    2   2   2


<a name="datachkdm"><h3>Data Checking</h3></a>

 Number of reflections on file:    19448
 Number outside resolution limit:      0
 Number of systematic absences:        0
 Number outside asymmetric unit:       0
 Number of reflections used:       19448

 Number of unobserved reflections:                  2189
 Number of centric reflections:                     2367
 Number of centric phases more than 4 degrees out:     0

 Program data read:
 Column:      MIN       MAX       MEAN X    MEAN X^2
    H          0.000    38.000    13.060     251.327
    K          0.000    47.000    14.820     332.473
    L          0.000    66.000    25.731     949.506
    S          0.003     0.160     0.085       0.009
    EPS       -4.000     2.000     1.509       4.025
    FO        -0.010   905.764   220.313   71790.328
    PHIO      -1.571     6.133     3.175      11.610
    FOMO       0.000     0.741     0.001       0.000
    HL-A      -0.838     0.747     0.000       0.000
    HL-B      -0.712     0.930     0.000       0.000
    HL-C       0.000     0.000     0.000       0.000
    HL-D       0.000     0.000     0.000       0.000

<a name="datascldm"><h3>Data Scaling</h3></a>

 Input data analysis:
   Estimated intensity scale factor =     14.737
   Estimated temperature factor     =     18.999

<applet width=" 400" height=" 300" code="JLogGraph.class" 
codebase="/home/sness/crystal/ccp4-5.99.3/bin"><param name="table" value="
 $TABLE: Analysis of input structure factors :
 $GRAPHS: Data completeness with resolution :N:2,4:
        : Mean F^2 with resolution          :N:2,5,6:
 $$
  res   1/resol^2  number    %present      expect.   obs. $$
 (lim)(4sin2th/l2)(reflns) (completeness)    (mean F^2)   $$
 10.00   0.007       362.        61.0   2079762.  753504.
  8.00   0.013       373.        70.5   1080658. 1141671.
  7.00   0.018       419.        80.3    616203.  921377.
  6.00   0.024       741.        80.8    638247.  846446.
  5.00   0.034      1413.        77.4   1079536. 1135613.
  4.50   0.045      1030.        65.3   1374101. 1506012.
  4.00   0.056      1536.        63.2   1591079. 1804027.
  3.60   0.070      1962.        64.0   1339951. 1688460.
  3.30   0.085      2170.        65.1   1260501. 1334481.
  3.00   0.101      2956.        62.0    934949. 1020829.
  2.80   0.119      1980.        44.3    801294.  717776.
  2.60   0.137      1728.        29.6    734755.  651931.
  2.40   0.153       589.         7.7    714557.  613637.
 $$
"><b>For inline graphs use a Java browser</b></applet>

FORMATTED      OLD     file opened on unit   8
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: HISTLIB, Filename: /home/sness/crystal/ccp4-5.99.3/lib/data/hist.lib
<!--SUMMARY_END--></FONT></B>


 HISTLIB opened:
  Number of histograms            =   18
  Number of entries per histogram =  100
 RESL  10.0  8.0  7.0  6.0  5.0  4.5  4.0  3.6  3.3  3.0  2.8  2.6  2.4  2.2  2.0  1.8  1.6  1.5


<a name="solmskdm"><h3>Initial Solvent Mask</h3></a>

 Auto Wang-radius   82.4

            The masked region occupies   0.0 % of the cell.
            Maps are x-y sections with the x-axis horizontal
            and the origin top left.

 Section   0 of 144

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 +++++++++++++++++++++++++++++++++++++++++++++++++++++                   

 USER EXTENSION SCHEME SELECTED 

 Extension is in steps of resolution only.

 Approximate number of starting reflections   19448 of   19448
<applet width=" 400" height=" 300" code="JLogGraph.class" 
codebase="/home/sness/crystal/ccp4-5.99.3/bin"><param name="table" value="
 $TABLE: Analysis of input figures of merit :
 $GRAPHS: Mean FOM with resolution :N:2,4:
 $$
  res   1/resol^2  number   mean_FOM$$
 (lim)(4sin2th/l2)(reflns) $$
 19.22   0.003         3.     0.000
 13.59   0.005       119.     0.011
 11.10   0.008       148.     0.013
  9.61   0.011       156.     0.007
  8.60   0.014       182.     0.005
  7.85   0.016       219.     0.006
  7.27   0.019       243.     0.000
  6.80   0.022       260.     0.000
  6.41   0.024       266.     0.000
  6.08   0.027       298.     0.002
  5.80   0.030       309.     0.000
  5.55   0.032       294.     0.000
  5.33   0.035       326.     0.000
  5.14   0.038       315.     0.000
  4.96   0.041       315.     0.001
  4.81   0.043       301.     0.000
  4.66   0.046       325.     0.002
  4.53   0.049       293.     0.002
  4.41   0.051       303.     0.000
  4.30   0.054       302.     0.007
  4.19   0.057       334.     0.003
  4.10   0.060       344.     0.000
  4.01   0.062       356.     0.000
  3.92   0.065       376.     0.000
  3.84   0.068       335.     0.000
  3.77   0.070       401.     0.000
  3.70   0.073       359.     0.000
  3.63   0.076       376.     0.000
  3.57   0.078       388.     0.000
  3.51   0.081       385.     0.000
  3.45   0.084       412.     0.000
  3.40   0.087       412.     0.000
  3.35   0.089       472.     0.000
  3.30   0.092       468.     0.000
  3.25   0.095       472.     0.000
  3.20   0.097       468.     0.000
  3.16   0.100       501.     0.000
  3.12   0.103       470.     0.000
  3.08   0.106       492.     0.000
  3.04   0.108       483.     0.000
  3.00   0.111       443.     0.000
  2.97   0.114       499.     0.000
  2.93   0.116       361.     0.000
  2.90   0.119       370.     0.000
  2.87   0.122       381.     0.000
  2.83   0.124       420.     0.000
  2.80   0.127       449.     0.000
  2.77   0.130       385.     0.000
  2.75   0.133       371.     0.000
  2.72   0.135       362.     0.001
  2.69   0.138       316.     0.000
  2.67   0.141       270.     0.000
  2.64   0.143       279.     0.000
  2.62   0.146       253.     0.000
  2.59   0.149       244.     0.000
  2.57   0.152       206.     0.000
  2.55   0.154       209.     0.000
  2.52   0.157       174.     0.000
  2.50   0.160       175.     0.001
 $$
"><b>For inline graphs use a Java browser</b></applet>

 Weights for including reflections
        by magnitude:  0.00
        by FOM:        0.00
        by resolution: 1.00

<hr>
</pre>

<a name="cyc0001dm"><h3>Cycle    1</h3></a>
<a href="#cyc0002dm">Next cycle</a>
<a href="#tocdm">Contents</a>
<pre>

  Effective resolution:  2.503 A
  Number of reflections included:   19448
  Number of reflections excluded:       0
./dm-command.com: line 12:   624 Killed                  dm HKLIN /home/sness/ccp4-sness/9_crank/workdb/crank.in.6_DM.mtz HKLOUT dm.out.mtz  <<END
mode SOLV
combine PERT
scheme ALL
ncycles AUTO
solc 0.622
ncsmask
LABIN  FP=1_SCALEIT_X1_D2_F SIGFP=1_SCALEIT_X1_D2_SIGF PHIO=5_BP3_PHIB FOMO=5_BP3_FOM HLA=5_BP3_HLA HLB=5_BP3_HLB HLC=5_BP3_HLC HLD=5_BP3_HLD
LABOUT  FDM=FDM PHIDM=PHIDM FOMDM=FOMDM HLADM=HLADM HLBDM=HLBDM HLCDM=HLCDM HLDDM=HLDDM
END

