Website disconnect to DB leads to ERROR 500

Upgraded to PHP 5.5 and MySQL 5.6 - Now and then server disconnects to DataBase. Need Help. Here is SQL Err Log:-

Version: '5.6.29'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MySQL Community Server (GPL)
160229 14:20:36 mysqld_safe Number of processes running now: 0
160229 14:20:36 mysqld_safe mysqld restarted
2016-02-29 14:20:36 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2016-02-29 14:20:36 0 [Note] /usr/sbin/mysqld (mysqld 5.6.29) starting as process 19086 ...
2016-02-29 14:20:36 19086 [Note] Plugin 'FEDERATED' is disabled.
2016-02-29 14:20:36 19086 [Note] InnoDB: Using atomics to ref count buffer pool pages
2016-02-29 14:20:36 19086 [Note] InnoDB: The InnoDB memory heap is disabled
2016-02-29 14:20:36 19086 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2016-02-29 14:20:36 19086 [Note] InnoDB: Memory barrier is not used
2016-02-29 14:20:36 19086 [Note] InnoDB: Compressed tables use zlib 1.2.3
2016-02-29 14:20:36 19086 [Note] InnoDB: Using Linux native AIO
2016-02-29 14:20:36 19086 [Note] InnoDB: Using CPU crc32 instructions
2016-02-29 14:20:36 19086 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2016-02-29 14:20:36 19086 [Note] InnoDB: Completed initialization of buffer pool
2016-02-29 14:20:36 19086 [Note] InnoDB: Highest supported file format is Barracuda.
2016-02-29 14:20:36 19086 [Note] InnoDB: The log sequence numbers 861036126 and 861036126 in ibdata files do not match the log sequence number 861341205 in the ib_logfiles!
2016-02-29 14:20:36 19086 [Note] InnoDB: Database was not shutdown normally!
2016-02-29 14:20:36 19086 [Note] InnoDB: Starting crash recovery.
2016-02-29 14:20:36 19086 [Note] InnoDB: Reading tablespace information from the .ibd files...
2016-02-29 14:20:36 19086 [Note] InnoDB: Restoring possible half-written data pages
2016-02-29 14:20:36 19086 [Note] InnoDB: from the doublewrite buffer...
2016-02-29 14:20:36 19086 [Note] InnoDB: 128 rollback segment(s) are active.
2016-02-29 14:20:36 19086 [Note] InnoDB: Waiting for purge to start
2016-02-29 14:20:36 19086 [Note] InnoDB: 5.6.29 started; log sequence number 861341205
2016-02-29 14:20:36 19086 [Note] Server hostname (bind-address): '*'; port: 3306
2016-02-29 14:20:36 19086 [Note] IPv6 is not available.
2016-02-29 14:20:36 19086 [Note]   - '0.0.0.0' resolves to '0.0.0.0';
2016-02-29 14:20:36 19086 [Note] Server socket created on IP: '0.0.0.0'.
2016-02-29 14:20:36 19086 [Note] Event Scheduler: Loaded 0 events
2016-02-29 14:20:36 19086 [Note] /usr/sbin/mysqld: ready for connections.
Website disconnect to DB leads to ERROR 500

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