Could you post the log from trying flashtool?
28/021/2017 21:21:03 - INFO - Device connected in flash mode 28/021/2017 21:21:23 - INFO - Selected Bundle for Sony Xperia X(F5121). FW release : 4.0.A.2.301_R8A. Customization : Customized TW 28/021/2017 21:21:23 - INFO - Preparing files for flashing 28/021/2017 21:21:48 - INFO - Please connect your device into flashmode. 28/021/2017 21:21:49 - INFO - Opening device for R/W 28/021/2017 21:21:49 - INFO - Device ready for R/W. 28/021/2017 21:21:49 - INFO - Reading device information 28/021/2017 21:21:49 - INFO - Phone ready for flashmode operations. 28/021/2017 21:21:49 - INFO - Opening TA partition 2 28/021/2017 21:21:49 - INFO - Current device : F5121 - CB512EFM5U - 1302-4771_R8A - 1300-4911_34.0.A.2.301 - GENERIC_34.0.A.2.301 28/021/2017 21:21:49 - INFO - Closing TA partition 28/021/2017 21:21:49 - INFO - Start Flashing 28/021/2017 21:21:49 - INFO - No loader in the bundle. Searching for one 28/021/2017 21:21:49 - INFO - No matching loader found 28/021/2017 21:21:49 - WARN - No loader found or set manually. Skipping loader 28/021/2017 21:21:49 - INFO - Loader : S1_Root_d553 - Version : 1299-4841_S1_Boot_MSM8956_LA1.0.1_73 / Boot version : 1299-4841_S1_Boot_MSM8956_LA1.0.1_73 / Bootloader status : ROOTABLE 28/021/2017 21:21:49 - INFO - Max packet size set to 4M 28/021/2017 21:21:49 - INFO - USB buffer size set to 512K 28/021/2017 21:21:50 - INFO - Parsing boot delivery 28/021/2017 21:21:52 - INFO - Found a template session. Using it : /home/arto/.flashTool/firmwares/prepared/F5121_4.0.A.2.301.fsc 28/021/2017 21:21:52 - INFO - Set loader configuration : [00 01 00 00 00 0C] 28/021/2017 21:21:52 - INFO - Opening TA partition 2 28/021/2017 21:21:52 - INFO - Writing TA unit 00002774. Value : 01 28/021/2017 21:21:52 - INFO - Closing TA partition 28/021/2017 21:21:55 - INFO - Processing partition.sin 28/021/2017 21:21:55 - INFO - Checking header 28/021/2017 21:21:55 - INFO - Flashing data 28/021/2017 21:21:55 - INFO - Opening TA partition 2 28/021/2017 21:21:55 - INFO - Processing cmnlib_S1_Boot_MSM8956_LA1_0_1_73_AID_4_PLATFORM-LOIRE-COM-LIVE-HWID009B00E1-SWID0C-APPID01-OEM1-AID4-DEBUG00_S1-BOOT-LIVE-D553-0004-MMC.sin 28/021/2017 21:21:55 - INFO - Checking header 28/021/2017 21:21:55 - INFO - Flashing data 28/021/2017 21:21:55 - INFO - Processing emmc_appsboot_S1_Boot_MSM8956_LA1_0_1_73_AID_4_PLATFORM-LOIRE-COM-LIVE-HWID009B00E1-SWID09-OEM1-AID4-DEBUG00_S1-BOOT-LIVE-D553-0004-MMC.sin 28/021/2017 21:21:55 - INFO - Checking header 28/021/2017 21:21:55 - INFO - Flashing data 28/021/2017 21:21:55 - INFO - Processing hyp_S1_Boot_MSM8956_LA1_0_1_73_AID_4_PLATFORM-LOIRE-COM-LIVE-HWID009B00E1-SWID15-OEM1-AID4-DEBUG00_S1-BOOT-LIVE-D553-0004-MMC.sin 28/021/2017 21:21:55 - INFO - Checking header 28/021/2017 21:21:55 - INFO - Flashing data 28/021/2017 21:21:55 - INFO - Processing keymaster_S1_Boot_MSM8956_LA1_0_1_73_AID_4_PLATFORM-LOIRE-COM-LIVE-HWID009B00E1-SWID0C-APPID01-OEM1-AID4-DEBUG00_S1-BOOT-LIVE-D553-0004-MMC.sin 28/021/2017 21:21:55 - INFO - Checking header 28/021/2017 21:21:55 - INFO - Flashing data 28/021/2017 21:21:56 - INFO - Processing rpm_S1_Boot_MSM8956_LA1_0_1_73_AID_4_PLATFORM-LOIRE-COM-LIVE-HWID009B00E1-SWID0A-OEM1-AID4-DEBUG00_S1-BOOT-LIVE-D553-0004-MMC.sin 28/021/2017 21:21:56 - INFO - Checking header 28/021/2017 21:21:56 - INFO - Flashing data 28/021/2017 21:21:56 - INFO - Processing s1sbl_S1_Boot_MSM8956_LA1_0_1_73_AID_4_S1-BOOT-LIVE-D553-0004-ELF_S1-BOOT-LIVE-D553-0004-MMC.sin 28/021/2017 21:21:56 - INFO - Checking header 28/021/2017 21:21:56 - INFO - Flashing data 28/021/2017 21:21:57 - INFO - Processing sbl1_S1_Boot_MSM8956_LA1_0_1_73_AID_4_PLATFORM-LOIRE-COM-LIVE-HWID009B00E1-SWID00-OEM1-AID4-DEBUG00_S1-BOOT-LIVE-D553-0004-MMC.sin 28/021/2017 21:21:57 - INFO - Checking header 28/021/2017 21:21:57 - INFO - Flashing data 28/021/2017 21:21:57 - INFO - Closing TA partition 28/021/2017 21:21:57 - INFO - Opening TA partition 2 28/021/2017 21:21:57 - INFO - Writing TA unit 0000084F. Value : 1A CE 33 00 01 00 08 03 00 02 04 02 05 00 02 02 80 00 10 05 00 01 02 71 00 00 05 00 04 82 82 00 10 02 00 04 85 05 00 03 02 82 00 10 05 00 05 82 71 00 00 02 00 05 85 12 00 02 00 A9 09 BE BA A9 09 00 00 B3 08 BE BA B3 08 00 00 04 00 03 00 02 00 04 00 04 00 B0 04 0E 00 06 00 B8 0B 01 4B 00 00 00 03 96 00 2C 01 03 00 09 00 01 28/021/2017 21:21:57 - INFO - Writing TA unit 000008FD. Value : 00 28/021/2017 21:21:57 - INFO - Closing TA partition 28/021/2017 21:21:57 - INFO - Opening TA partition 2 28/021/2017 21:21:57 - INFO - Processing tzs1attest_S1_Boot_MSM8956_LA1_0_1_73_AID_4_PLATFORM-LOIRE-COM-LIVE-HWID009B00E1-SWID0C-APPID01-OEM1-AID4-DEBUG00_S1-BOOT-LIVE-D553-0004-MMC.sin 28/021/2017 21:21:57 - INFO - Checking header 28/021/2017 21:21:57 - INFO - Flashing data 28/021/2017 21:21:57 - INFO - Processing tz_S1_Boot_MSM8956_LA1_0_1_73_AID_4_PLATFORM-LOIRE-COM-LIVE-HWID009B00E1-SWID07-OEM1-AID4-DEBUG00_S1-BOOT-LIVE-D553-0004-MMC.sin 28/021/2017 21:21:57 - INFO - Checking header 28/021/2017 21:21:57 - INFO - Flashing data 28/021/2017 21:21:58 - INFO - Processing tzs1sbl_S1_Boot_MSM8956_LA1_0_1_73_AID_4_PLATFORM-LOIRE-COM-LIVE-HWID009B00E1-SWID0C-APPID01-OEM1-AID4-DEBUG00_S1-BOOT-LIVE-D553-0004-MMC.sin 28/021/2017 21:21:58 - INFO - Checking header 28/021/2017 21:21:58 - INFO - Flashing data 28/021/2017 21:21:58 - INFO - Closing TA partition 28/021/2017 21:21:58 - INFO - Opening TA partition 2 28/021/2017 21:21:58 - INFO - Processing apps_log.sin 28/021/2017 21:21:58 - INFO - Checking header 28/021/2017 21:21:58 - INFO - Flashing data 28/022/2017 21:22:00 - INFO - Processing diag.sin 28/022/2017 21:22:00 - INFO - Checking header 28/022/2017 21:22:00 - INFO - Flashing data 28/022/2017 21:22:00 - WARN - ssd is excluded from bundle 28/022/2017 21:22:00 - INFO - Processing adspso.sin 28/022/2017 21:22:00 - INFO - Checking header 28/022/2017 21:22:00 - INFO - Flashing data 28/022/2017 21:22:01 - INFO - Processing cache.sin 28/022/2017 21:22:01 - INFO - Checking header 28/022/2017 21:22:01 - INFO - Flashing data 28/022/2017 21:22:01 - INFO - Processing modem.sin 28/022/2017 21:22:01 - INFO - Checking header 28/022/2017 21:22:01 - INFO - Flashing data 28/022/2017 21:22:04 - INFO - Processing Qnovo.sin 28/022/2017 21:22:04 - INFO - Checking header 28/022/2017 21:22:04 - INFO - Flashing data 28/022/2017 21:22:05 - INFO - Processing amss_fs_1.sin 28/022/2017 21:22:05 - INFO - Checking header 28/022/2017 21:22:05 - INFO - Flashing data 28/022/2017 21:22:06 - INFO - Processing amss_fs_2.sin 28/022/2017 21:22:06 - INFO - Checking header 28/022/2017 21:22:06 - INFO - Flashing data 28/022/2017 21:22:06 - INFO - Processing amss_fsg.sin 28/022/2017 21:22:06 - INFO - Checking header 28/022/2017 21:22:06 - INFO - Flashing data 28/022/2017 21:22:06 - INFO - Processing persist.sin 28/022/2017 21:22:06 - INFO - Checking header 28/022/2017 21:22:06 - INFO - Flashing data 28/022/2017 21:22:06 - INFO - Processing kernel.sin 28/022/2017 21:22:06 - INFO - Checking header 28/022/2017 21:22:06 - INFO - Flashing data 28/022/2017 21:22:09 - INFO - Processing fotakernel.sin 28/022/2017 21:22:09 - INFO - Checking header 28/022/2017 21:22:09 - INFO - Flashing data 28/022/2017 21:22:25 - INFO - Processing ramdump.sin 28/022/2017 21:22:25 - INFO - Checking header 28/022/2017 21:22:25 - INFO - Flashing data 28/022/2017 21:22:27 - INFO - Processing system.sin 28/022/2017 21:22:27 - INFO - Checking header 28/022/2017 21:22:27 - INFO - Flashing data 28/026/2017 21:26:04 - INFO - Closing TA partition 28/026/2017 21:26:04 - INFO - Opening TA partition 2 28/026/2017 21:26:04 - INFO - Processing oem.sin 28/026/2017 21:26:04 - INFO - Checking header 28/026/2017 21:26:04 - INFO - Flashing data 28/026/2017 21:26:09 - WARN - userdata is excluded from bundle 28/026/2017 21:26:09 - INFO - Closing TA partition 28/026/2017 21:26:09 - INFO - Opening TA partition 2 28/026/2017 21:26:09 - INFO - Writing TA unit 000008A4. Value : 00 00 00 00 00 00 00 00 00 00 00 00 00 00 28/026/2017 21:26:09 - INFO - Closing TA partition 28/026/2017 21:26:10 - INFO - Opening TA partition 2 28/026/2017 21:26:10 - INFO - Writing TA unit 00000964. Value : 00 28/026/2017 21:26:10 - INFO - Closing TA partition 28/026/2017 21:26:10 - INFO - Opening TA partition 2 28/026/2017 21:26:10 - INFO - Writing TA unit 00000907. Value : 00 28/026/2017 21:26:10 - INFO - Closing TA partition 28/026/2017 21:26:10 - INFO - Opening TA partition 2 28/026/2017 21:26:10 - INFO - Writing TA unit 0000091A. Value : 00 28/026/2017 21:26:10 - INFO - Closing TA partition 28/026/2017 21:26:10 - INFO - Opening TA partition 2 28/026/2017 21:26:10 - INFO - Writing TA unit 000009F6. Value : 01 28/026/2017 21:26:10 - INFO - Closing TA partition 28/026/2017 21:26:11 - INFO - Opening TA partition 2 28/026/2017 21:26:11 - INFO - Writing TA unit 000009F9. Value : 76 69 72 67 69 6E 2C 6E 6F 74 69 6D 65 73 74 61 6D 70 00 28/026/2017 21:26:11 - INFO - Closing TA partition 28/026/2017 21:26:11 - INFO - Opening TA partition 2 28/026/2017 21:26:11 - INFO - Processing elabel.sin 28/026/2017 21:26:11 - INFO - Checking header 28/026/2017 21:26:11 - INFO - Flashing data 28/026/2017 21:26:12 - INFO - Closing TA partition 28/026/2017 21:26:12 - INFO - Opening TA partition 2 28/026/2017 21:26:12 - INFO - Writing TA unit 00002725. Value : 32 30 31 37 2D 30 39 2D 32 38 20 32 31 3A 32 36 3A 31 32 00 28/026/2017 21:26:12 - INFO - Writing TA unit 00002774. Value : 00 28/026/2017 21:26:12 - INFO - Closing TA partition 28/026/2017 21:26:12 - INFO - Ending flash session 28/026/2017 21:26:12 - INFO - Flashing finished. 28/026/2017 21:26:12 - INFO - Please unplug and start your phone 28/026/2017 21:26:12 - INFO - For flashtool, Unknown Sources and Debugging must be checked in phone settings