[edit: remove junk text at the end]
lsim() wants the input to be the time domain signal. You are passing the frequency domain signal Xs to lsim(). Maybe fixing that will help. I encourage you to think about the frequencies you are using to define the pole and zero locations, and the time vector you pass to lsim(). You define the pole-zero locations with frequencies of 1000 and 5000 Hz. But the time vector, t, which you pass to lsim() is [0,1,2,3,...], which implies a sampling rate of 1 Hz. A 1 Hz-sampled signal does not cotain power at any frequencies above 0.5 Hz. To address the mismatch between the implied sampling rate and the desired filter frequencies, adjust the time vector, which should be t=[0,1,2,...]/fs; where fs=sampling rate in Hz. You define vectors f and w, but you do not do anything with them. What was your goal for those vectors?
Your code and your written description of hte notch filter mention two frequencies, 1 and 5 kHz. Do you want two sharp notch filters - one at 1 kHz and one at 5 kHz? Or do you want a "wide" notch (i.e. a band-stop) covering 1 to 5 kHz? Your poles and zeros suggest two sharp notches, but you only mention one notch filter in your text.
I am not sure why you want to use lsim(). I wouldn't. I would start with a standard filter routine. If it produces unacceptable resuts - and that can happen, especially with higher order filters - then try something else. Here is a notch filter at 1 kHz, designed and then applied to the signal
x=load('mysignal.txt'); % load audio signal file saved as text file
fs=44.1e3; % specify sampling rate (Hz)
bsFilter = designfilt('bandstopfir', ... % response type
'FilterOrder',102, ... % filter order
'PassbandFrequency1',900, ... % band edge
'StopbandFrequency1',950, ... % band edge
'StopbandFrequency2',1050, ... % band edge
'PassbandFrequency2',1100, ... % band edge
'SampleRate',fs) % sampling rate
y = filter(bsFilter,x);
I used an FIR filter above, since FIR filters often give nicer results four audio, due to their linear phase response (i.e. all frequencies experience equal delay). I used order=52 because a sharp notch requires a high order.
If you also want a notch at 5 kHz, then create another bandstop filter, and pass the already-filtered signal through it.
