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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>
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