private byte[] sign(byte[] pdf, Certificate certificate, PrivateKey privateKey) throws KeyStoreException, IOException, NoSuchAlgorithmException, CertificateException, UnrecoverableKeyException, DocumentException, XmlDSignException, InternalCryptoException {
Certificate[] chain = new Certificate[] {certificate};

PdfReader reader = new PdfReader(pdf);
ByteArrayOutputStream out = new ByteArrayOutputStream();
PdfStamper stp = PdfStamper.createSignature(reader, out, '\0');
PdfSignatureAppearance sap = stp.getSignatureAppearance();

sap.setCrypto(privateKey, chain, null, PdfName.ADOBE_CryptoProPDF);
sap.setReason("I'm the author");
sap.setLocation("Lisbon");
// comment next line to have an invisible signature
sap.setVisibleSignature(new Rectangle(100, 100, 200, 200), 1, null);
stp.close();

return out.toByteArray();
}

private byte[] a(byte[] pdf, X509Certificate certificate, PrivateKey privateKey) throws KeyStoreException, IOException, NoSuchAlgorithmException, CertificateException, UnrecoverableKeyException, DocumentException, XmlDSignException, InternalCryptoException, CryptoDataException {
PdfReader reader = new PdfReader(pdf);
ByteArrayOutputStream out = new ByteArrayOutputStream();
PdfStamper st = PdfStamper.createSignature(reader, out, '\0');

PdfSignatureAppearance sap = st.getSignatureAppearance();

X509Certificate[] chain = new X509Certificate[] {certificate};

sap.setCrypto(null, chain, null, null);
sap.setReason("I like to sign");
sap.setLocation("Universe");
sap.setAcro6Layers(true);
sap.setRender(PdfSignatureAppearance.SignatureRenderNameAndDescription);
sap.setSignDate(new GregorianCalendar());

// Выбираем подходящий тип фильтра
PdfName filterName = new PdfName("CryptoPro#20PDF");

// Создаем подпись
PdfSignature dic = new PdfSignature(filterName, PdfName.ADBE_PKCS7_DETACHED);
dic.setDate(new PdfDate(sap.getSignDate()));
dic.setName(PdfPKCS7.getSubjectFields(chain[0]).getField("CN"));
if (sap.getReason() != null) {
dic.setReason(sap.getReason());
}
if (sap.getLocation() != null) {
dic.setLocation(sap.getLocation());
}
sap.setCryptoDictionary(dic);

int intCSize = 100000;
HashMap<PdfName, Integer> hashtable = new HashMap<PdfName, Integer>();
hashtable.put(PdfName.CONTENTS, intCSize * 2 + 2);
sap.preClose(hashtable);

// Вычисляем подпись

byte[] pk = cryptoService.signData(IOUtils.toByteArray(sap.getRangeStream()), certificate.getEncoded(), null, null);

// Помещаем подпись в документ
PdfDictionary dic2 = new PdfDictionary();
byte[] outc = Arrays.copyOf(pk, pk.length);
dic2.put(PdfName.CONTENTS, new PdfString(outc).setHexWriting(true));
sap.close(dic2);

return out.toByteArray();
}

Error during signature verification.

Signature contains incorrect, unrecognized, corrupted or suspicious data.
Support Information: SigDict /Contents illegal data

Simple35CS.exe Pdf.Sign not_signed.pdf "тут имя сертификата (DN)"