Sun 30 Dec 03:45:07 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2aj7-2.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aj7-2.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aj7-2.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 30 Dec 03:46:19 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 512 and 0 Target number of residues in the AU: 512 Target solvent content: 0.5104 Checking the provided sequence file Detected sequence length: 163 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 326 Adjusted target solvent content: 0.69 Input MTZ file: 2aj7-2.2-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 173 Cell parameters: 108.801 108.801 82.811 90.000 90.000 120.000 Input sequence file: 2aj7-2.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 1.00 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 94.224 2.240 Wilson plot Bfac: 25.68 26900 reflections ( 99.98 % complete ) and 0 restraints for refining 2908 atoms. Observations/parameters ratio is 2.31 ------------------------------------------------------ Starting model: R = 0.3466 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3029 (Rfree = 0.000) for 2908 atoms. Found 72 (72 requested) and removed 37 (36 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.32 1.78 NCS extension: 0 residues added, 2943 seeds are put forward Round 1: 240 peptides, 20 chains. Longest chain 51 peptides. Score 0.640 Round 2: 259 peptides, 19 chains. Longest chain 54 peptides. Score 0.686 Round 3: 262 peptides, 16 chains. Longest chain 51 peptides. Score 0.717 Round 4: 279 peptides, 11 chains. Longest chain 58 peptides. Score 0.782 Round 5: 289 peptides, 10 chains. Longest chain 89 peptides. Score 0.802 Taking the results from Round 5 Chains 10, Residues 279, Estimated correctness of the model 94.7 % 6 chains (240 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 139 B and 143 B 9 chains (282 residues) following loop building 5 chains (243 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 3071 restraints for refining 2830 atoms. 959 conditional restraints added. Observations/parameters ratio is 2.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2964 (Rfree = 0.000) for 2830 atoms. Found 70 (70 requested) and removed 38 (35 requested) atoms. Cycle 2: After refmac, R = 0.2710 (Rfree = 0.000) for 2845 atoms. Found 69 (69 requested) and removed 35 (35 requested) atoms. Cycle 3: After refmac, R = 0.2513 (Rfree = 0.000) for 2860 atoms. Found 68 (68 requested) and removed 30 (35 requested) atoms. Cycle 4: After refmac, R = 0.2381 (Rfree = 0.000) for 2888 atoms. Found 68 (68 requested) and removed 27 (35 requested) atoms. Cycle 5: After refmac, R = 0.2300 (Rfree = 0.000) for 2918 atoms. Found 69 (69 requested) and removed 24 (36 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.21 1.69 NCS extension: 19 residues added (27 deleted due to clashes), 2991 seeds are put forward Round 1: 283 peptides, 7 chains. Longest chain 101 peptides. Score 0.816 Round 2: 289 peptides, 6 chains. Longest chain 102 peptides. Score 0.829 Round 3: 291 peptides, 5 chains. Longest chain 102 peptides. Score 0.838 Round 4: 286 peptides, 6 chains. Longest chain 102 peptides. Score 0.826 Round 5: 284 peptides, 7 chains. Longest chain 102 peptides. Score 0.817 Taking the results from Round 3 Chains 6, Residues 286, Estimated correctness of the model 96.4 % 4 chains (273 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 111 A and 115 A 4 chains (287 residues) following loop building 3 chains (276 residues) in sequence following loop building ------------------------------------------------------ QUITTING ... ARP/wARP module stopped with an error message: REFMAC5 *** Look for error message in the file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-parrot-hancs/2aj7-2_warpNtrace_refine.last.log QUITTING ... ARP/wARP module stopped with an error message: REFMAC5 The last 15 lines of the log file: ##### ERROR : GLY : duplicated atom_name : "C ". ##### chain: QQQ residue: 11 ##### ERROR : GLY : duplicated atom_name : "O ". ##### chain: QQQ residue: 11 ##### IERR = 1 ##### ##### There is an error. See above ##### ===> Error: Fatal error. Cannot continue ##### ##### Refmac: Fatal error. Cannot continue ##### Refmac: Fatal error. Cannot continue ##### Times: User: 10.3s System: 0.1s Elapsed: 0:15 ##### ##### ##### *** Look for error message in the file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-parrot-hancs/2aj7-2_warpNtrace_refine.last.log Sun 30 Dec 04:09:12 GMT 2018 QUITTING ... ARP/wARP module stopped with an error message: /opt/apps/easybuild/software/chem/ccp4/7.0.066/arp_warp_8.0/bin/bin-x86_64-Linux/warp_tracing.sh *** Look for error message in the file: where the output of warp_tracing.sh went to TimeTaking 2880.33