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[ccp4bb]: REFMAC5 under CCP4 4.1



hi,

I tried running REFMAC5 with identical script and input i used a couple
months ago.  back then, it was stable.  now, it distorts my protein
terribly and the R factor climbs from 0.24 up to 0.55.  the differences:
1) back then I was using a Digital Unix Alpha, now i am on Linux (I hope
this is irrelevant)
2) back then I was using an early release of REFMAC5 under CCP4 4.0.1. now
I am using CCP4 v4.1 with the REFMAC5 release contained therein.

is there either a bug or a required change to input scripts?  I couldn't
check the PROBLEMS page as the CCP4 web site seems to be down this
weekend. (i hope the mailing lists are working)

here's my script, the output of the new run and the diff between that and
the old run are attached.

thanks,

------------------
#!/bin/csh -f
#
refmac5 \
HKLIN   ../../mtz/gn11_free.mtz \
HKLOUT   refm01.mtz \
XYZIN   begin.pdb \
XYZOUT   refm01.pdb \
>refmac.out \
<<EOF
#
LABIN FP=FP11 SIGFP=SIGFP11  FREE=FreeR_flag
LABO FC=FC PHIC=PHIC    FWT=2FOFCWT PHWT=PH2FOFCWT -
                     DELFWT=FOFCWT  PHDELWT=PHFOFCWT
MAKE HYDR ALL
MAKE CHECK 0
REFI TYPE REST
REFI RESI MLKF
REFI BREF MIXED
#
SCAL TYPE BULK
#NCYC 5
MONI FEW
end
EOF
#

=======================================================================
"Words, I've noticed, describe just about anything."  - James Lileks
=======================================================================
                        David J. Schuller
                        modern man in a post-modern world
                        MacCHESS, Cornell University
                        djs63@cornell.edu
1,2c1
< <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
< <pre>
---
> <!--SUMMARY_BEGIN-->
7,12c6,11
< 1###############################################################
<  ###############################################################
<  ###############################################################
<  ### CCP PROGRAM SUITE: Refmac_5.0.32    VERSION 4.1: 22/01/01##
<  ###############################################################
<  User: schuller  Run date: 18/ 2/01  Run time:16:17:35
---
> 1##########################################################
>  ##########################################################
>  ##########################################################
>  ### CCP PROGRAM SUITE: Refmac_5.0  VERSION 4.0: 14/07/00##
>  ##########################################################
>  User: schuller  Run date:  8/11/00  Run time:10:50:04
21c20
< <!--SUMMARY_END--></FONT></B>
---
> <!--SUMMARY_END-->
45,50c44,48
< 
<   (Q)QOPEN: file opened on unit  1      Status: READONLY
< <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<  Logical Name: HKLIN      Filename: ../../mtz/gn11_free.mtz
< <!--SUMMARY_END--></FONT></B>
< 
---
> <!--SUMMARY_BEGIN-->
>   (Q)QOPEN allocated #  1
>  User:   schuller             Logical Name: HKLIN
>  Status: READONLY   Filename: ../../mtz/gn11_free.mtz
> <!--SUMMARY_END-->
84,85c82,83
< Dictionary files for restraints : /usr/apps/ccp4_master/ccp4-4.1/lib/data/monomers/mon*cif
< Parameters for new entry and VDW: /usr/apps/ccp4_master/ccp4-4.1/lib/data/monomers/ener_lib.cif
---
> Dictionary files for restraints : /usr/share/local/ccp4_master/refmac5/dic/mon*cif
> Parameters for new entry and VDW: /usr/share/local/ccp4_master/refmac5/dic/ener_lib.cif
89,92c87
<     Links between monomers will be checked. Only those links present in the coordinate file will be used
<     Standard sugar links will be analysed and used
<     For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
<     Symmetry related links will be analysed and used
---
>     Symmetry related links be analysed and used
156c151
<           Distance for acceptor - H    = vdw1+     ( 0.20)
---
>           Distance for acceptor - H    = vdw1+vdw2+( 0.20)
172c167
<      Thermal parameters                      3.00A
---
>      Thermal parameters                      0.03A
178c173,179
<  Input file :begin.pdb
---
>  Input file : begin.pdb
>   ------------------------------
>   ---  LIBRARY OF MONOMERS   ---
>  _lib_name         mon_lib
>  _lib_version      3.1
>  _lib_update       16/07/00
>   ------------------------------
185,186c186,229
<   NUMBER OF MONOMERS IN THE LIBRARY          :  2407
<                 with complete description    :   336
---
>   ------------------------------
>   ---  LIBRARY OF MONOMERS   ---
>  _lib_name         mon_lib
>  _lib_version      3.1
>  _lib_update       16/07/00
>   ------------------------------
>   ------------------------------
>   ---  LIBRARY OF MONOMERS   ---
>  _lib_name         mon_lib
>  _lib_version      3.1
>  _lib_update       16/07/00
>   ------------------------------
>   ------------------------------
>   ---  LIBRARY OF MONOMERS   ---
>  _lib_name         mon_lib
>  _lib_version      3.1
>  _lib_update       16/07/00
>   ------------------------------
>   ------------------------------
>   ---  LIBRARY OF MONOMERS   ---
>  _lib_name         mon_lib
>  _lib_version      3.1
>  _lib_update       16/07/00
>   ------------------------------
>   ------------------------------
>   ---  LIBRARY OF MONOMERS   ---
>  _lib_name         mon_lib
>  _lib_version      3.1
>  _lib_update       16/07/00
>   ------------------------------
>   ------------------------------
>   ---  LIBRARY OF MONOMERS   ---
>  _lib_name         mon_lib
>  _lib_version      3.1
>  _lib_update       16/07/00
>   ------------------------------
>   ------------------------------
>   ---  LIBRARY OF MONOMERS   ---
>  _lib_name         mon_lib
>  _lib_version      3.1
>  _lib_update       16/07/00
>   ------------------------------
>   NUMBER OF MONOMERS IN THE LIBRARY          :  2406
>                 with complete description    :   335
194,196c237
< <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<  Logical name: ATOMSF, Filename: /usr/apps/ccp4_master/ccp4-4.1/lib/data/atomsf.lib
< <!--SUMMARY_END--></FONT></B>
---
>  Logical name: ATOMSF, Full name: /usr/share/local/ccp4_master/ccp4/lib/data/atomsf.lib
200,202c241
< <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<  Logical name: SYMOP, Filename: /usr/apps/ccp4_master/ccp4-4.1/lib/data/symop.lib
< <!--SUMMARY_END--></FONT></B>
---
>  Logical name: SYMOP, Full name: /usr/share/local/ccp4_master/ccp4/lib/data/symop.lib
205d243
<            Different chains have the same chain id.
208c246
<   Number of chains   :       3
---
>   Number of chaines  :       3
222,224c260
< <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<  Logical name: SYMOP, Filename: /usr/apps/ccp4_master/ccp4-4.1/lib/data/symop.lib
< <!--SUMMARY_END--></FONT></B>
---
>  Logical name: SYMOP, Full name: /usr/share/local/ccp4_master/ccp4/lib/data/symop.lib
235,237c271
< <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<  Logical name: SYMOP, Filename: /usr/apps/ccp4_master/ccp4-4.1/lib/data/symop.lib
< <!--SUMMARY_END--></FONT></B>
---
>  Logical name: SYMOP, Full name: /usr/share/local/ccp4_master/ccp4/lib/data/symop.lib
241,243c275
< <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<  Logical name: SYMOP, Filename: /usr/apps/ccp4_master/ccp4-4.1/lib/data/symop.lib
< <!--SUMMARY_END--></FONT></B>
---
>  Logical name: SYMOP, Full name: /usr/share/local/ccp4_master/ccp4/lib/data/symop.lib
264c296
<   S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669
---
>   S      6.2915   2.4386   3.0353  32.3337   1.9891   0.6785   1.5410  81.6937   1.1407
268d299
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
277,278c308,309
< Bond distances: refined atoms                  1677     0.031     0.021
< Bond distances: others                         1463     0.000     0.020
---
> Bond distances: refined atoms                  3136     0.023     0.021
> Bond angles  : refined atoms                   5675     1.950     2.591
280,282d310
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
285,287c313,315
< Overall               : scale =   1.016, B  =   0.610
< Babinet"s bulk solvent: scale =   0.216, B  = 464.683
< Partial structure    1: scale =   1.617, B  =  28.110
---
> Overall               : scale =   1.017, B  =   0.592
> Babinet"s bulk solvent: scale =   0.222, B  = 448.354
> Partial structure    1: scale =   1.620, B  =  27.833
291c319
< Overall sigmaA parameters  : sigmaA0 =   0.895, B_sigmaA  =   0.420
---
> Overall sigmaA parameters  : sigmaA0 =   0.895, B_sigmaA  =   0.430
293c321
< SigmaA for partial structure  1: scale =   0.196, B  =  40.872
---
> SigmaA for partial structure  1: scale =   0.203, B  =  43.662
297c325
< Overall R factor                     =     0.2500
---
> Overall R factor                     =     0.2501
303,307d330
<  U before setting    0.276       0.116       0.195E-01  -0.610E-01  -0.133       0.618E-01
< Atom    3222 X   201FE                tends to have small eigenvalue. Reset it
< Eigenvalues    0.359       0.966E-01  -0.445E-01
<  U after setting    0.284       0.119       0.779E-01  -0.663E-01  -0.111       0.475E-01
< Eigenvalues    0.359       0.966E-01   0.253E-01
312,316d334
<     ****                Sphericity outliers                 ****
<  
< U values different from sphere >  10.00Sigma will be monitored
< X 205 MET SD    U value= 0.4904 0.4198 0.3963 0.1107 0.1791 0.0326 Delta= 0.309 Sigma=  0.025
<  
319,320c337,338
< Bond distances: refined atoms                  1677     0.116     0.021
< Bond distances: others                         1463     0.030     0.020
---
> Bond distances: refined atoms                  3136     0.024     0.021
> Bond angles  : refined atoms                   5675     1.880     2.591
322,324d339
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
327,329c342,344
< Overall               : scale =   1.072, B  =   7.544
< Babinet"s bulk solvent: scale =   0.680, B  = 464.696
< Partial structure    1: scale =   1.668, B  =  35.525
---
> Overall               : scale =   1.016, B  =   0.173
> Babinet"s bulk solvent: scale =   0.229, B  = 448.353
> Partial structure    1: scale =   1.614, B  =  28.245
333c348
< Overall sigmaA parameters  : sigmaA0 =   0.910, B_sigmaA  =   1.908
---
> Overall sigmaA parameters  : sigmaA0 =   0.895, B_sigmaA  =   0.328
335c350
< SigmaA for partial structure  1: scale =   0.190, B  =  49.369
---
> SigmaA for partial structure  1: scale =   0.216, B  =  48.293
339,341c354,356
< Overall R factor                     =     0.2617
< Free R factor                        =     0.3192
< Overall figure of merit              =     0.6676
---
> Overall R factor                     =     0.2442
> Free R factor                        =     0.2830
> Overall figure of merit              =     0.7524
345,359d359
<  U before setting   -0.920E-01  -0.110E-01   0.447      -0.398E-01  -0.635E-01   0.935E-01
< Atom     360 X    24SD                tends to have small eigenvalue. Reset it
< Eigenvalues   -0.110      -0.205E-01   0.474
<  U after setting    0.321E-01   0.429E-01   0.450      -0.109E-01  -0.537E-01   0.862E-01
< Eigenvalues    0.253E-01   0.253E-01   0.474
<  U before setting    0.499E-01  -0.757E-01   0.107      -0.679E-01  -0.974E-01   0.753E-01
< Atom    3092 X   197SD                tends to have small eigenvalue. Reset it
< Eigenvalues   -0.224E-01  -0.112       0.215
<  U after setting    0.884E-01   0.458E-01   0.131      -0.359E-01  -0.817E-01   0.465E-01
< Eigenvalues    0.253E-01   0.253E-01   0.215
<  U before setting    0.751        4.10       -4.27       -2.37        1.08       -2.47
< Atom    3222 X   201FE                tends to have small eigenvalue. Reset it
< Eigenvalues   -0.471        6.03       -4.98
<  U after setting     1.18        4.49       0.410       -2.27       0.667       -1.31
< Eigenvalues    0.253E-01    6.03       0.253E-01
364,372d363
<     ****                Sphericity outliers                 ****
<  
< U values different from sphere >  10.00Sigma will be monitored
< X  31 MET SD    U value= 0.1277 0.1384 0.5451-0.0109-0.0537 0.0862 Delta= 0.366 Sigma=  0.025
< X  75 MET SD    U value= 0.3026 0.4412 0.5267-0.0579-0.0439 0.2955 Delta= 0.459 Sigma=  0.025
< X 113 CYS SG    U value= 0.3120 0.3648 0.2657-0.1881-0.0204 0.0316 Delta= 0.280 Sigma=  0.025
< X 205 MET SD    U value= 0.4299 0.2701 0.5355 0.0493 0.1152 0.0007 Delta= 0.259 Sigma=  0.025
< X 300 HEM FE    U value= 1.2779 4.5842 0.5051-2.2725 0.6668-1.3096 Delta= 4.903 Sigma=  0.025
<  
375,376c366,367
< Bond distances: refined atoms                  1677     0.119     0.021
< Bond distances: others                         1463     0.029     0.020
---
> Bond distances: refined atoms                  3136     0.024     0.021
> Bond angles  : refined atoms                   5675     1.904     2.591
378,380d368
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
383,385c371,373
< Overall               : scale =   1.040, B  =   7.584
< Babinet"s bulk solvent: scale =   0.691, B  = 464.719
< Partial structure    1: scale =   1.607, B  =  40.055
---
> Overall               : scale =   1.014, B  =   0.200
> Babinet"s bulk solvent: scale =   0.220, B  = 448.353
> Partial structure    1: scale =   1.611, B  =  28.455
389c377
< Overall sigmaA parameters  : sigmaA0 =   0.896, B_sigmaA  =   2.339
---
> Overall sigmaA parameters  : sigmaA0 =   0.897, B_sigmaA  =   0.310
391c379
< SigmaA for partial structure  1: scale =   0.173, B  =  47.623
---
> SigmaA for partial structure  1: scale =   0.213, B  =  46.971
395,397c383,385
< Overall R factor                     =     0.3305
< Free R factor                        =     0.3392
< Overall figure of merit              =     0.6313
---
> Overall R factor                     =     0.2424
> Free R factor                        =     0.2801
> Overall figure of merit              =     0.7554
401,424d388
<  U before setting    0.232       0.317       0.184      -0.246      -0.344E-01   0.325E-01
< Atom    1725 X   106SG                tends to have small eigenvalue. Reset it
< Eigenvalues    0.244E-01   0.531       0.178
<  U after setting    0.232       0.317       0.184      -0.246      -0.344E-01   0.325E-01
< Eigenvalues    0.253E-01   0.531       0.178
<  U before setting    0.190        1.20       -1.16       0.277E-01  -0.139      -0.208
< Atom    3092 X   197SD                tends to have small eigenvalue. Reset it
< Eigenvalues    0.202        1.22       -1.19
<  U after setting    0.202        1.21       0.364E-01   0.379E-01  -0.206E-01  -0.105
< Eigenvalues    0.202        1.22       0.253E-01
<  U before setting    0.219       0.371       0.110       0.172       0.363       0.583E-01
< Atom    3109 X   198SD                tends to have small eigenvalue. Reset it
< Eigenvalues    0.640       0.272      -0.211
<  U after setting    0.325       0.375       0.237       0.153       0.247       0.799E-01
< Eigenvalues    0.272       0.640       0.253E-01
<  U before setting    0.628        12.8       -3.95       -2.84       -1.63        2.06
< Atom    3222 X   201FE                tends to have small eigenvalue. Reset it
< Eigenvalues    0.279        13.8       -4.54
<  U after setting    0.945        12.8       0.282       -2.92      -0.467        1.74
< Eigenvalues    0.279        13.8       0.253E-01
<  U before setting    0.945        12.8       0.282       -2.92      -0.467        1.74
< Atom    3222 X   201FE                tends to have large eigenvalue. Reset it
< Eigenvalues    0.279        13.8       0.253E-01
<  U after setting    0.568        5.92       0.151       -1.31      -0.245       0.793
429,438d392
<     ****                Sphericity outliers                 ****
<  
< U values different from sphere >  10.00Sigma will be monitored
< X  31 MET SD    U value= 0.2079 0.2049 0.6667-0.0568-0.1376 0.0844 Delta= 0.447 Sigma=  0.025
< X  75 MET SD    U value= 0.4090 0.5429 0.6290-0.0330-0.0646 0.2716 Delta= 0.427 Sigma=  0.025
< X 113 CYS SG    U value= 0.3286 0.4133 0.2802-0.2457-0.0344 0.0325 Delta= 0.366 Sigma=  0.025
< X 204 MET SD    U value= 0.2980 1.3048 0.1324 0.0379-0.0206-0.1051 Delta= 0.912 Sigma=  0.025
< X 205 MET SD    U value= 0.4207 0.4709 0.3335 0.1527 0.2473 0.0799 Delta= 0.437 Sigma=  0.025
< X 300 HEM FE    U value= 0.6643 6.0135 0.2469-1.3115-0.2452 0.7930 Delta= 5.050 Sigma=  0.025
<  
441,442c395,396
< Bond distances: refined atoms                  1677     0.228     0.021
< Bond distances: others                         1463     0.091     0.020
---
> Bond distances: refined atoms                  3136     0.024     0.021
> Bond angles  : refined atoms                   5675     1.947     2.591
444,446d397
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
449,451c400,402
< Overall               : scale =   1.239, B  =  12.153
< Babinet"s bulk solvent: scale =   0.499, B  =  88.601
< Partial structure    1: scale =   1.883, B  =  51.629
---
> Overall               : scale =   1.013, B  =   0.209
> Babinet"s bulk solvent: scale =   0.215, B  = 448.353
> Partial structure    1: scale =   1.608, B  =  28.358
455c406
< Overall sigmaA parameters  : sigmaA0 =   0.876, B_sigmaA  =   7.579
---
> Overall sigmaA parameters  : sigmaA0 =   0.898, B_sigmaA  =   0.306
457c408
< SigmaA for partial structure  1: scale =   0.192, B  =  67.062
---
> SigmaA for partial structure  1: scale =   0.211, B  =  45.899
461,463c412,414
< Overall R factor                     =     0.4054
< Free R factor                        =     0.4353
< Overall figure of merit              =     0.4264
---
> Overall R factor                     =     0.2415
> Free R factor                        =     0.2781
> Overall figure of merit              =     0.7571
467,500d417
<  U before setting    -1.10       0.698E-01   0.477      -0.521      -0.653       0.580
< Atom     360 X    24SD                tends to have small eigenvalue. Reset it
< Eigenvalues    -1.40      -0.340        1.19
<  U after setting    0.162       0.381       0.700      -0.221      -0.304       0.490
< Eigenvalues    0.253E-01   0.253E-01    1.19
<  U before setting    0.278       0.443      -0.168      -0.953E-01  -0.310       0.899
< Atom    1118 X    68SD                tends to have small eigenvalue. Reset it
< Eigenvalues    0.237        1.16      -0.847
<  U after setting    0.306       0.710       0.410      -0.181      -0.184       0.506
< Eigenvalues    0.237        1.16       0.253E-01
<  U before setting    0.534E-01   0.130       0.130E-01  -0.403       0.224E-01   0.208
< Atom    1725 X   106SG                tends to have small eigenvalue. Reset it
< Eigenvalues   -0.380       0.536       0.402E-01
<  U after setting    0.218       0.308       0.743E-01  -0.231      -0.782E-01   0.104
< Eigenvalues    0.253E-01   0.536       0.402E-01
<  U before setting   -0.259        1.27       0.220E-01   0.298      -0.176      -0.172
< Atom    3092 X   197SD                tends to have small eigenvalue. Reset it
< Eigenvalues   -0.370        1.36       0.459E-01
<  U after setting    0.783E-01    1.28       0.729E-01   0.251      -0.453E-01  -0.190
< Eigenvalues    0.253E-01    1.36       0.459E-01
<  U before setting    0.377       0.304       0.225       0.857E-01   0.317       0.256E-01
< Atom    3109 X   198SD                tends to have small eigenvalue. Reset it
< Eigenvalues    0.648       0.287      -0.282E-01
<  U after setting    0.398       0.304       0.257       0.822E-01   0.291       0.298E-01
< Eigenvalues    0.648       0.287       0.253E-01
<  U before setting     1.22        6.70      -0.761      -0.230       0.432       0.627
< Atom    3222 X   201FE                tends to have small eigenvalue. Reset it
< Eigenvalues     1.31        6.76      -0.908
<  U after setting     1.26        6.71       0.126      -0.213       0.243       0.548
< Eigenvalues     1.31        6.76       0.253E-01
<  U before setting     1.26        6.71       0.126      -0.213       0.243       0.548
< Atom    3222 X   201FE                tends to have large eigenvalue. Reset it
< Eigenvalues     1.31        6.76       0.253E-01
<  U after setting     1.26        6.28       0.123      -0.199       0.245       0.514
505,514d421
<     ****                Sphericity outliers                 ****
<  
< U values different from sphere >  10.00Sigma will be monitored
< X  31 MET SD    U value= 0.3162 0.5346 0.8541-0.2206-0.3040 0.4897 Delta= 0.953 Sigma=  0.025
< X  75 MET SD    U value= 0.4595 0.8641 0.5634-0.1809-0.1842 0.5055 Delta= 0.856 Sigma=  0.025
< X 113 CYS SG    U value= 0.3723 0.4623 0.2282-0.2313-0.0782 0.1038 Delta= 0.411 Sigma=  0.025
< X 204 MET SD    U value= 0.2322 1.4339 0.2268 0.2508-0.0453-0.1904 Delta= 1.081 Sigma=  0.025
< X 205 MET SD    U value= 0.5520 0.4582 0.4114 0.0822 0.2912 0.0298 Delta= 0.442 Sigma=  0.025
< X 300 HEM FE    U value= 1.4135 6.4377 0.2769-0.1985 0.2445 0.5140 Delta= 4.714 Sigma=  0.025
<  
517,518c424,425
< Bond distances: refined atoms                  1677     0.359     0.021
< Bond distances: others                         1463     0.153     0.020
---
> Bond distances: refined atoms                  3136     0.024     0.021
> Bond angles  : refined atoms                   5675     1.987     2.591
520,522d426
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
525,527c429,431
< Overall               : scale =   0.912, B  =   7.248
< Babinet"s bulk solvent: scale =   0.717, B  = 200.000
< Partial structure    1: scale =   1.327, B  =  57.527
---
> Overall               : scale =   1.013, B  =   0.223
> Babinet"s bulk solvent: scale =   0.213, B  = 448.353
> Partial structure    1: scale =   1.606, B  =  28.377
531c435
< Overall sigmaA parameters  : sigmaA0 =   0.737, B_sigmaA  =  12.562
---
> Overall sigmaA parameters  : sigmaA0 =   0.898, B_sigmaA  =   0.309
533c437
< SigmaA for partial structure  1: scale =   0.237, B  = 129.757
---
> SigmaA for partial structure  1: scale =   0.209, B  =  46.859
537,539c441,443
< Overall R factor                     =     0.4781
< Free R factor                        =     0.5144
< Overall figure of merit              =     0.2655
---
> Overall R factor                     =     0.2410
> Free R factor                        =     0.2773
> Overall figure of merit              =     0.7578
543,572d446
<  U before setting   -0.713E-01   0.207       0.367       0.132      -0.305       0.868
< Atom     360 X    24SD                tends to have small eigenvalue. Reset it
< Eigenvalues    0.549E-01  -0.727        1.17
<  U after setting    0.640E-01   0.523       0.668      -0.752E-01  -0.103       0.560
< Eigenvalues    0.549E-01   0.253E-01    1.17
<  U before setting    0.528       0.804       0.112E-01   0.195      -0.686      -0.489
< Atom    1725 X   106SG                tends to have small eigenvalue. Reset it
< Eigenvalues     1.37       0.505      -0.533
<  U after setting    0.666       0.834       0.401       0.260      -0.454      -0.380
< Eigenvalues     1.37       0.505       0.253E-01
<  U before setting   -0.109        1.47      -0.632E-02   0.785      -0.385      -0.707
< Atom    3092 X   197SD                tends to have small eigenvalue. Reset it
< Eigenvalues   -0.474        2.10      -0.272
<  U after setting    0.306        1.55       0.288       0.654      -0.272      -0.634
< Eigenvalues    0.253E-01    2.10       0.253E-01
<  U before setting    0.571      -0.418E-01   0.182       0.133       0.215      -0.715E-01
< Atom    3109 X   198SD                tends to have small eigenvalue. Reset it
< Eigenvalues    0.678      -0.121       0.154
<  U after setting    0.583       0.674E-01   0.207       0.962E-01   0.197      -0.194E-01
< Eigenvalues    0.678       0.253E-01   0.154
<  
<     ****                Sphericity outliers                 ****
<  
< U values different from sphere >  10.00Sigma will be monitored
< X  31 MET SD    U value= 0.1558 0.6148 0.7596-0.0752-0.1029 0.5600 Delta= 0.927 Sigma=  0.025
< X  75 MET SD    U value= 0.4208 0.9266 0.6560 0.0091-0.1916 0.3916 Delta= 0.713 Sigma=  0.025
< X 113 CYS SG    U value= 0.7581 0.9257 0.4932 0.2597-0.4539-0.3799 Delta= 0.965 Sigma=  0.025
< X 204 MET SD    U value= 0.3976 1.6437 0.3802 0.6544-0.2717-0.6338 Delta= 1.690 Sigma=  0.025
< X 205 MET SD    U value= 0.6753 0.1592 0.2986 0.0962 0.1970-0.0194 Delta= 0.489 Sigma=  0.025
< X 300 HEM FE    U value= 2.3823 2.3639 4.1402-0.3537 0.6849-0.0380 Delta= 1.809 Sigma=  0.025
576,577c450,451
< Bond distances: refined atoms                  1677     0.647     0.021
< Bond distances: others                         1463     0.404     0.020
---
> Bond distances: refined atoms                  3136     0.024     0.021
> Bond angles  : refined atoms                   5675     2.017     2.591
579,581d452
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
<  In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
584,586c455,457
< Overall               : scale =   0.764, B  =  11.519
< Babinet"s bulk solvent: scale =   0.758, B  = 200.000
< Partial structure    1: scale =   1.070, B  =  71.476
---
> Overall               : scale =   1.012, B  =   0.224
> Babinet"s bulk solvent: scale =   0.210, B  = 448.354
> Partial structure    1: scale =   1.606, B  =  28.519
590c461
< Overall sigmaA parameters  : sigmaA0 =   0.713, B_sigmaA  =  20.639
---
> Overall sigmaA parameters  : sigmaA0 =   0.899, B_sigmaA  =   0.314
592c463
< SigmaA for partial structure  1: scale =   0.001, B  = 129.677
---
> SigmaA for partial structure  1: scale =   0.209, B  =  47.500
596,598c467,469
< Overall R factor                     =     0.5496
< Free R factor                        =     0.5494
< Overall figure of merit              =     0.2655
---
> Overall R factor                     =     0.2407
> Free R factor                        =     0.2766
> Overall figure of merit              =     0.7578
600,605c471,475
< 
<   (Q)QOPEN: file opened on unit  2      Status: UNKNOWN
< <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<  Logical Name: HKLOUT      Filename: refm01.mtz
< <!--SUMMARY_END--></FONT></B>
< 
---
> <!--SUMMARY_BEGIN-->
>   (Q)QOPEN allocated #  2
>  User:   schuller             Logical Name: HKLOUT
>  Status: UNKNOWN    Filename: refm01.mtz
> <!--SUMMARY_END-->
626c496
<  * Dataset ID, project name, dataset name, cell dimensions, wavelength:
---
>  * Dataset ID, project name, dataset name:
630,631d499
<              63.1670   63.1670  100.3780   90.0000   90.0000   90.0000
<  
646,647c514,515
<  FP11                           F               1.4253          1583.6095        1
<  SIGFP11                        Q               1.0318            54.8579        1
---
>  FP11                           F               1.0756          1195.0848        1
>  SIGFP11                        Q               0.7787            41.3995        1
649c517
<  FC                             F               0.0009          8352.2686        1
---
>  FC                             F               0.0203          8780.1807        1
651c519
<  2FOFCWT                        F               0.0001          3174.9519        1
---
>  2FOFCWT                        F               0.0019          2836.4822        1
653c521
<  FOFCWT                         F               0.0000          3175.0449        1
---
>  FOFCWT                         F               0.0000          2836.7539        1
659c527
<     63.1670   63.1670  100.3780   90.0000   90.0000   90.0000
---
>     63.167   63.167  100.378   90.000   90.000   90.000
719,720c587,588
<   Time in seconds: CPU =       171.35
<              Elapsed =         178.00
---
>   Time in seconds: CPU =       251.04
>              Elapsed =         256.00
732,737c600,605
<          1   0.250   0.287    0.746    0.031    2.362    0.156
<          2   0.262   0.319    0.668    0.116    5.956    0.457
<          3   0.330   0.339    0.631    0.119    6.384    0.387
<          4   0.405   0.435    0.426    0.228   11.443    0.809
<          5   0.478   0.514    0.266    0.359   18.983    1.322
<          6   0.550   0.549    0.266    0.647   31.034    2.491
---
>          1   0.250   0.286    0.746    0.023    1.950    0.156
>          2   0.244   0.283    0.752    0.024    1.880    0.159
>          3   0.242   0.280    0.755    0.024    1.904    0.159
>          4   0.242   0.278    0.757    0.024    1.947    0.159
>          5   0.241   0.277    0.758    0.024    1.987    0.159
>          6   0.241   0.277    0.758    0.024    2.017    0.159
740,747c608,611
< <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<  Refmac_5.0.32:  End of Refmac_5.0.32
<  Times: User:     205.5s System:    3.2s Elapsed:    3:36
< </pre>
< <!--SUMMARY_END--></FONT></B>
< <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
< </html>
< <!--SUMMARY_END--></FONT></B>
---
> <!--SUMMARY_BEGIN-->
>  Refmac_5.0.27:  End of Refmac_5.0.27
>  Times: User:     269.3s System:    6.3s Elapsed:    4:42
> <!--SUMMARY_END-->
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>




1###############################################################
 ###############################################################
 ###############################################################
 ### CCP PROGRAM SUITE: Refmac_5.0.32    VERSION 4.1: 22/01/01##
 ###############################################################
 User: schuller  Run date: 18/ 2/01  Run time:16:17:35


 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.


<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ comment $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 Comment line--- #
 Data line--- LABIN FP=FP11 SIGFP=SIGFP11  FREE=FreeR_flag
 Data line--- LABO FC=FC PHIC=PHIC    FWT=2FOFCWT PHWT=PH2FOFCWT                      DELFWT=FOFCWT  PHDELWT=PHFOFCWT
 Data line--- MAKE HYDR ALL
 Data line--- MAKE CHECK 0
 Data line--- REFI TYPE REST
 Data line--- REFI RESI MLKF
 Data line--- REFI BREF MIXED
 Comment line--- #
 Data line--- SCAL TYPE BULK
 Comment line--- #NCYC 5
 Data line--- MONI FEW
 Data line--- end

  (Q)QOPEN: file opened on unit  1      Status: READONLY
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Logical Name: HKLIN      Filename: ../../mtz/gn11_free.mtz
<!--SUMMARY_END--></FONT></B>

 * Input Program Labels :
 
 H K L FP SIGFP FREE FPART1 PHIP1 FPART2 PHIP2 FPART3 PHIP3 HLA HLB HLC HLD FOM
 PHIB
 
 * Input File Labels :
 
 H K L FP11 SIGFP11 dum2 FreeR_flag
 
 * Lookup Table : the number indicates the input column no.
 * Array element n corresponds to the nth program label
 
     1    2    3    4    5    7    0    0    0    0    0    0    0    0    0
     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
     0    0    0    0
 
 
    ****           Input and Default parameters#            ****
 
 
Input coordinate file.  Logical name - XYZIN actual file name  - begin.pdb
Output coordinate file. Logical name - XYZOUT actual file name - refm01.pdb
Input reflection file.  Logical name - HKLIN actual file name  - ../../mtz/gn11_free.mtz
Output reflection file. Logical name - HKLOUT actual file name - refm01.mtz
 
Cell from mtz :    63.167    63.167   100.378    90.000    90.000    90.000
Space group from mtz: number -   96; name - P43212
 
  Refinement type                        : Restrained
 
 
    ****                 Makecif parameters                 ****
 
Dictionary files for restraints : /usr/apps/ccp4_master/ccp4-4.1/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /usr/apps/ccp4_master/ccp4-4.1/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically
 
 
  Residual                               : Rice Maximum Likelihood for Fs
 
    ****          Least-square scaling parameters           ****
 
Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Bulk solvent based on Babinet"s principle
Constant bulk solvent in non protein region
Probe radii for non-ions     1.400
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800
 
  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0222
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    53.4522  1.4997
  Estimated number of reflections :      39642
  Free R exclusion - flag equals:     0
  Weighting by comparison of trace of matrix
  Weighting parameters   :     0.5000
  Refinement cycles       :     5
  Scaling type                           :
          Bulk solvent using using Babinet principle
  using working set of reflns but not experimental sigmas
 
  Estimation of SigmaA Using 2 Gaussians:
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas
 
  Scaling and SigmaA resln:    53.4522  1.4997
 
  Damping factors:     1.0000  1.0000
 
 
    ****          Geometry restraints and weights           ****
 
 
                                              Sigma:
 Bonding distances
          Weight =  1.00
 
 Bond angles
          Weight =  1.00
 
 Planar groups
          WEIGHT= 1.00
 
 Chiral centers
          Weight= 1.00
 
 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.30
          Sigma for VDW trhough torsion angle     =  0.50
          Sigma for HBOND                         =  0.50
          Sigma for metal-ion                     =  0.50
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.20)
          VDW distance through torsion = vdw1+vdw2+(-0.75)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)
 
 TORSION ANGLES
          Weight= 1.00
 
 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)         1.50A**2
     Main chain angle (1-3 neighbour)        2.00A**2
     Side chain bond                         3.00A**2
     Side chain angle                        4.50A**2
 
 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.03A
     Thermal parameters                      3.00A
     Occupancy parameters                    0.20A
 
Monitoring style is "FEW". Minimum information will be printed out
---------------------------------------------------------------
 
 Input file :begin.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      3.1
 _lib_update       16/07/00
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          :  2407
                with complete description    :   336
  NUMBER OF MODIFICATIONS                    :    37
  NUMBER OF LINKS                            :    62
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

 FORMATTED      OLD     file opened on unit  45
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Logical name: ATOMSF, Filename: /usr/apps/ccp4_master/ccp4-4.1/lib/data/atomsf.lib
<!--SUMMARY_END--></FONT></B>


 FORMATTED      OLD     file opened on unit   8
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Logical name: SYMOP, Filename: /usr/apps/ccp4_master/ccp4-4.1/lib/data/symop.lib
<!--SUMMARY_END--></FONT></B>

  WARNING: Chain_list is not correct. Program changed it.
           Different chains have the same chain id.
  Number of atoms    :    1870
  Number of residues :     442
  Number of chains   :       3
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     connection is found (not be used) dist=   2.048 ideal_dist=   1.935
            ch:XX res:  23  HIS      at:NE2  --> ch:Xa res: 300  HEM      at:FE
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------

 FORMATTED      OLD     file opened on unit   8
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Logical name: SYMOP, Filename: /usr/apps/ccp4_master/ccp4-4.1/lib/data/symop.lib
<!--SUMMARY_END--></FONT></B>

  Number of chains                  :       3
  Total number of monomers          :     442
  Number of atoms                   :    3959
  Number of missing atoms           :      26
  Number of rebuilding atoms        :    2063
  Number of unknoun atoms           :       0
  Number of deleted atoms           :       0

 FORMATTED      OLD     file opened on unit   8
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Logical name: SYMOP, Filename: /usr/apps/ccp4_master/ccp4-4.1/lib/data/symop.lib
<!--SUMMARY_END--></FONT></B>


 FORMATTED      OLD     file opened on unit   8
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Logical name: SYMOP, Filename: /usr/apps/ccp4_master/ccp4-4.1/lib/data/symop.lib
<!--SUMMARY_END--></FONT></B>

 
 
 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c
 
 
  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
  S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669
  FE    11.7695   4.7611   7.3573   0.3072   3.5222  15.3535   2.3045  76.8805   1.0369
 
 
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 Number of reflections in file      33282
 Number of reflection read          33282
 
 
     CGMAT cycle number =      1
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1677     0.031     0.021
Bond distances: others                         1463     0.000     0.020
-------------------------------------------------------------------------------
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 
-----------------------------------------------------------------------------
Overall               : scale =   1.016, B  =   0.610
Babinet"s bulk solvent: scale =   0.216, B  = 464.683
Partial structure    1: scale =   1.617, B  =  28.110
Overall anisotropic scale factors
   B11 =  0.14 B22 =  0.14 B33 = -0.28 B12 =  0.00 B13 =  0.00 B23 =  0.00
 
Overall sigmaA parameters  : sigmaA0 =   0.895, B_sigmaA  =   0.420
Babinet"s scale for sigmaA : scale =    -0.001, B  =        150.000
SigmaA for partial structure  1: scale =   0.196, B  =  40.872
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2500
Free R factor                        =     0.2865
Overall figure of merit              =     0.7460
-----------------------------------------------------------------------------
 
 
 U before setting    0.276       0.116       0.195E-01  -0.610E-01  -0.133       0.618E-01
Atom    3222 X   201FE                tends to have small eigenvalue. Reset it
Eigenvalues    0.359       0.966E-01  -0.445E-01
 U after setting    0.284       0.119       0.779E-01  -0.663E-01  -0.111       0.475E-01
Eigenvalues    0.359       0.966E-01   0.253E-01
 
 
     CGMAT cycle number =      2
 
    ****                Sphericity outliers                 ****
 
U values different from sphere >  10.00Sigma will be monitored
X 205 MET SD    U value= 0.4904 0.4198 0.3963 0.1107 0.1791 0.0326 Delta= 0.309 Sigma=  0.025
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1677     0.116     0.021
Bond distances: others                         1463     0.030     0.020
-------------------------------------------------------------------------------
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 
-----------------------------------------------------------------------------
Overall               : scale =   1.072, B  =   7.544
Babinet"s bulk solvent: scale =   0.680, B  = 464.696
Partial structure    1: scale =   1.668, B  =  35.525
Overall anisotropic scale factors
   B11 =  0.14 B22 =  0.14 B33 = -0.28 B12 =  0.00 B13 =  0.00 B23 =  0.00
 
Overall sigmaA parameters  : sigmaA0 =   0.910, B_sigmaA  =   1.908
Babinet"s scale for sigmaA : scale =    -0.001, B  =        150.000
SigmaA for partial structure  1: scale =   0.190, B  =  49.369
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2617
Free R factor                        =     0.3192
Overall figure of merit              =     0.6676
-----------------------------------------------------------------------------
 
 
 U before setting   -0.920E-01  -0.110E-01   0.447      -0.398E-01  -0.635E-01   0.935E-01
Atom     360 X    24SD                tends to have small eigenvalue. Reset it
Eigenvalues   -0.110      -0.205E-01   0.474
 U after setting    0.321E-01   0.429E-01   0.450      -0.109E-01  -0.537E-01   0.862E-01
Eigenvalues    0.253E-01   0.253E-01   0.474
 U before setting    0.499E-01  -0.757E-01   0.107      -0.679E-01  -0.974E-01   0.753E-01
Atom    3092 X   197SD                tends to have small eigenvalue. Reset it
Eigenvalues   -0.224E-01  -0.112       0.215
 U after setting    0.884E-01   0.458E-01   0.131      -0.359E-01  -0.817E-01   0.465E-01
Eigenvalues    0.253E-01   0.253E-01   0.215
 U before setting    0.751        4.10       -4.27       -2.37        1.08       -2.47
Atom    3222 X   201FE                tends to have small eigenvalue. Reset it
Eigenvalues   -0.471        6.03       -4.98
 U after setting     1.18        4.49       0.410       -2.27       0.667       -1.31
Eigenvalues    0.253E-01    6.03       0.253E-01
 
 
     CGMAT cycle number =      3
 
    ****                Sphericity outliers                 ****
 
U values different from sphere >  10.00Sigma will be monitored
X  31 MET SD    U value= 0.1277 0.1384 0.5451-0.0109-0.0537 0.0862 Delta= 0.366 Sigma=  0.025
X  75 MET SD    U value= 0.3026 0.4412 0.5267-0.0579-0.0439 0.2955 Delta= 0.459 Sigma=  0.025
X 113 CYS SG    U value= 0.3120 0.3648 0.2657-0.1881-0.0204 0.0316 Delta= 0.280 Sigma=  0.025
X 205 MET SD    U value= 0.4299 0.2701 0.5355 0.0493 0.1152 0.0007 Delta= 0.259 Sigma=  0.025
X 300 HEM FE    U value= 1.2779 4.5842 0.5051-2.2725 0.6668-1.3096 Delta= 4.903 Sigma=  0.025
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1677     0.119     0.021
Bond distances: others                         1463     0.029     0.020
-------------------------------------------------------------------------------
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 
-----------------------------------------------------------------------------
Overall               : scale =   1.040, B  =   7.584
Babinet"s bulk solvent: scale =   0.691, B  = 464.719
Partial structure    1: scale =   1.607, B  =  40.055
Overall anisotropic scale factors
   B11 =  0.14 B22 =  0.14 B33 = -0.28 B12 =  0.00 B13 =  0.00 B23 =  0.00
 
Overall sigmaA parameters  : sigmaA0 =   0.896, B_sigmaA  =   2.339
Babinet"s scale for sigmaA : scale =    -0.001, B  =        150.000
SigmaA for partial structure  1: scale =   0.173, B  =  47.623
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.3305
Free R factor                        =     0.3392
Overall figure of merit              =     0.6313
-----------------------------------------------------------------------------
 
 
 U before setting    0.232       0.317       0.184      -0.246      -0.344E-01   0.325E-01
Atom    1725 X   106SG                tends to have small eigenvalue. Reset it
Eigenvalues    0.244E-01   0.531       0.178
 U after setting    0.232       0.317       0.184      -0.246      -0.344E-01   0.325E-01
Eigenvalues    0.253E-01   0.531       0.178
 U before setting    0.190        1.20       -1.16       0.277E-01  -0.139      -0.208
Atom    3092 X   197SD                tends to have small eigenvalue. Reset it
Eigenvalues    0.202        1.22       -1.19
 U after setting    0.202        1.21       0.364E-01   0.379E-01  -0.206E-01  -0.105
Eigenvalues    0.202        1.22       0.253E-01
 U before setting    0.219       0.371       0.110       0.172       0.363       0.583E-01
Atom    3109 X   198SD                tends to have small eigenvalue. Reset it
Eigenvalues    0.640       0.272      -0.211
 U after setting    0.325       0.375       0.237       0.153       0.247       0.799E-01
Eigenvalues    0.272       0.640       0.253E-01
 U before setting    0.628        12.8       -3.95       -2.84       -1.63        2.06
Atom    3222 X   201FE                tends to have small eigenvalue. Reset it
Eigenvalues    0.279        13.8       -4.54
 U after setting    0.945        12.8       0.282       -2.92      -0.467        1.74
Eigenvalues    0.279        13.8       0.253E-01
 U before setting    0.945        12.8       0.282       -2.92      -0.467        1.74
Atom    3222 X   201FE                tends to have large eigenvalue. Reset it
Eigenvalues    0.279        13.8       0.253E-01
 U after setting    0.568        5.92       0.151       -1.31      -0.245       0.793
 
 
     CGMAT cycle number =      4
 
    ****                Sphericity outliers                 ****
 
U values different from sphere >  10.00Sigma will be monitored
X  31 MET SD    U value= 0.2079 0.2049 0.6667-0.0568-0.1376 0.0844 Delta= 0.447 Sigma=  0.025
X  75 MET SD    U value= 0.4090 0.5429 0.6290-0.0330-0.0646 0.2716 Delta= 0.427 Sigma=  0.025
X 113 CYS SG    U value= 0.3286 0.4133 0.2802-0.2457-0.0344 0.0325 Delta= 0.366 Sigma=  0.025
X 204 MET SD    U value= 0.2980 1.3048 0.1324 0.0379-0.0206-0.1051 Delta= 0.912 Sigma=  0.025
X 205 MET SD    U value= 0.4207 0.4709 0.3335 0.1527 0.2473 0.0799 Delta= 0.437 Sigma=  0.025
X 300 HEM FE    U value= 0.6643 6.0135 0.2469-1.3115-0.2452 0.7930 Delta= 5.050 Sigma=  0.025
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1677     0.228     0.021
Bond distances: others                         1463     0.091     0.020
-------------------------------------------------------------------------------
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 
-----------------------------------------------------------------------------
Overall               : scale =   1.239, B  =  12.153
Babinet"s bulk solvent: scale =   0.499, B  =  88.601
Partial structure    1: scale =   1.883, B  =  51.629
Overall anisotropic scale factors
   B11 =  0.14 B22 =  0.14 B33 = -0.28 B12 =  0.00 B13 =  0.00 B23 =  0.00
 
Overall sigmaA parameters  : sigmaA0 =   0.876, B_sigmaA  =   7.579
Babinet"s scale for sigmaA : scale =    -0.001, B  =        150.000
SigmaA for partial structure  1: scale =   0.192, B  =  67.062
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.4054
Free R factor                        =     0.4353
Overall figure of merit              =     0.4264
-----------------------------------------------------------------------------
 
 
 U before setting    -1.10       0.698E-01   0.477      -0.521      -0.653       0.580
Atom     360 X    24SD                tends to have small eigenvalue. Reset it
Eigenvalues    -1.40      -0.340        1.19
 U after setting    0.162       0.381       0.700      -0.221      -0.304       0.490
Eigenvalues    0.253E-01   0.253E-01    1.19
 U before setting    0.278       0.443      -0.168      -0.953E-01  -0.310       0.899
Atom    1118 X    68SD                tends to have small eigenvalue. Reset it
Eigenvalues    0.237        1.16      -0.847
 U after setting    0.306       0.710       0.410      -0.181      -0.184       0.506
Eigenvalues    0.237        1.16       0.253E-01
 U before setting    0.534E-01   0.130       0.130E-01  -0.403       0.224E-01   0.208
Atom    1725 X   106SG                tends to have small eigenvalue. Reset it
Eigenvalues   -0.380       0.536       0.402E-01
 U after setting    0.218       0.308       0.743E-01  -0.231      -0.782E-01   0.104
Eigenvalues    0.253E-01   0.536       0.402E-01
 U before setting   -0.259        1.27       0.220E-01   0.298      -0.176      -0.172
Atom    3092 X   197SD                tends to have small eigenvalue. Reset it
Eigenvalues   -0.370        1.36       0.459E-01
 U after setting    0.783E-01    1.28       0.729E-01   0.251      -0.453E-01  -0.190
Eigenvalues    0.253E-01    1.36       0.459E-01
 U before setting    0.377       0.304       0.225       0.857E-01   0.317       0.256E-01
Atom    3109 X   198SD                tends to have small eigenvalue. Reset it
Eigenvalues    0.648       0.287      -0.282E-01
 U after setting    0.398       0.304       0.257       0.822E-01   0.291       0.298E-01
Eigenvalues    0.648       0.287       0.253E-01
 U before setting     1.22        6.70      -0.761      -0.230       0.432       0.627
Atom    3222 X   201FE                tends to have small eigenvalue. Reset it
Eigenvalues     1.31        6.76      -0.908
 U after setting     1.26        6.71       0.126      -0.213       0.243       0.548
Eigenvalues     1.31        6.76       0.253E-01
 U before setting     1.26        6.71       0.126      -0.213       0.243       0.548
Atom    3222 X   201FE                tends to have large eigenvalue. Reset it
Eigenvalues     1.31        6.76       0.253E-01
 U after setting     1.26        6.28       0.123      -0.199       0.245       0.514
 
 
     CGMAT cycle number =      5
 
    ****                Sphericity outliers                 ****
 
U values different from sphere >  10.00Sigma will be monitored
X  31 MET SD    U value= 0.3162 0.5346 0.8541-0.2206-0.3040 0.4897 Delta= 0.953 Sigma=  0.025
X  75 MET SD    U value= 0.4595 0.8641 0.5634-0.1809-0.1842 0.5055 Delta= 0.856 Sigma=  0.025
X 113 CYS SG    U value= 0.3723 0.4623 0.2282-0.2313-0.0782 0.1038 Delta= 0.411 Sigma=  0.025
X 204 MET SD    U value= 0.2322 1.4339 0.2268 0.2508-0.0453-0.1904 Delta= 1.081 Sigma=  0.025
X 205 MET SD    U value= 0.5520 0.4582 0.4114 0.0822 0.2912 0.0298 Delta= 0.442 Sigma=  0.025
X 300 HEM FE    U value= 1.4135 6.4377 0.2769-0.1985 0.2445 0.5140 Delta= 4.714 Sigma=  0.025
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1677     0.359     0.021
Bond distances: others                         1463     0.153     0.020
-------------------------------------------------------------------------------
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 
-----------------------------------------------------------------------------
Overall               : scale =   0.912, B  =   7.248
Babinet"s bulk solvent: scale =   0.717, B  = 200.000
Partial structure    1: scale =   1.327, B  =  57.527
Overall anisotropic scale factors
   B11 =  0.14 B22 =  0.14 B33 = -0.28 B12 =  0.00 B13 =  0.00 B23 =  0.00
 
Overall sigmaA parameters  : sigmaA0 =   0.737, B_sigmaA  =  12.562
Babinet"s scale for sigmaA : scale =    -0.001, B  =        150.000
SigmaA for partial structure  1: scale =   0.237, B  = 129.757
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.4781
Free R factor                        =     0.5144
Overall figure of merit              =     0.2655
-----------------------------------------------------------------------------
 
 
 U before setting   -0.713E-01   0.207       0.367       0.132      -0.305       0.868
Atom     360 X    24SD                tends to have small eigenvalue. Reset it
Eigenvalues    0.549E-01  -0.727        1.17
 U after setting    0.640E-01   0.523       0.668      -0.752E-01  -0.103       0.560
Eigenvalues    0.549E-01   0.253E-01    1.17
 U before setting    0.528       0.804       0.112E-01   0.195      -0.686      -0.489
Atom    1725 X   106SG                tends to have small eigenvalue. Reset it
Eigenvalues     1.37       0.505      -0.533
 U after setting    0.666       0.834       0.401       0.260      -0.454      -0.380
Eigenvalues     1.37       0.505       0.253E-01
 U before setting   -0.109        1.47      -0.632E-02   0.785      -0.385      -0.707
Atom    3092 X   197SD                tends to have small eigenvalue. Reset it
Eigenvalues   -0.474        2.10      -0.272
 U after setting    0.306        1.55       0.288       0.654      -0.272      -0.634
Eigenvalues    0.253E-01    2.10       0.253E-01
 U before setting    0.571      -0.418E-01   0.182       0.133       0.215      -0.715E-01
Atom    3109 X   198SD                tends to have small eigenvalue. Reset it
Eigenvalues    0.678      -0.121       0.154
 U after setting    0.583       0.674E-01   0.207       0.962E-01   0.197      -0.194E-01
Eigenvalues    0.678       0.253E-01   0.154
 
    ****                Sphericity outliers                 ****
 
U values different from sphere >  10.00Sigma will be monitored
X  31 MET SD    U value= 0.1558 0.6148 0.7596-0.0752-0.1029 0.5600 Delta= 0.927 Sigma=  0.025
X  75 MET SD    U value= 0.4208 0.9266 0.6560 0.0091-0.1916 0.3916 Delta= 0.713 Sigma=  0.025
X 113 CYS SG    U value= 0.7581 0.9257 0.4932 0.2597-0.4539-0.3799 Delta= 0.965 Sigma=  0.025
X 204 MET SD    U value= 0.3976 1.6437 0.3802 0.6544-0.2717-0.6338 Delta= 1.690 Sigma=  0.025
X 205 MET SD    U value= 0.6753 0.1592 0.2986 0.0962 0.1970-0.0194 Delta= 0.489 Sigma=  0.025
X 300 HEM FE    U value= 2.3823 2.3639 4.1402-0.3537 0.6849-0.0380 Delta= 1.809 Sigma=  0.025
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1677     0.647     0.021
Bond distances: others                         1463     0.404     0.020
-------------------------------------------------------------------------------
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 In resolution bins  21, i.e. between resolutions    53.452-   53.452 too few reflections
 
-----------------------------------------------------------------------------
Overall               : scale =   0.764, B  =  11.519
Babinet"s bulk solvent: scale =   0.758, B  = 200.000
Partial structure    1: scale =   1.070, B  =  71.476
Overall anisotropic scale factors
   B11 =  0.14 B22 =  0.14 B33 = -0.28 B12 =  0.00 B13 =  0.00 B23 =  0.00
 
Overall sigmaA parameters  : sigmaA0 =   0.713, B_sigmaA  =  20.639
Babinet"s scale for sigmaA : scale =    -0.001, B  =        150.000
SigmaA for partial structure  1: scale =   0.001, B  = 129.677
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.5496
Free R factor                        =     0.5494
Overall figure of merit              =     0.2655
-----------------------------------------------------------------------------

  (Q)QOPEN: file opened on unit  2      Status: UNKNOWN
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Logical Name: HKLOUT      Filename: refm01.mtz
<!--SUMMARY_END--></FONT></B>

 * Output Program Labels :
 
 H K L FP11 SIGFP11 FreeR_flag FC PHIC FWT PHWT DELFWT PHDELWT FOM
 
 * Output File Labels :
 
 H K L FP11 SIGFP11 FreeR_flag FC PHIC 2FOFCWT PH2FOFCWT FOFCWT PHFOFCWT FOM
 
 * Output File Column Types :
 
 H H H F Q I F P F P F P W
 
 HEADER INFORMATION FOR OUTPUT MTZ FILE ON INDEX  2
 
 * Title:
 
    Output mtz file from refmac
 
 * Number of Datasets =   1
 
 * Dataset ID, project name, dataset name, cell dimensions, wavelength:
 
        1 unknown
          unknown290800
             63.1670   63.1670  100.3780   90.0000   90.0000   90.0000
 
 
 * Number of Columns =  13
 
 * Number of Reflections =  33281
 
 * Missing value set to NaN in output mtz  file
 
 * There is no History information in this MTZ file
 
 * Column Labels, Types, Ranges [and Dataset IDs] :
 
 H                              H                    0                 42        1
 K                              H                    0                 29        1
 L                              H                    0                 66        1
 FP11                           F               1.4253          1583.6095        1
 SIGFP11                        Q               1.0318            54.8579        1
 FreeR_flag                     I               0.0000            19.0000        1
 FC                             F               0.0009          8352.2686        1
 PHIC                           P            -180.0000           180.0000        1
 2FOFCWT                        F               0.0001          3174.9519        1
 PH2FOFCWT                      P               0.0000           360.0000        1
 FOFCWT                         F               0.0000          3175.0449        1
 PHFOFCWT                       P               0.0000           360.0000        1
 FOM                            W               0.0000             1.0000        1
 
 * Cell Dimensions :
 
    63.1670   63.1670  100.3780   90.0000   90.0000   90.0000
 
 *  Resolution Range :
 
      0.00050     0.44465      (   44.666 -     1.500 A )
 
 * Sort Order :
 
      1     2     3     0     0
 
 * Number of Symmetry Operations =   8
 * Number of Primitive Operations =   8
 * Space Group =  96      P43212
 * Lattice Type = P
 * Point Group Name = PG422
 
 * Symmetry Operations :
 
 Symmetry  1     X,   Y,   Z
   1.00  0.00  0.00  0.00
   0.00  1.00  0.00  0.00
   0.00  0.00  1.00  0.00
   0.00  0.00  0.00  1.00
 Symmetry  2     -X,  -Y,   Z+1/2
  -1.00  0.00  0.00  0.00
   0.00 -1.00  0.00  0.00
   0.00  0.00  1.00  0.50
   0.00  0.00  0.00  1.00
 Symmetry  3     -Y+1/2,   X+1/2,   Z+3/4
   0.00 -1.00  0.00  0.50
   1.00  0.00  0.00  0.50
   0.00  0.00  1.00  0.75
   0.00  0.00  0.00  1.00
 Symmetry  4     Y+1/2,  -X+1/2,   Z+1/4
   0.00  1.00  0.00  0.50
  -1.00  0.00  0.00  0.50
   0.00  0.00  1.00  0.25
   0.00  0.00  0.00  1.00
 Symmetry  5     -X+1/2,   Y+1/2,  -Z+3/4
  -1.00  0.00  0.00  0.50
   0.00  1.00  0.00  0.50
   0.00  0.00 -1.00  0.75
   0.00  0.00  0.00  1.00
 Symmetry  6     X+1/2,  -Y+1/2,  -Z+1/4
   1.00  0.00  0.00  0.50
   0.00 -1.00  0.00  0.50
   0.00  0.00 -1.00  0.25
   0.00  0.00  0.00  1.00
 Symmetry  7     Y,   X,  -Z
   0.00  1.00  0.00  0.00
   1.00  0.00  0.00  0.00
   0.00  0.00 -1.00  0.00
   0.00  0.00  0.00  1.00
 Symmetry  8     -Y,  -X,  -Z+1/2
   0.00 -1.00  0.00  0.00
  -1.00  0.00  0.00  0.00
   0.00  0.00 -1.00  0.50
   0.00  0.00  0.00  1.00
 
 
  Time in seconds: CPU =       171.35
             Elapsed =         178.00
 
    **** Things for loggraph, R factor and others vs cycle  ****
 
 
$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:Geometry vs cycle:N:1,5,6,7:
$$
Ncyc Rfact Rfree  FOM rmsBOND rmsANGLE rmsCHIRAL $$
$$
         1   0.250   0.287    0.746    0.031    2.362    0.156
         2   0.262   0.319    0.668    0.116    5.956    0.457
         3   0.330   0.339    0.631    0.119    6.384    0.387
         4   0.405   0.435    0.426    0.228   11.443    0.809
         5   0.478   0.514    0.266    0.359   18.983    1.322
         6   0.550   0.549    0.266    0.647   31.034    2.491
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac_5.0.32:  End of Refmac_5.0.32
 Times: User:     205.5s System:    3.2s Elapsed:    3:36
</pre>
<!--SUMMARY_END--></FONT></B>
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<!--SUMMARY_END--></FONT></B>