Errors from the output of PDB by I-TASSER

We are using CCP4 AMPLE online. But it shows several errors.

1. For the first time we tried, it shows that the it doesn't I-TASSER format (tar. bz2). It can only support tar. bz, zip, tar, such formats.

2. So for the second time, we deleted "2" directly and uploaded again. It gives the error as below:
*** ERROR ***
The following pdb files have errors:

/data1/serv7/AMPLE/WangCQian/8483366406/AMPLE_0/models/threading3.pdb: file /data1/serv7/AMPLE/WangCQian/8483366406/AMPLE_0/models/threading3.pdb, line 6:
ATOM 1005 CA ARG 5 60.848 145.702 -1.147 4 GLU
------------------------------------------------------------^
not a floating-point number.
/data1/serv7/AMPLE/WangCQian/8483366406/AMPLE_0/models/threading5.pdb: file /data1/serv7/AMPLE/WangCQian/8483366406/AMPLE_0/models/threading5.pdb, line 6:
ATOM 1001 CA THR 3 25.299 32.249 89.671 8 HIS
------------------------------------------------------------^
not a floating-point number.
/data1/serv7/AMPLE/WangCQian/8483366406/AMPLE_0/models/threading6.pdb: file /data1/serv7/AMPLE/WangCQian/8483366406/AMPLE_0/models/threading6.pdb, line 6:
ATOM 5 CA ARG 5 60.283 -7.095 35.062 3 THR
------------------------------------------------------------^
not a floating-point number.

3. For third time, we first unzip the original I-TASSER output and compress it back to .zip file. And another error showed up:
2017-03-23 17:31:08,008 - root [462] - INFO - #########################################################################
#########################################################################
#########################################################################
# CCP4: AMPLE - Ab Initio Modelling Molecular Replacement #
#########################################################################

The authors of specific programs should be referenced where applicable:

AMPLE: J. Bibby, R. M. Keegan, O. Mayans, M. D. Winn and D. J. Rigden.
AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using
rapidly computed ab initio models. (2012). Acta Cryst. D68, 1622-1631 [ doi:10.1107/S0907444912039194 ]

Routine phasing of coiled-coil protein crystal structures with AMPLE (2015). Thomas, J. M. H.,
Keegan, R. M., Bibby, J., Winn, M. D., Mayans, O. and Rigden, D. J. IUCrJ 2, 198-206.
[doi:10.1107/S2052252515002080]

CCP4: Collaborative Computational Project, Number 4. (1994), The CCP4 Suite: Programs
for Protein Crystallography. Acta Cryst. D50, 760-763

MaxCluster: http://www.sbg.bio.ic.ac.uk/maxcluster/

MOLREP: A.A.Vagin & A.Teplyakov (1997) J. Appl. Cryst. 30, 1022-1025

MrBUMP: R.M.Keegan and M.D.Winn (2007) Acta Cryst. D63, 447-457

PHASER: McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D.,
Storoni, L.C. & Read, R.J. (2007)
Phaser crystallographic software J. Appl. Cryst. 40, 658-674

REFMAC: G.N. Murshudov, A.A.Vagin and E.J.Dodson, (1997) Refinement of Macromolecular
Structures by the Maximum-Likelihood Method. Acta Cryst. D53, 240-255

SCWRL: G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack, Jr. Improved prediction of protein
side-chain conformations with SCWRL4. Proteins (2009).

SHELXE: "Extending molecular-replacement solutions with SHELXE". Thorn, A. and Sheldrick, G. M. (2013),
Acta Crystallographica D, 69: 2251-2256. doi: 10.1107/S0907444913027534

SPICKER: Y. Zhang, J. Skolnick, SPICKER: Approach to clustering protein structures for
near-native model selection, Journal of Computational Chemistry, 2004 25: 865-871

Theseus: THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures.
Theobald, Douglas L. & Wuttke, Deborah S. (2006b) Bioinformatics 22(17):2171-2172 [Open Access]
Supplementary Materials for Theobald and Wuttke 2006b.

2017-03-23 17:31:08,008 - root [463] - INFO - AMPLE version: 1.1.0
2017-03-23 17:31:08,008 - root [464] - INFO - Running with CCP4 version: 7.0.19 from directory: /data1/opt/ccp4-updated/7.0/ccp4-7.0
2017-03-23 17:31:08,019 - root [465] - INFO - Running on host: comp14.local
2017-03-23 17:31:08,025 - root [466] - INFO - Running on platform: Linux-2.6.18-194.el5-x86_64-with-redhat-5.5-Final
2017-03-23 17:31:08,026 - root [467] - INFO - Job started at: Thu, 23 Mar 2017 17:31:08
2017-03-23 17:31:08,026 - root [468] - INFO - Invoked with command-line:
/data1/opt/ccp4-updated/7.0/ccp4-7.0/lib/py2/ample/__main__.py -fasta input/MonC1pcoldIsequenceNoHis.seq -mtz input/monC1LeftA12_xdsF_207A.mtz -models input/S321250_results.zip -webserver_uri ../../

2017-03-23 17:31:08,026 - root [469] - INFO - Running in directory: /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0

2017-03-23 17:31:08,030 - root [268] - INFO - Fasta is 496 amino acids long
2017-03-23 17:31:08,071 - ample.util.options_processor [111] - INFO - Using MTZ file: /data1/serv7/AMPLE/WangCQian/0585159494/input/monC1LeftA12_xdsF_207A.mtz
2017-03-23 17:31:08,072 - ample.util.options_processor [284] - INFO - Using arpwarp script: /data1/opt/ccp4-updated/7.0/arp_warp_7.6/bin/bin-x86_64-Linux/auto_tracing.sh
2017-03-23 17:31:08,152 - ample.util.options_processor [330] - INFO - Cannot find Scwrl executable: Scwrl4
2017-03-23 17:31:08,154 - ample.util.options_processor [361] - INFO - NOT making Fragments
2017-03-23 17:31:08,154 - ample.util.options_processor [366] - INFO - NOT making Rosetta Models
2017-03-23 17:31:08,154 - ample.util.options_processor [370] - INFO - Rebuilding in Bucaneer
2017-03-23 17:31:08,154 - ample.util.options_processor [375] - INFO - Rebuilding in ARP/wARP
2017-03-23 17:31:08,155 - ample.util.options_processor [385] - INFO - *** Purge mode specified - all intermediate files will be deleted ***
2017-03-23 17:31:08,155 - root [493] - INFO - All needed programs are found, continuing...
2017-03-23 17:31:08,178 - ample.util.config_util [303] - INFO - AMPLE configuration written to: /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/ampl_.ini
2017-03-23 17:31:08,180 - root [315] - INFO - Importing models from directory: /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models

2017-03-23 17:31:08,181 - ample.util.ample_util [210] - INFO - Extracting files from zipfile: /data1/serv7/AMPLE/WangCQian/0585159494/input/S321250_results.zip
2017-03-23 17:31:08,628 - root [141] - INFO - Checking pdbs in directory: /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models
2017-03-23 17:31:13,932 - root [213] - CRITICAL - *** ERROR ***
The following pdb files have errors:

/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading3.pdb: file /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading3.pdb, line 6:
ATOM 1005 CA ARG 5 60.848 145.702 -1.147 4 GLU
------------------------------------------------------------^
not a floating-point number.
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading5.pdb: file /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading5.pdb, line 6:
ATOM 1001 CA THR 3 25.299 32.249 89.671 8 HIS
------------------------------------------------------------^
not a floating-point number.
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading6.pdb: file /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading6.pdb, line 6:
ATOM 5 CA ARG 5 60.283 -7.095 35.062 3 THR
------------------------------------------------------------^
not a floating-point number.
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/model5.pdb: ENDMDL record missing at end of input.
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading8.pdb: file /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading8.pdb, line 6:
ATOM 1 CA PRO 6 27.189 52.925 51.930 1 PRO
------------------------------------------------------------^
not a floating-point number.
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/model4.pdb: ENDMDL record missing at end of input.
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/model3.pdb: ENDMDL record missing at end of input.
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading1.pdb: file /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading1.pdb, line 6:
ATOM 1004 CA THR 4 27.252 52.549 50.518 1 PRO
------------------------------------------------------------^
not a floating-point number.
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/model2.pdb: ENDMDL record missing at end of input.
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading9.pdb: file /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading9.pdb, line 6:
ATOM 1006 CA PRO 6 27.252 52.549 50.518 1 PRO
------------------------------------------------------------^
not a floating-point number.
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading7.pdb: file /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading7.pdb, line 6:
ATOM 1001 CA THR 3 25.299 32.249 89.671 8 HIS
------------------------------------------------------------^
not a floating-point number.
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading2.pdb: file /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading2.pdb, line 6:
ATOM 1001 CA MET 1 63.235 -9.550 35.087 2 MET
------------------------------------------------------------^
not a floating-point number.
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading4.pdb: file /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading4.pdb, line 6:
ATOM 1001 CA ARG 5 46.099 -5.363 30.098 8 THR
------------------------------------------------------------^
not a floating-point number.

The following pdb files have more than one chain:

/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/model1_2dkiA.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/CH_FN_2WETB00.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/CH_complex2.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/model1_2r0gA.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/CH_complex3.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/model1_2o9zB.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/model1_5uaoA.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/CH_complex5.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/model1_3e1tA.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/CH_CF_1phhA_BS02_DHB.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/model1_4cy6A.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/CH_FN_2FJAA01.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/CH_TM_2qa1A_BS02_FAD.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/model1_3i3lA.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/model1_5dbjE.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/CH_complex4.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/CH_complex1.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/CH_FN_1D4EA00.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/model1_3ihgA.pdb
/data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/model1_1pn0C.pdb

The following pdb files have differing sequences from the reference sequence:

MTTTRPAHAVVLGASMAGTLAAHVLARHVDAVTVVERDALPEEPQHRKGVPQARHAHLLWSNGARLIEEMLPGTTDRLLAAGARRLGFPEDLVTLTGQGWQHRFPATQFALVASRPLLDLTVRQQALGADNITVRQRTEAVELTGSGGGSGGRVTGVVVRDLDSGRQEQLEADLVIDATGRGSRLKQWLAALGVPALEEDVVDAGVAYATRLFKAPPGATTHFPAVNIAADDRVREPGRFGVVYPIEGGRWLATLSCTRGAQLPTHEDEFIPFAENLNHPILADLLRDAEPLTPVFGSRSGANRRLYPERLEQWPDGLLVIGDSLTAFNPIYGHGMSSAARCATTIDREFERSVQEGTGSARAGTRALQKAIGAAVDDPWILAATKDIDYVNCRVSATDPRLIGVDTEQRLRFAEAITAASIRSPKASEIVTDVMSLNAPQAELGSNRFLMAMRADERLPELTAPPFLPEELAVVGLDAATISPTPTPTPTAAVR

PDB: /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/models/threading10.pdb
RPAHAVVLGASMAGTLAAHVLARHVDAVTVVERDALPEEPQHRKGVPQARHLWSNGARLIEEMGTTDRLLAAGARRLGFPEDLVTLTGQGWPATQFALVASRPLLDLTVRQQALGDNITVRQRTEAVELTGSGGGVVVRDLDGRQEQLEADLVIDATGRGSRLKQWLAAVPALEEDVVDAGVAYATRLFKAPPGATTHFPAVNIAAVREPGRFGVVYPIEGGRWLATLSCTRGAQLPTHEDEFIPFAENNHPILADLLRDAEPPVFGSRSGANRRLYLEQWPDGLLVIGDSLTAFNPIYGHGMSSAARCATTIDREFERVQEGTGSARAGTRALQKAIGAAVDDPWILAATKDPRLIGVDTEQRLRFAEAITAASIRKASEIVTDVMSLNAPQAELGSNRFLMAMRADERLPELTAPPFLPEELAVVGLDAATISP

2017-03-23 17:31:13,935 - root [59] - CRITICAL - **********************************************************************
******************** AMPLE ERROR *******************
**********************************************************************

Problem importing pdb files - please check the log for more information

**********************************************************************

More information may be found in the debug log file: /data1/serv7/AMPLE/WangCQian/0585159494/AMPLE_0/debug.log

Could you please help us solve this issue? Thanks!