null Tue 25 Dec 19:27:57 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 2aj7-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aj7-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aj7-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-3.6-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/2aj7-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-3.6-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 ============================================================ Tue 25 Dec 19:28:06 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/2aj7-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-3.6-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 389 and 0 Target number of residues in the AU: 389 Target solvent content: 0.6280 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: 2aj7-3.6-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: 2aj7-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 1.15 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 3 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 3.601 Wilson plot Bfac: 65.23 6555 reflections ( 99.92 % complete ) and 0 restraints for refining 2891 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3262 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3309 (Rfree = 0.000) for 2891 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 2.76 Search for helices and strands: 0 residues in 0 chains, 2936 seeds are put forward NCS extension: 0 residues added, 2936 seeds are put forward Round 1: 175 peptides, 30 chains. Longest chain 12 peptides. Score 0.356 Round 2: 212 peptides, 25 chains. Longest chain 16 peptides. Score 0.523 Round 3: 227 peptides, 27 chains. Longest chain 22 peptides. Score 0.537 Round 4: 229 peptides, 25 chains. Longest chain 22 peptides. Score 0.564 Round 5: 227 peptides, 23 chains. Longest chain 38 peptides. Score 0.581 Taking the results from Round 5 Chains 24, Residues 204, Estimated correctness of the model 7.0 % 1 chains (36 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 4656 restraints for refining 2363 atoms. 3699 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3016 (Rfree = 0.000) for 2363 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 2: After refmac, R = 0.2909 (Rfree = 0.000) for 2306 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 3: After refmac, R = 0.2754 (Rfree = 0.000) for 2276 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 4: After refmac, R = 0.2525 (Rfree = 0.000) for 2256 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 5: After refmac, R = 0.2596 (Rfree = 0.000) for 2236 atoms. Found 12 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 2.62 Search for helices and strands: 0 residues in 0 chains, 2295 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2307 seeds are put forward Round 1: 213 peptides, 28 chains. Longest chain 19 peptides. Score 0.490 Round 2: 235 peptides, 18 chains. Longest chain 54 peptides. Score 0.650 Round 3: 228 peptides, 23 chains. Longest chain 29 peptides. Score 0.583 Round 4: 242 peptides, 23 chains. Longest chain 41 peptides. Score 0.614 Round 5: 243 peptides, 23 chains. Longest chain 37 peptides. Score 0.616 Taking the results from Round 2 Chains 19, Residues 217, Estimated correctness of the model 33.1 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 4499 restraints for refining 2364 atoms. 3479 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3227 (Rfree = 0.000) for 2364 atoms. Found 11 (15 requested) and removed 18 (7 requested) atoms. Cycle 7: After refmac, R = 0.2935 (Rfree = 0.000) for 2342 atoms. Found 10 (15 requested) and removed 18 (7 requested) atoms. Cycle 8: After refmac, R = 0.2831 (Rfree = 0.000) for 2324 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. Cycle 9: After refmac, R = 0.2851 (Rfree = 0.000) for 2315 atoms. Found 11 (14 requested) and removed 13 (7 requested) atoms. Cycle 10: After refmac, R = 0.2778 (Rfree = 0.000) for 2302 atoms. Found 7 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 2.57 Search for helices and strands: 0 residues in 0 chains, 2367 seeds are put forward NCS extension: 52 residues added (8 deleted due to clashes), 2419 seeds are put forward Round 1: 220 peptides, 27 chains. Longest chain 32 peptides. Score 0.519 Round 2: 229 peptides, 24 chains. Longest chain 26 peptides. Score 0.575 Round 3: 242 peptides, 24 chains. Longest chain 25 peptides. Score 0.603 Round 4: 229 peptides, 25 chains. Longest chain 26 peptides. Score 0.564 Round 5: 244 peptides, 24 chains. Longest chain 35 peptides. Score 0.608 Taking the results from Round 5 Chains 24, Residues 220, Estimated correctness of the model 17.7 % 1 chains (29 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 4628 restraints for refining 2364 atoms. 3639 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3083 (Rfree = 0.000) for 2364 atoms. Found 14 (15 requested) and removed 14 (7 requested) atoms. Cycle 12: After refmac, R = 0.2966 (Rfree = 0.000) for 2342 atoms. Found 12 (15 requested) and removed 13 (7 requested) atoms. Cycle 13: After refmac, R = 0.2805 (Rfree = 0.000) for 2325 atoms. Found 3 (15 requested) and removed 14 (7 requested) atoms. Cycle 14: After refmac, R = 0.2695 (Rfree = 0.000) for 2303 atoms. Found 4 (14 requested) and removed 11 (7 requested) atoms. Cycle 15: After refmac, R = 0.2741 (Rfree = 0.000) for 2294 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 2.58 Search for helices and strands: 0 residues in 0 chains, 2365 seeds are put forward NCS extension: 34 residues added (7 deleted due to clashes), 2399 seeds are put forward Round 1: 219 peptides, 27 chains. Longest chain 24 peptides. Score 0.517 Round 2: 234 peptides, 24 chains. Longest chain 30 peptides. Score 0.586 Round 3: 235 peptides, 23 chains. Longest chain 35 peptides. Score 0.599 Round 4: 237 peptides, 25 chains. Longest chain 29 peptides. Score 0.582 Round 5: 237 peptides, 24 chains. Longest chain 41 peptides. Score 0.592 Taking the results from Round 3 Chains 24, Residues 212, Estimated correctness of the model 14.2 % 2 chains (56 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 4430 restraints for refining 2364 atoms. 3361 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3106 (Rfree = 0.000) for 2364 atoms. Found 13 (15 requested) and removed 19 (7 requested) atoms. Cycle 17: After refmac, R = 0.2931 (Rfree = 0.000) for 2339 atoms. Found 10 (15 requested) and removed 12 (7 requested) atoms. Cycle 18: After refmac, R = 0.2725 (Rfree = 0.000) for 2326 atoms. Found 3 (14 requested) and removed 15 (7 requested) atoms. Cycle 19: After refmac, R = 0.2795 (Rfree = 0.000) for 2308 atoms. Found 9 (14 requested) and removed 13 (7 requested) atoms. Cycle 20: After refmac, R = 0.2641 (Rfree = 0.000) for 2302 atoms. Found 7 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 2.60 Search for helices and strands: 0 residues in 0 chains, 2365 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2391 seeds are put forward Round 1: 210 peptides, 27 chains. Longest chain 26 peptides. Score 0.494 Round 2: 216 peptides, 23 chains. Longest chain 18 peptides. Score 0.555 Round 3: 229 peptides, 26 chains. Longest chain 22 peptides. Score 0.553 Round 4: 227 peptides, 26 chains. Longest chain 27 peptides. Score 0.548 Round 5: 232 peptides, 24 chains. Longest chain 24 peptides. Score 0.581 Taking the results from Round 5 Chains 26, Residues 208, Estimated correctness of the model 7.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 4897 restraints for refining 2364 atoms. 4028 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2962 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 22: After refmac, R = 0.2823 (Rfree = 0.000) for 2343 atoms. Found 8 (15 requested) and removed 11 (7 requested) atoms. Cycle 23: After refmac, R = 0.2685 (Rfree = 0.000) for 2327 atoms. Found 4 (14 requested) and removed 13 (7 requested) atoms. Cycle 24: After refmac, R = 0.2590 (Rfree = 0.000) for 2309 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.2598 (Rfree = 0.000) for 2296 atoms. Found 4 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 2.55 Search for helices and strands: 0 residues in 0 chains, 2350 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 2385 seeds are put forward Round 1: 218 peptides, 27 chains. Longest chain 27 peptides. Score 0.514 Round 2: 245 peptides, 24 chains. Longest chain 31 peptides. Score 0.610 Round 3: 230 peptides, 19 chains. Longest chain 45 peptides. Score 0.629 Round 4: 227 peptides, 21 chains. Longest chain 38 peptides. Score 0.602 Round 5: 231 peptides, 21 chains. Longest chain 50 peptides. Score 0.611 Taking the results from Round 3 Chains 22, Residues 211, Estimated correctness of the model 25.6 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 4645 restraints for refining 2364 atoms. 3684 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2972 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 27: After refmac, R = 0.2880 (Rfree = 0.000) for 2353 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 28: After refmac, R = 0.2789 (Rfree = 0.000) for 2345 atoms. Found 13 (15 requested) and removed 12 (7 requested) atoms. Cycle 29: After refmac, R = 0.2652 (Rfree = 0.000) for 2341 atoms. Found 5 (15 requested) and removed 16 (7 requested) atoms. Cycle 30: After refmac, R = 0.2743 (Rfree = 0.000) for 2324 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 2.58 Search for helices and strands: 0 residues in 0 chains, 2401 seeds are put forward NCS extension: 49 residues added (2 deleted due to clashes), 2450 seeds are put forward Round 1: 207 peptides, 27 chains. Longest chain 23 peptides. Score 0.486 Round 2: 213 peptides, 24 chains. Longest chain 21 peptides. Score 0.537 Round 3: 219 peptides, 25 chains. Longest chain 26 peptides. Score 0.540 Round 4: 217 peptides, 23 chains. Longest chain 21 peptides. Score 0.558 Round 5: 227 peptides, 25 chains. Longest chain 21 peptides. Score 0.559 Taking the results from Round 5 Chains 27, Residues 202, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 4906 restraints for refining 2363 atoms. 4077 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3060 (Rfree = 0.000) for 2363 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 32: After refmac, R = 0.2854 (Rfree = 0.000) for 2345 atoms. Found 10 (15 requested) and removed 8 (7 requested) atoms. Cycle 33: After refmac, R = 0.2815 (Rfree = 0.000) for 2327 atoms. Found 12 (15 requested) and removed 10 (7 requested) atoms. Cycle 34: After refmac, R = 0.2811 (Rfree = 0.000) for 2321 atoms. Found 9 (14 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.2766 (Rfree = 0.000) for 2319 atoms. Found 6 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 2.58 Search for helices and strands: 0 residues in 0 chains, 2410 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2426 seeds are put forward Round 1: 191 peptides, 22 chains. Longest chain 30 peptides. Score 0.505 Round 2: 193 peptides, 22 chains. Longest chain 24 peptides. Score 0.510 Round 3: 199 peptides, 24 chains. Longest chain 21 peptides. Score 0.501 Round 4: 208 peptides, 26 chains. Longest chain 29 peptides. Score 0.501 Round 5: 211 peptides, 26 chains. Longest chain 24 peptides. Score 0.508 Taking the results from Round 2 Chains 23, Residues 171, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 5087 restraints for refining 2364 atoms. 4366 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2826 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 37: After refmac, R = 0.2567 (Rfree = 0.000) for 2340 atoms. Found 8 (15 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.2652 (Rfree = 0.000) for 2330 atoms. Found 8 (15 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.2412 (Rfree = 0.000) for 2317 atoms. Found 6 (14 requested) and removed 8 (7 requested) atoms. Cycle 40: After refmac, R = 0.2582 (Rfree = 0.000) for 2311 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 2.58 Search for helices and strands: 0 residues in 0 chains, 2377 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2398 seeds are put forward Round 1: 191 peptides, 29 chains. Longest chain 21 peptides. Score 0.417 Round 2: 211 peptides, 25 chains. Longest chain 19 peptides. Score 0.520 Round 3: 204 peptides, 22 chains. Longest chain 18 peptides. Score 0.538 Round 4: 207 peptides, 24 chains. Longest chain 23 peptides. Score 0.522 Round 5: 208 peptides, 23 chains. Longest chain 22 peptides. Score 0.536 Taking the results from Round 3 Chains 22, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 5082 restraints for refining 2363 atoms. 4376 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2651 (Rfree = 0.000) for 2363 atoms. Found 7 (15 requested) and removed 9 (7 requested) atoms. Cycle 42: After refmac, R = 0.2518 (Rfree = 0.000) for 2354 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 43: After refmac, R = 0.2542 (Rfree = 0.000) for 2354 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.2410 (Rfree = 0.000) for 2355 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 45: After refmac, R = 0.2540 (Rfree = 0.000) for 2355 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 2.52 Search for helices and strands: 0 residues in 0 chains, 2423 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2444 seeds are put forward Round 1: 183 peptides, 27 chains. Longest chain 16 peptides. Score 0.420 Round 2: 201 peptides, 23 chains. Longest chain 20 peptides. Score 0.518 Round 3: 203 peptides, 22 chains. Longest chain 28 peptides. Score 0.535 Round 4: 217 peptides, 23 chains. Longest chain 27 peptides. Score 0.558 Round 5: 221 peptides, 26 chains. Longest chain 27 peptides. Score 0.533 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2aj7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6555 reflections ( 99.92 % complete ) and 5044 restraints for refining 2364 atoms. 4291 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2748 (Rfree = 0.000) for 2364 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2687 (Rfree = 0.000) for 2340 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2475 (Rfree = 0.000) for 2327 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2408 (Rfree = 0.000) for 2317 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:27:31 GMT 2018 Job finished. TimeTaking 59.57 Used memory is bytes: 6152904