You can also deploy the contract using the contract instance. Consider the following example of deploying a contract in both v0.2x.x and v1.x.x to understand more:

var bytecode = output.contracts["HelloWorld"].bytecode;
var abi = output.contracts["HelloWorld"].interface;

// For v0.2x.x
var helloworldContract = web3.eth.contract(abi); 
var helloworld = helloworldContract.new({
      from: "0xce5C2D181f6DD99091351f6E6056c333A969AEC9",      
      data: byteCode,      
      gas: 4700000    
}, function (e, contract){     
    if (typeof contract.address !== "undefined") {          
        console.log("address: " + contract.address);     
    }  
});

// For v1.x.x
var helloWorld = new web3.eth.Contract(abi);
helloWorld.deploy({
    data: byteCode,
    arguments: [] // Constructor arguments
})
.send({
    from: "0x1234567890123456789012345678901234567891",
    gas: 4700000
})
.on("error", function(error){ 
    console.error(error); 
})
.on("receipt", function(receipt) {
   console.log(receipt.contractAddress);
});

For larger contracts, you may have to increase the gas amount for execution. This can be estimated with the contract instance:

// For v0.2x.x
var gas = web3.eth.estimateGas({
    data: byteCode
});
console.log(gas);

// For v1.x.x
helloWorld.deploy({     
    data: byteCode,     
    arguments: [] 
}) 
.estimateGas(function(err, gas){     
    console.log(gas); 
});