I'm not familiar with this output (XDS?) but I would guess Rw-lin
(not Rw-pim or rim, although those are theoretically more useful)
is the R-factor to use for Rsym (or Rmerge if you are merging datasets
previously reduced from multiple crystals).
I think "observed" means, out of all the spots that you "measured", those
that pass your criterion for being observed and were actually used in
data processing, so I think the numbers here apply.
"R-free error" depends on the number of reflections set aside for the "free"
set, so you can't get it at this stage. After choosing a free set and refining your
structure, you can use CNS xtal_pdbsubmission.inp or sum such to give this and other
statistics.
so: 0.1797, NULL, and "don't know".
james09 pruza wrote:
> Dear All CCP4bbers,
>
> Please help me in finding *R-sym I *(observed), *R-merge I*(obseved),
> *R-Free Error i*n the data provided below. If I am not wrong, Can anyone
> suggest me the difference between R-sym and R-merge?
>
> Thanks in advance for the help.
>
> James*
> *
>
> R-values of internal consistency :
> ======== --------------------
> (Anomalous scaling counts I+ and I- as separate hkl.)
>
> R-merge ( sum |Ij-<I>| / sum |<I>| ) = 23.4 % ( 21.57 % for Fsq > 0)
> where <I>=sum(Ij)/N, j=1...N,
> calculated from 188629 observations of 60655 /+//-/ reflexions
>
> - dito within user-defined resolution: 23.4 %
> calculated from 188182 observations of 60508 /+//-/ reflexions
>
>
> Sigma-weighted R-merge :
> ( sum wj*|Ij-<I>| / sum |<I>| ) = 19.1 %
> where <I>=sum(wj*Ij), j=1...N,
> with sum(wj)=1,
> calculated from 133636 observations of 60655 /+//-/ reflexions
>
> - dito within user-defined resolution: 19.1 %
> calculated from 133323 observations of 60508 /+//-/ reflexions
>
>
> Multiplicity of accepted measurements for unique reflexions, and
> completeness C
> in equal-volume shells (on average 4161 possible unique reflexions each):
> Shell- 1* 2* 3* 4* 5-6* 7-8* 9-12* 13-16* >16*
> total C[%]
> limits [A] ----- ----- ----- ----- ----- ----- ----- ----- -----
> ----- ----
> inf. - 30.0 excluded... (but see right
> below) 0.0
> 30.0 - 6.46 221 878 805 1620 597 0 0 0 0
> 4121 95.1
> 6.46 - 5.13 73 659 726 1850 840 0 0 0 0
> 4148 98.9
> 5.13 - 4.48 80 687 841 1823 712 0 0 0 0
> 4143 99.1
> 4.48 - 4.07 72 673 802 1778 772 0 0 0 0
> 4097 99.3
> 4.07 - 3.78 94 595 735 1862 831 0 0 0 0
> 4117 99.4
> 3.78 - 3.56 108 563 738 1883 856 0 0 0 0
> 4148 99.7
> 3.56 - 3.38 81 519 689 1968 886 0 0 0 0
> 4143 99.8
> 3.38 - 3.23 49 465 731 1976 877 0 0 0 0
> 4098 100.0
> 3.23 - 3.11 58 485 772 1950 875 0 0 0 0
> 4140 100.0
> 3.11 - 3.00 39 457 768 1944 832 0 0 0 0
> 4040 98.8
> - - - - - - ----- ----- ----- ----- ----- ----- ----- ----- -----
> ----- ----
> * 30.0 - 3.00 875 5981 7607 18654 8078 0 0 0 0
> 41195 99.0
> ----------- ----- ----- ----- ----- ----- ----- ----- ----- -----
> ----- ----
> Below specified lower-resolution limit :
> inf. - 30.0 0 1 0 0 0 0 0 0 0 1
> Beyond specified high-resolution limit :
> 3.00 - 2.99 0 37 25 51 9 0 0 0 0 122
>
> Same multiplicities as relative percentages [%] and <average multiplicity>
> (total measured unique reflexions in each shell = 100.%)
> 30.0 - 6.46 5.4 21.3 19.5 39.3 14.5 . . . . <3.38>
> 6.46 - 5.13 1.8 15.9 17.5 44.6 20.3 . . . . <3.67>
> 5.13 - 4.48 1.9 16.6 20.3 44.0 17.2 . . . . <3.58>
> 4.48 - 4.07 1.8 16.4 19.6 43.4 18.8 . . . . <3.61>
> 4.07 - 3.78 2.3 14.5 17.9 45.2 20.2 . . . . <3.67>
> 3.78 - 3.56 2.6 13.6 17.8 45.4 20.6 . . . . <3.68>
> 3.56 - 3.38 2.0 12.5 16.6 47.5 21.4 . . . . <3.74>
> 3.38 - 3.23 1.2 11.3 17.8 48.2 21.4 . . . . <3.78>
> 3.23 - 3.11 1.4 11.7 18.6 47.1 21.1 . . . . <3.76>
> 3.11 - 3.00 1.0 11.3 19.0 48.1 20.6 . . . . <3.77>
> - - - - - - ----- ----- ----- ----- ----- ----- ----- ----- ----- ->>>
> * 30.0 - 3.00 2.1 14.5 18.5 45.3 19.6 0.0 0.0 0.0 0.0
> 100. <3.66>
> ----------- ----- ----- ----- ----- ----- ----- ----- ----- -----
> ==== ------
> Below specified lower-resolution limit :
> inf. - 30.0 . 100.0 . . . . . . . <2.00>
> Beyond specified high-resolution limit :
> 3.00 - 2.99 . 30.3 20.5 41.8 7.4 . . . . <3.27>
>
>
> Multiplicity of centric measurements
> Shell- 1* 2* 3* 4* 5-6* 7-8* 9-12* >13* total /
> poss. C[%]
> limits [A] ----- ----- ----- ----- ----- ----- ----- ----- -----
> ----- ----
> 30.0 - 6.46 93 354 32 2 0 0 0 0 481
> 566 85.0
> 6.46 - 5.13 37 251 28 0 0 0 0 0 316
> 334 94.6
> 5.13 - 4.48 39 209 16 0 0 0 0 0 264
> 281 94.0
> 4.48 - 4.07 24 193 17 0 0 0 0 0 234
> 249 94.0
> 4.07 - 3.78 25 169 21 0 0 0 0 0 215
> 223 96.4
> 3.78 - 3.56 34 161 18 0 0 0 0 0 213
> 220 96.8
> 3.56 - 3.38 25 157 17 0 0 0 0 0 199
> 204 97.5
> 3.38 - 3.23 26 145 21 0 0 0 0 0 192
> 192 100.0
> 3.23 - 3.11 26 138 23 0 0 0 0 0 187
> 187 100.0
> 3.11 - 3.00 27 129 19 0 0 0 0 0 175
> 175 100.0
> - - - - - - ----- ----- ----- ----- ----- ----- ----- ----- -----
> ----- ----
> * 30.0 - 3.00 356 1906 212 2 0 0 0 0 2476
> 2631 94.1
>
>
> Multiplicity of acentric measurements for Bijvoet /-/ and /+/ separately :
> Shell- 1* 2* 3* 4* 5-6* 7-8* 9-12* >13* total /
> poss. C[%]
> limits [A] ----- ----- ----- ----- ----- ----- ----- ----- -----
> ----- ----
> 30.0 - 6.46 1530 4572 790 0 0 0 0 0 6892
> 7534 91.5
> 6.46 - 5.13 1503 4925 1077 0 0 0 0 0 7505
> 7720 97.2
> 5.13 - 4.48 1786 4813 974 0 0 0 0 0 7573
> 7796 97.1
> 4.48 - 4.07 1811 4668 1066 0 0 0 0 0 7545
> 7754 97.3
> 4.07 - 3.78 1686 4685 1209 0 0 0 0 0 7580
> 7834 96.8
> 3.78 - 3.56 1756 4595 1308 0 0 0 0 0 7659
> 7882 97.2
> 3.56 - 3.38 1785 4558 1407 0 0 0 0 0 7750
> 7896 98.2
> 3.38 - 3.23 1784 4527 1425 0 0 0 0 0 7736
> 7812 99.0
> 3.23 - 3.11 1833 4549 1415 0 0 0 0 0 7797
> 7908 98.6
> 3.11 - 3.00 1819 4405 1420 0 0 0 0 0 7644
> 7826 97.7
> - - - - - - ----- ----- ----- ----- ----- ----- ----- ----- -----
> ----- ----
> * 30.0 - 3.00 17293 46297 12091 0 0 0 0 0 75681
> 77962 97.1
>
>
> Anomalous R-value :
> ( sum |<I+>-<I->| / sum |<I+>+<I->| ) = 17.5 %
> where <I>=sum(Ij)/N,
> calculated from 37074 anomalous pairs (with 143188 measurements:
> multiplicity 2.1 <-> 78993
> measurements for I+
> multiplicity 1.7 <-> 64195
> measurements for I-
> Weighted anomalous R-value :
> ( sum |<I+>-<I->| / sum |<I+>+<I->| ) = 18.4 %
> where <I>=sum(wj*Ij) with sum(wj)=1,
> calculated from 37074 anomalous pairs
>
>
> Table of s-dependent anomalous, and centric, R-factors in equal-volume
> shells :
> R_ano. = sum { |<I+> - <I->| } / sum { |<I+> + <I->| }
> R_cen. = linear R_merge for centric reflexions only.
> centric
> Resolution s Bijvoet-pairs <I> R_ano.
> measurements R_cen.
> -----[A]---- ------------- ------- --[%]-- |
> ------- --[%]--
> 30.0 - 6.46 0.000 - 0.077 3252 10168. 12.79 |
> 806 29.64
> 6.46 - 5.13 0.077 - 0.097 3673 2734. 15.19 |
> 564 20.88
> 5.13 - 4.48 0.097 - 0.112 3694 4719. 16.01 |
> 440 24.88
> 4.48 - 4.07 0.112 - 0.123 3682 4326. 17.18 |
> 418 23.54
> 4.07 - 3.78 0.123 - 0.132 3678 2602. 19.76 |
> 375 27.71
> 3.78 - 3.56 0.132 - 0.141 3724 1490. 22.87 |
> 337 29.09
> 3.56 - 3.38 0.141 - 0.148 3806 1032. 26.32 |
> 317 34.76
> 3.38 - 3.23 0.148 - 0.155 3830 728. 31.24 |
> 317 35.64
> 3.23 - 3.11 0.155 - 0.161 3844 470. 38.98 |
> 292 47.76
> 3.11 - 3.00 0.161 - 0.167 3779 358. 48.06 |
> 250 59.71
> - - - - - - -------- ------- ------- |
> ------- --[%]--
> * 30.0 - 3.00 total : 36962 2745. 17.45% |
> 4116 28.09%
> -------- ------- ------- -------
> Below specified lower-resolution limit :
> inf. - 30.0 0.000 - 0.017 1 110. 19.20 | 0
> Beyond specified high-resolution limit :
> 3.00 - 2.99 0.167 - 0.167 111 340. 44.46 | 0
>
> Summary of neg. <I> : 179 centric reflexions
> 2886 /I-/
> 2594 /I+/
> including 0 pairs with *both* mates <=0
>
>
> Tables of s-dependent R-factors in equal-volume shells :
> (Single measurements or negative <I> omitted from all sums.)
> R_linear = sum { |I - <I>| } / sum {I}
> R_square = SQRT( sum{|I - <I>|**2} / sum{I**2} )
>
> Resolution s measurements I<0 <I> <I/s> R_squ. R_lin.
> -----[A]---- ------------- -------- ----- ------- -----
> --[%]-- --[%]--
> 30.0 - 6.46 0.000 - 0.077 12293 119 10081. 5.2
> 27.28 18.23
> 6.46 - 5.13 0.077 - 0.097 13386 394 2490. 2.7
> 19.45 18.50
> 5.13 - 4.48 0.097 - 0.112 12787 359 4220. 3.0
> 21.40 18.89
> 4.48 - 4.07 0.112 - 0.123 12670 452 3638. 2.5
> 21.79 21.21
> 4.07 - 3.78 0.123 - 0.132 12819 799 2102. 1.6
> 23.85 26.60
> 3.78 - 3.56 0.132 - 0.141 12820 940 1335. 1.1 26.50
> 32.14
> 3.56 - 3.38 0.141 - 0.148 12270 1186 958. 0.9
> 30.64 37.29
> 3.38 - 3.23 0.148 - 0.155 12071 1438 661. 0.6
> 36.79 44.73
> 3.23 - 3.11 0.155 - 0.161 11613 1619 463. 0.5
> 43.91 53.68
> 3.11 - 3.00 0.161 - 0.167 10870 1708 376. 0.4
> 51.01 61.37
> - - - - - - ------ ------ ------- -----
> ------- -------
> * 30.0 - 3.00 total : 123599 9014 2674. 1.9
> 26.11% 22.61%
> ------
> ------ =======
> 4515 non-pos. <I> with 9771 measurements omitted from this table.
>
> Table of <<I>/sigma(<I>)> for mean values on output file:
> ================
> Resolution <I> /0/ /+/ /-/ sig<0
> -----[A]---- ------------- ------------- -------------
> ------------- -----
> 30.0 - 6.46 4121 7.7 481 4.5 3551 5.8 3341
> 5.7 0
> 6.46 - 5.13 4148 4.6 316 2.5 3797 3.5 3708
> 3.2 0
> 5.13 - 4.48 4143 5.0 264 2.6 3838 3.8 3735
> 3.5 0
> 4.48 - 4.07 4097 4.3 234 2.1 3835 3.2 3710
> 3.0 0
> 4.07 - 3.78 4117 3.0 215 1.7 3863 2.2 3717
> 2.1 0
> 3.78 - 3.56 4148 2.2 213 1.6 3915 1.6 3744
> 1.5 0
> 3.56 - 3.38 4143 1.6 199 1.3 3938 1.2 3812
> 1.1 0
> 3.38 - 3.23 4098 1.2 192 0.9 3896 0.8 3840
> 0.8 0
> 3.23 - 3.11 4140 0.8 187 0.5 3946 0.6 3851
> 0.6 0
> 3.11 - 3.00 4040 0.6 175 0.4 3853 0.4 3791
> 0.4 0
> - - - - - - ------------- ------------- -------------
> ------------- -----
> * 30.0 - 3.00 41195 3.1 2476 2.2 38432 2.3 37249
> 2.1 0
> ------------- ------------- -------------
> ------------- -----
> Below specified lower-resolution limit :
> inf. - 30.0 1 -1.0 0 ... 1 -0.2 1
> -1.0 0
> Beyond specified high-resolution limit :
> 3.00 - 2.99 122 0.6 10 0.6 112 0.4 111
> 0.4 0
>
> Multiplicity-independent and sigma-weighted R-factors :
> PCV = "pooled coefficient of variation"
> R_rim = "redundancy-independent merging R-factor" = R_meas.
> R_pim = "precision-indicating merging R-factor"
> Rw_xxx = sigma-weighted R-factors, where :
> <Iw> = sum{ w * I } with sum{ w } = 1
> .. defined as:
> PCV = sum{ SQRT[ sum{ |Ij - <Ihkl>|**2 }/(n-1) ] } / sum{ <I> }
> h j h
> R_rim = sum{ SQRT[n/(n-1)] * sum{ |I - <Ihkl>| } } / sum{ I }
> R_pim = sum{ SQRT[1/(n-1)] * sum{ |I - <Ihkl>| } } / sum{ I } )
> Rw_rim = sum{ SQRT[n/(n-1)] * sum{ w * |I - <Iw>| } } / sum{<Iw>}
> Rw_pim = sum{ SQRT[1/(n-1)] * sum{ w * |I - <Iw>| } } / sum{<Iw>}
> Rw_squ = SQRT[ sum{ w * |I - <Iw>|**2 } / sum{<Iw>**2} ]
> Rw_lin = sum{ w * |I - <Iw>| } / sum{<Iw>}
>
> Resolution /+//-/ PCV R_rim R_pim Rw_rim Rw_pim
> Rw_squ. Rw_lin.
> -----[A]---- -------- --[%]-- --[%]-- --[%]-- --[%]-- --[%]--
> --[%]-- --[%]--
> 30.0 - 6.46 5734 25.53 24.98 16.99 13.73 9.41
> 11.97 9.96
> 6.46 - 5.13 6143 25.77 25.31 17.18 22.87 15.69
> 15.44 16.57
> 5.13 - 4.48 5903 26.43 25.94 17.69 21.78 14.98
> 15.39 15.75
> 4.48 - 4.07 5800 29.69 29.07 19.78 25.73 17.66
> 18.16 18.65
> 4.07 - 3.78 5810 36.85 36.38 24.69 32.42 22.21
> 20.15 23.54
> 3.78 - 3.56 5768 44.37 43.66 29.37 40.40 27.53
> 25.67 29.44
> 3.56 - 3.38 5475 51.15 50.32 33.56 46.70 31.61
> 30.79 34.22
> 3.38 - 3.23 5375 61.60 60.34 40.23 56.21 38.02
> 37.98 41.20
> 3.23 - 3.11 5175 73.50 72.31 48.10 66.85 45.19
> 46.53 49.03
> 3.11 - 3.00 4833 83.97 82.72 55.07 77.06 52.10
> 57.35 56.51
> --------- ------- ------- ------- ------- -------
> ------- -------
> * total : 56016 31.39% 30.88% 20.91% 24.72% 16.90%
> 13.95% 17.97%
