Table 1. List of parameters in the model and of their values.

Binding energies are expressed in units of $k_{B}T$, and times in days (d) or hours (h). The last nine parameters were inferred within selection variant (C), except ${ϵ}_{\text{Ag}}$, whose reported value refers to variant (A), which includes Ag-binding selection.

Values of model parameters
Symbol	Value	Meaning	Source
$T_{\text{turn}}$	12 h	Duration of an evolution turn	Wang et al., 2015
$T_{\text{GC}}$	6 d	Time for GC formation after injection	De Silva and Klein, 2015; Jacob et al., 1993; McHeyzer-Williams et al., 1993
$N_{\max }$	2500	GC max population size	Eisen, 2014; Tas et al., 2016
$N_i$	2500	Initial GC population size	Eisen, 2014; Tas et al., 2016
$N_{\text{found}}$	100	Number of GC founder clones	Tas et al., 2016; Mesin et al., 2016
$p_{\text{diff}}$	10%	Probability of differentiation	Wang et al., 2015; Meyer-Hermann et al., 2012; Oprea and Perelson, 1997
${\tau }_{\text{diff}}$	11 d	Switch time in MC/PC differentiation	Weisel et al., 2016
$\mathrm{\Delta }{\tau }_{\text{diff}}$	2 d	Switching timescale in MC/PC differentiation	Weisel et al., 2016
$p_{\text{mut}}$	14%	Prob. of mutation per division	Wang et al., 2015; McKean et al., 1984; Kleinstein et al., 2003
$p_{\text{s}},p_{\text{l}},p_{\text{aa}}$	50%, 30%, 20%	Probability of a mutation to be silent/lethal/affinity-affecting	Zhang and Shakhnovich, 2010; Wang et al., 2015; Wang, 2017
$K_{\text{aa}}(\mathrm{\Delta }ϵ)$	Equation 18	Distribution of affinity-affecting mutations	Ovchinnikov et al., 2018
$k^{+}$	0.98 /d	Ag release rate	MacLean et al., 2001
$k_{\mathrm{\varnothing }}^{-}$	${\displaystyle 1.22\times {10}^{-2}/\mathrm{d}}$	Ag decay rate	Tew and Mandel, 1979
$a$	0.12	Baseline selection success probability	Max-likelihood fit
$b$	0.66	Baseline selection failure probability	Max-likelihood fit
${\mu }_{\text{naive}}$	-14.60	Mean binding energy of seeder clones generated by naive precursors	Max-likelihood fit
${\sigma }_{\text{naive}}$	1.66	Standard deviation of the seeder clones binding energy distribution	Max-likelihood fit
$k_B^{-}$	$2.07\times {10}^{-5}/\mathrm{d}$	Ag consumption rate per B-cell	Max-likelihood fit
$\alpha$	${\displaystyle 2.3\times {10}^{-2}\mu \mathrm{g}}$	Concentration to dosage conversion factor	Max-likelihood fit
$g_{\text{recall}}$	0.56	MC fraction in Ab-SC population for measurement 1 day after boost	Max-likelihood fit
$g_{\text{imm}}$	0	MC fraction in Ab-SC population for measurement 4 days after second injection	Max-likelihood fit
${ϵ}_{\text{Ag}}$	-13.59	Threshold Ag binding energy ${}^{(A)}$	Max-likelihood fit