null Sun 23 Dec 22:22:42 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 2ppv-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ppv-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ppv-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-4.0-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/2ppv-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-4.0-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 23 Dec 22:23:43 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/2ppv-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-4.0-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 285 and 0 Target number of residues in the AU: 285 Target solvent content: 0.6987 Checking the provided sequence file Detected sequence length: 332 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 332 Adjusted target solvent content: 0.65 Input MTZ file: 2ppv-4.0-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: 20 Cell parameters: 133.390 136.620 56.180 90.000 90.000 90.000 Input sequence file: 2ppv-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2656 target number of atoms Had to go as low as 0.95 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.185 4.000 Wilson plot Bfac: 120.03 4560 reflections ( 99.32 % complete ) and 0 restraints for refining 2939 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3562 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3632 (Rfree = 0.000) for 2939 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.21 3.43 Search for helices and strands: 0 residues in 0 chains, 2986 seeds are put forward Round 1: 130 peptides, 23 chains. Longest chain 9 peptides. Score 0.321 Round 2: 158 peptides, 20 chains. Longest chain 25 peptides. Score 0.460 Round 3: 181 peptides, 23 chains. Longest chain 24 peptides. Score 0.487 Round 4: 176 peptides, 20 chains. Longest chain 26 peptides. Score 0.513 Round 5: 180 peptides, 21 chains. Longest chain 24 peptides. Score 0.511 Taking the results from Round 4 Chains 20, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4560 reflections ( 99.32 % complete ) and 5598 restraints for refining 2398 atoms. 4994 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2812 (Rfree = 0.000) for 2398 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 2: After refmac, R = 0.2548 (Rfree = 0.000) for 2347 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 3: After refmac, R = 0.2361 (Rfree = 0.000) for 2324 atoms. Found 5 (11 requested) and removed 10 (5 requested) atoms. Cycle 4: After refmac, R = 0.2381 (Rfree = 0.000) for 2310 atoms. Found 10 (11 requested) and removed 11 (5 requested) atoms. Cycle 5: After refmac, R = 0.2477 (Rfree = 0.000) for 2299 atoms. Found 6 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.18 3.40 Search for helices and strands: 0 residues in 0 chains, 2409 seeds are put forward Round 1: 165 peptides, 23 chains. Longest chain 17 peptides. Score 0.439 Round 2: 184 peptides, 22 chains. Longest chain 16 peptides. Score 0.509 Round 3: 180 peptides, 22 chains. Longest chain 22 peptides. Score 0.497 Round 4: 170 peptides, 19 chains. Longest chain 24 peptides. Score 0.509 Round 5: 176 peptides, 19 chains. Longest chain 18 peptides. Score 0.526 Taking the results from Round 5 Chains 20, Residues 157, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4560 reflections ( 99.32 % complete ) and 5591 restraints for refining 2398 atoms. 4950 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2545 (Rfree = 0.000) for 2398 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 7: After refmac, R = 0.2581 (Rfree = 0.000) for 2345 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 8: After refmac, R = 0.2495 (Rfree = 0.000) for 2316 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 9: After refmac, R = 0.2491 (Rfree = 0.000) for 2282 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 10: After refmac, R = 0.2593 (Rfree = 0.000) for 2257 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.18 3.40 Search for helices and strands: 0 residues in 0 chains, 2369 seeds are put forward Round 1: 157 peptides, 24 chains. Longest chain 13 peptides. Score 0.399 Round 2: 175 peptides, 20 chains. Longest chain 17 peptides. Score 0.510 Round 3: 189 peptides, 22 chains. Longest chain 16 peptides. Score 0.523 Round 4: 188 peptides, 24 chains. Longest chain 19 peptides. Score 0.494 Round 5: 180 peptides, 23 chains. Longest chain 18 peptides. Score 0.484 Taking the results from Round 3 Chains 22, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4560 reflections ( 99.32 % complete ) and 5185 restraints for refining 2344 atoms. 4539 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2555 (Rfree = 0.000) for 2344 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 12: After refmac, R = 0.2655 (Rfree = 0.000) for 2306 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 13: After refmac, R = 0.2740 (Rfree = 0.000) for 2273 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 14: After refmac, R = 0.2675 (Rfree = 0.000) for 2249 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 15: After refmac, R = 0.2620 (Rfree = 0.000) for 2237 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.14 3.37 Search for helices and strands: 0 residues in 0 chains, 2352 seeds are put forward Round 1: 158 peptides, 24 chains. Longest chain 11 peptides. Score 0.402 Round 2: 185 peptides, 24 chains. Longest chain 14 peptides. Score 0.485 Round 3: 178 peptides, 22 chains. Longest chain 18 peptides. Score 0.492 Round 4: 178 peptides, 22 chains. Longest chain 28 peptides. Score 0.492 Round 5: 191 peptides, 23 chains. Longest chain 17 peptides. Score 0.515 Taking the results from Round 5 Chains 25, Residues 168, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4560 reflections ( 99.32 % complete ) and 5334 restraints for refining 2399 atoms. 4649 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2819 (Rfree = 0.000) for 2399 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 17: After refmac, R = 0.2615 (Rfree = 0.000) for 2366 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 18: After refmac, R = 0.2444 (Rfree = 0.000) for 2344 atoms. Found 7 (11 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.2638 (Rfree = 0.000) for 2325 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 20: After refmac, R = 0.2498 (Rfree = 0.000) for 2315 atoms. Found 7 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.15 3.38 Search for helices and strands: 0 residues in 0 chains, 2436 seeds are put forward Round 1: 166 peptides, 28 chains. Longest chain 12 peptides. Score 0.370 Round 2: 183 peptides, 24 chains. Longest chain 14 peptides. Score 0.479 Round 3: 200 peptides, 25 chains. Longest chain 24 peptides. Score 0.515 Round 4: 203 peptides, 24 chains. Longest chain 19 peptides. Score 0.536 Round 5: 171 peptides, 19 chains. Longest chain 16 peptides. Score 0.512 Taking the results from Round 4 Chains 24, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4560 reflections ( 99.32 % complete ) and 5353 restraints for refining 2399 atoms. 4661 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2645 (Rfree = 0.000) for 2399 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 22: After refmac, R = 0.2605 (Rfree = 0.000) for 2360 atoms. Found 8 (11 requested) and removed 14 (5 requested) atoms. Cycle 23: After refmac, R = 0.2689 (Rfree = 0.000) for 2333 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 24: After refmac, R = 0.2657 (Rfree = 0.000) for 2307 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 25: After refmac, R = 0.2402 (Rfree = 0.000) for 2289 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.13 3.36 Search for helices and strands: 0 residues in 0 chains, 2431 seeds are put forward Round 1: 154 peptides, 29 chains. Longest chain 10 peptides. Score 0.313 Round 2: 166 peptides, 27 chains. Longest chain 10 peptides. Score 0.384 Round 3: 168 peptides, 27 chains. Longest chain 10 peptides. Score 0.391 Round 4: 158 peptides, 23 chains. Longest chain 14 peptides. Score 0.417 Round 5: 174 peptides, 27 chains. Longest chain 16 peptides. Score 0.410 Taking the results from Round 4 Chains 23, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4560 reflections ( 99.32 % complete ) and 5505 restraints for refining 2399 atoms. 4988 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2765 (Rfree = 0.000) for 2399 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 27: After refmac, R = 0.2546 (Rfree = 0.000) for 2362 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 28: After refmac, R = 0.2556 (Rfree = 0.000) for 2336 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 29: After refmac, R = 0.2390 (Rfree = 0.000) for 2322 atoms. Found 7 (11 requested) and removed 11 (5 requested) atoms. Cycle 30: After refmac, R = 0.2140 (Rfree = 0.000) for 2304 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.07 3.31 Search for helices and strands: 0 residues in 0 chains, 2406 seeds are put forward Round 1: 130 peptides, 25 chains. Longest chain 9 peptides. Score 0.289 Round 2: 154 peptides, 25 chains. Longest chain 12 peptides. Score 0.374 Round 3: 159 peptides, 22 chains. Longest chain 12 peptides. Score 0.434 Round 4: 162 peptides, 21 chains. Longest chain 21 peptides. Score 0.458 Round 5: 172 peptides, 24 chains. Longest chain 13 peptides. Score 0.446 Taking the results from Round 4 Chains 21, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4560 reflections ( 99.32 % complete ) and 5480 restraints for refining 2376 atoms. 4937 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2391 (Rfree = 0.000) for 2376 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 32: After refmac, R = 0.2420 (Rfree = 0.000) for 2351 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 33: After refmac, R = 0.2309 (Rfree = 0.000) for 2329 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 34: After refmac, R = 0.2671 (Rfree = 0.000) for 2320 atoms. Found 11 (11 requested) and removed 21 (5 requested) atoms. Cycle 35: After refmac, R = 0.2089 (Rfree = 0.000) for 2296 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 4.16 3.39 Search for helices and strands: 0 residues in 0 chains, 2380 seeds are put forward Round 1: 140 peptides, 29 chains. Longest chain 9 peptides. Score 0.262 Round 2: 174 peptides, 29 chains. Longest chain 15 peptides. Score 0.382 Round 3: 172 peptides, 23 chains. Longest chain 13 peptides. Score 0.460 Round 4: 166 peptides, 22 chains. Longest chain 22 peptides. Score 0.456 Round 5: 176 peptides, 23 chains. Longest chain 22 peptides. Score 0.472 Taking the results from Round 5 Chains 23, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4560 reflections ( 99.32 % complete ) and 5431 restraints for refining 2399 atoms. 4842 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2740 (Rfree = 0.000) for 2399 atoms. Found 9 (11 requested) and removed 15 (5 requested) atoms. Cycle 37: After refmac, R = 0.2410 (Rfree = 0.000) for 2379 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 38: After refmac, R = 0.2400 (Rfree = 0.000) for 2366 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 39: After refmac, R = 0.2568 (Rfree = 0.000) for 2359 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 40: After refmac, R = 0.2552 (Rfree = 0.000) for 2343 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.20 3.42 Search for helices and strands: 0 residues in 0 chains, 2448 seeds are put forward Round 1: 138 peptides, 28 chains. Longest chain 8 peptides. Score 0.271 Round 2: 166 peptides, 25 chains. Longest chain 17 peptides. Score 0.413 Round 3: 171 peptides, 26 chains. Longest chain 13 peptides. Score 0.415 Round 4: 162 peptides, 23 chains. Longest chain 19 peptides. Score 0.429 Round 5: 169 peptides, 25 chains. Longest chain 17 peptides. Score 0.423 Taking the results from Round 4 Chains 23, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4560 reflections ( 99.32 % complete ) and 5471 restraints for refining 2398 atoms. 4938 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2641 (Rfree = 0.000) for 2398 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 42: After refmac, R = 0.2380 (Rfree = 0.000) for 2382 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 43: After refmac, R = 0.2375 (Rfree = 0.000) for 2377 atoms. Found 8 (11 requested) and removed 13 (5 requested) atoms. Cycle 44: After refmac, R = 0.2196 (Rfree = 0.000) for 2358 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2096 (Rfree = 0.000) for 2346 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.14 3.37 Search for helices and strands: 0 residues in 0 chains, 2451 seeds are put forward Round 1: 124 peptides, 26 chains. Longest chain 11 peptides. Score 0.249 Round 2: 159 peptides, 26 chains. Longest chain 15 peptides. Score 0.376 Round 3: 168 peptides, 28 chains. Longest chain 19 peptides. Score 0.376 Round 4: 174 peptides, 27 chains. Longest chain 16 peptides. Score 0.410 Round 5: 159 peptides, 27 chains. Longest chain 12 peptides. Score 0.361 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 147, 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 2ppv-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4560 reflections ( 99.32 % complete ) and 5611 restraints for refining 2398 atoms. 5050 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2530 (Rfree = 0.000) for 2398 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2509 (Rfree = 0.000) for 2368 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2567 (Rfree = 0.000) for 2345 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2669 (Rfree = 0.000) for 2326 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:52:53 GMT 2018 Job finished. TimeTaking 90.19 Used memory is bytes: 13781472