I don't really understand what you want and the example solution throws away
quite a lot of data, so consider this alternative:
data.out2 <- read.table(textConnection("id ? rater.1 n.1 ? rater.2 n.2
rater.3 n.3 ? rater.4 n.4
11 ? 11 0.1183333 ?79 ? ? ? ?NA ?NA ? ? ? ?NA ?NA ? ? ? ?NA ?NA
114 114 0.2478709 113 ? ? ? ?NA ?NA ? ? ? ?NA ?NA ? ? ? ?NA ?NA
12 ? 12 0.3130655 ?54 0.3668242 ?54 ? ? ? ?NA ?NA ? ? ? ?NA ?NA
121 121 0.2400000 331 ? ? ? ?NA ?NA ? ? ? ?NA ?NA ? ? ? ?NA ?NA
122 122 0.3004164 ?25 0.1046278 ?25 0.2424871 ?25 0.2796937 ?25
125 125 0.1634865 190 ? ? ? ?NA ?NA ? ? ? ?NA ?NA ? ? ? ?NA ?NA"), header=T,
stringsAsFactors=F)