null Sun 23 Dec 22:22:46 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 2hxv-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hxv-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hxv-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-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/2hxv-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-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 22:22:56 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/2hxv-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-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 254 and 0 Target number of residues in the AU: 254 Target solvent content: 0.6550 Checking the provided sequence file Detected sequence length: 360 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 360 Adjusted target solvent content: 0.51 Input MTZ file: 2hxv-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: 97 Cell parameters: 104.410 104.410 146.200 90.000 90.000 90.000 Input sequence file: 2hxv-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2880 target number of atoms Had to go as low as 0.70 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: 84.967 4.001 Wilson plot Bfac: 80.99 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3626 reflections ( 99.23 % complete ) and 0 restraints for refining 3180 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3435 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3427 (Rfree = 0.000) for 3180 atoms. Found 15 (15 requested) and removed 39 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.65 Search for helices and strands: 0 residues in 0 chains, 3196 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 7 peptides. Score 0.221 Round 2: 120 peptides, 21 chains. Longest chain 12 peptides. Score 0.344 Round 3: 142 peptides, 28 chains. Longest chain 7 peptides. Score 0.309 Round 4: 146 peptides, 25 chains. Longest chain 12 peptides. Score 0.381 Round 5: 164 peptides, 28 chains. Longest chain 13 peptides. Score 0.402 Taking the results from Round 5 Chains 28, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3626 reflections ( 99.23 % complete ) and 6095 restraints for refining 2535 atoms. 5579 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2699 (Rfree = 0.000) for 2535 atoms. Found 9 (12 requested) and removed 34 (6 requested) atoms. Cycle 2: After refmac, R = 0.2632 (Rfree = 0.000) for 2479 atoms. Found 5 (11 requested) and removed 18 (5 requested) atoms. Cycle 3: After refmac, R = 0.2466 (Rfree = 0.000) for 2451 atoms. Found 5 (11 requested) and removed 21 (5 requested) atoms. Cycle 4: After refmac, R = 0.2355 (Rfree = 0.000) for 2426 atoms. Found 2 (11 requested) and removed 12 (5 requested) atoms. Cycle 5: After refmac, R = 0.2280 (Rfree = 0.000) for 2411 atoms. Found 2 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.58 Search for helices and strands: 0 residues in 0 chains, 2460 seeds are put forward Round 1: 133 peptides, 28 chains. Longest chain 9 peptides. Score 0.268 Round 2: 167 peptides, 30 chains. Longest chain 12 peptides. Score 0.379 Round 3: 170 peptides, 29 chains. Longest chain 15 peptides. Score 0.408 Round 4: 185 peptides, 31 chains. Longest chain 13 peptides. Score 0.433 Round 5: 168 peptides, 27 chains. Longest chain 16 peptides. Score 0.435 Taking the results from Round 5 Chains 27, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3626 reflections ( 99.23 % complete ) and 5757 restraints for refining 2441 atoms. 5220 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2563 (Rfree = 0.000) for 2441 atoms. Found 11 (11 requested) and removed 57 (5 requested) atoms. Cycle 7: After refmac, R = 0.2330 (Rfree = 0.000) for 2377 atoms. Found 4 (11 requested) and removed 18 (5 requested) atoms. Cycle 8: After refmac, R = 0.2241 (Rfree = 0.000) for 2351 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 9: After refmac, R = 0.2172 (Rfree = 0.000) for 2343 atoms. Found 1 (11 requested) and removed 13 (5 requested) atoms. Cycle 10: After refmac, R = 0.2173 (Rfree = 0.000) for 2326 atoms. Found 5 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 2414 seeds are put forward Round 1: 155 peptides, 30 chains. Longest chain 10 peptides. Score 0.329 Round 2: 166 peptides, 30 chains. Longest chain 10 peptides. Score 0.375 Round 3: 168 peptides, 25 chains. Longest chain 15 peptides. Score 0.468 Round 4: 167 peptides, 29 chains. Longest chain 12 peptides. Score 0.396 Round 5: 167 peptides, 26 chains. Longest chain 22 peptides. Score 0.448 Taking the results from Round 3 Chains 25, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3626 reflections ( 99.23 % complete ) and 5327 restraints for refining 2401 atoms. 4780 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2536 (Rfree = 0.000) for 2401 atoms. Found 7 (11 requested) and removed 49 (5 requested) atoms. Cycle 12: After refmac, R = 0.2249 (Rfree = 0.000) for 2349 atoms. Found 4 (11 requested) and removed 26 (5 requested) atoms. Cycle 13: After refmac, R = 0.2221 (Rfree = 0.000) for 2319 atoms. Found 2 (11 requested) and removed 48 (5 requested) atoms. Cycle 14: After refmac, R = 0.2219 (Rfree = 0.000) for 2268 atoms. Found 1 (10 requested) and removed 17 (5 requested) atoms. Cycle 15: After refmac, R = 0.2211 (Rfree = 0.000) for 2250 atoms. Found 3 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.64 Search for helices and strands: 0 residues in 0 chains, 2314 seeds are put forward Round 1: 130 peptides, 27 chains. Longest chain 9 peptides. Score 0.274 Round 2: 169 peptides, 33 chains. Longest chain 9 peptides. Score 0.334 Round 3: 150 peptides, 28 chains. Longest chain 9 peptides. Score 0.344 Round 4: 151 peptides, 26 chains. Longest chain 10 peptides. Score 0.384 Round 5: 148 peptides, 25 chains. Longest chain 11 peptides. Score 0.389 Taking the results from Round 5 Chains 26, Residues 123, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3626 reflections ( 99.23 % complete ) and 5364 restraints for refining 2379 atoms. 4855 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2514 (Rfree = 0.000) for 2379 atoms. Found 10 (11 requested) and removed 70 (5 requested) atoms. Cycle 17: After refmac, R = 0.2391 (Rfree = 0.000) for 2307 atoms. Found 5 (11 requested) and removed 33 (5 requested) atoms. Cycle 18: After refmac, R = 0.2427 (Rfree = 0.000) for 2277 atoms. Found 2 (10 requested) and removed 29 (5 requested) atoms. Cycle 19: After refmac, R = 0.2447 (Rfree = 0.000) for 2250 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. Cycle 20: After refmac, R = 0.2462 (Rfree = 0.000) for 2244 atoms. Found 0 (10 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.64 Search for helices and strands: 0 residues in 0 chains, 2311 seeds are put forward Round 1: 126 peptides, 27 chains. Longest chain 7 peptides. Score 0.255 Round 2: 138 peptides, 24 chains. Longest chain 14 peptides. Score 0.366 Round 3: 141 peptides, 25 chains. Longest chain 12 peptides. Score 0.360 Round 4: 156 peptides, 26 chains. Longest chain 11 peptides. Score 0.404 Round 5: 150 peptides, 27 chains. Longest chain 13 peptides. Score 0.362 Taking the results from Round 4 Chains 26, Residues 130, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3626 reflections ( 99.23 % complete ) and 5407 restraints for refining 2372 atoms. 4878 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2618 (Rfree = 0.000) for 2372 atoms. Found 10 (11 requested) and removed 28 (5 requested) atoms. Cycle 22: After refmac, R = 0.2526 (Rfree = 0.000) for 2349 atoms. Found 8 (11 requested) and removed 11 (5 requested) atoms. Cycle 23: After refmac, R = 0.2538 (Rfree = 0.000) for 2346 atoms. Found 0 (11 requested) and removed 9 (5 requested) atoms. Cycle 24: After refmac, R = 0.2529 (Rfree = 0.000) for 2335 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 25: After refmac, R = 0.2541 (Rfree = 0.000) for 2331 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 2371 seeds are put forward Round 1: 136 peptides, 27 chains. Longest chain 9 peptides. Score 0.301 Round 2: 155 peptides, 26 chains. Longest chain 18 peptides. Score 0.400 Round 3: 167 peptides, 26 chains. Longest chain 21 peptides. Score 0.448 Round 4: 150 peptides, 24 chains. Longest chain 9 peptides. Score 0.415 Round 5: 154 peptides, 27 chains. Longest chain 11 peptides. Score 0.378 Taking the results from Round 3 Chains 27, Residues 141, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3626 reflections ( 99.23 % complete ) and 5420 restraints for refining 2436 atoms. 4843 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2658 (Rfree = 0.000) for 2436 atoms. Found 11 (11 requested) and removed 39 (5 requested) atoms. Cycle 27: After refmac, R = 0.2552 (Rfree = 0.000) for 2397 atoms. Found 7 (11 requested) and removed 26 (5 requested) atoms. Cycle 28: After refmac, R = 0.2512 (Rfree = 0.000) for 2373 atoms. Found 8 (11 requested) and removed 15 (5 requested) atoms. Cycle 29: After refmac, R = 0.2507 (Rfree = 0.000) for 2365 atoms. Found 0 (11 requested) and removed 9 (5 requested) atoms. Cycle 30: After refmac, R = 0.2474 (Rfree = 0.000) for 2353 atoms. Found 7 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 2417 seeds are put forward Round 1: 124 peptides, 25 chains. Longest chain 8 peptides. Score 0.285 Round 2: 139 peptides, 23 chains. Longest chain 14 peptides. Score 0.388 Round 3: 148 peptides, 24 chains. Longest chain 14 peptides. Score 0.407 Round 4: 155 peptides, 27 chains. Longest chain 13 peptides. Score 0.383 Round 5: 148 peptides, 23 chains. Longest chain 13 peptides. Score 0.425 Taking the results from Round 5 Chains 23, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3626 reflections ( 99.23 % complete ) and 5857 restraints for refining 2480 atoms. 5380 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2623 (Rfree = 0.000) for 2480 atoms. Found 11 (11 requested) and removed 29 (5 requested) atoms. Cycle 32: After refmac, R = 0.2544 (Rfree = 0.000) for 2460 atoms. Found 9 (11 requested) and removed 17 (5 requested) atoms. Cycle 33: After refmac, R = 0.2513 (Rfree = 0.000) for 2449 atoms. Found 4 (11 requested) and removed 9 (5 requested) atoms. Cycle 34: After refmac, R = 0.2510 (Rfree = 0.000) for 2440 atoms. Found 4 (11 requested) and removed 13 (5 requested) atoms. Cycle 35: After refmac, R = 0.2543 (Rfree = 0.000) for 2430 atoms. Found 1 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.56 Search for helices and strands: 0 residues in 0 chains, 2476 seeds are put forward Round 1: 114 peptides, 25 chains. Longest chain 8 peptides. Score 0.237 Round 2: 126 peptides, 25 chains. Longest chain 7 peptides. Score 0.294 Round 3: 140 peptides, 25 chains. Longest chain 11 peptides. Score 0.356 Round 4: 138 peptides, 26 chains. Longest chain 12 peptides. Score 0.329 Round 5: 136 peptides, 25 chains. Longest chain 13 peptides. Score 0.339 Taking the results from Round 3 Chains 25, Residues 115, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3626 reflections ( 99.23 % complete ) and 5839 restraints for refining 2481 atoms. 5386 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2528 (Rfree = 0.000) for 2481 atoms. Found 11 (11 requested) and removed 42 (5 requested) atoms. Cycle 37: After refmac, R = 0.2420 (Rfree = 0.000) for 2436 atoms. Found 6 (11 requested) and removed 14 (5 requested) atoms. Cycle 38: After refmac, R = 0.2389 (Rfree = 0.000) for 2424 atoms. Found 2 (11 requested) and removed 12 (5 requested) atoms. Cycle 39: After refmac, R = 0.2374 (Rfree = 0.000) for 2412 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2351 (Rfree = 0.000) for 2401 atoms. Found 3 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 3.57 Search for helices and strands: 0 residues in 0 chains, 2444 seeds are put forward Round 1: 100 peptides, 23 chains. Longest chain 6 peptides. Score 0.209 Round 2: 108 peptides, 23 chains. Longest chain 6 peptides. Score 0.249 Round 3: 117 peptides, 25 chains. Longest chain 8 peptides. Score 0.252 Round 4: 118 peptides, 24 chains. Longest chain 9 peptides. Score 0.276 Round 5: 119 peptides, 24 chains. Longest chain 9 peptides. Score 0.281 Taking the results from Round 5 Chains 24, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3626 reflections ( 99.23 % complete ) and 5920 restraints for refining 2442 atoms. 5564 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2573 (Rfree = 0.000) for 2442 atoms. Found 8 (11 requested) and removed 24 (5 requested) atoms. Cycle 42: After refmac, R = 0.2557 (Rfree = 0.000) for 2419 atoms. Found 5 (11 requested) and removed 10 (5 requested) atoms. Cycle 43: After refmac, R = 0.2533 (Rfree = 0.000) for 2414 atoms. Found 0 (11 requested) and removed 12 (5 requested) atoms. Cycle 44: After refmac, R = 0.2515 (Rfree = 0.000) for 2402 atoms. Found 1 (11 requested) and removed 9 (5 requested) atoms. Cycle 45: After refmac, R = 0.2494 (Rfree = 0.000) for 2393 atoms. Found 1 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 2425 seeds are put forward Round 1: 75 peptides, 18 chains. Longest chain 5 peptides. Score 0.184 Round 2: 76 peptides, 16 chains. Longest chain 8 peptides. Score 0.236 Round 3: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.263 Round 4: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.254 Round 5: 81 peptides, 15 chains. Longest chain 8 peptides. Score 0.285 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 66, 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 2hxv-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3626 reflections ( 99.23 % complete ) and 5893 restraints for refining 2390 atoms. 5644 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2496 (Rfree = 0.000) for 2390 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2450 (Rfree = 0.000) for 2381 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2450 (Rfree = 0.000) for 2373 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2446 (Rfree = 0.000) for 2367 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:09:12 GMT 2018 Job finished. TimeTaking 46.43 Used memory is bytes: 7431376