Mon 24 Dec 07:36:26 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2nuj-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2nuj-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2nuj-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.6-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:36:30 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/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.6-parrot-noncs/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 322 and 0 Target number of residues in the AU: 322 Target solvent content: 0.6255 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: 0.62 Input MTZ file: 2nuj-3.6-parrot-noncs.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: 91 Cell parameters: 78.401 78.401 151.418 90.000 90.000 90.000 Input sequence file: 2nuj-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 0.90 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: 78.401 3.600 Wilson plot Bfac: 63.74 5780 reflections ( 97.59 % complete ) and 0 restraints for refining 2901 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3554 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3226 (Rfree = 0.000) for 2901 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 2.83 Search for helices and strands: 0 residues in 0 chains, 2923 seeds are put forward NCS extension: 0 residues added, 2923 seeds are put forward Round 1: 153 peptides, 29 chains. Longest chain 11 peptides. Score 0.320 Round 2: 188 peptides, 28 chains. Longest chain 11 peptides. Score 0.459 Round 3: 196 peptides, 29 chains. Longest chain 24 peptides. Score 0.470 Round 4: 197 peptides, 27 chains. Longest chain 22 peptides. Score 0.502 Round 5: 209 peptides, 27 chains. Longest chain 19 peptides. Score 0.537 Taking the results from Round 5 Chains 27, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4830 restraints for refining 2364 atoms. 4129 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2824 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 2: After refmac, R = 0.2901 (Rfree = 0.000) for 2340 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 3: After refmac, R = 0.2868 (Rfree = 0.000) for 2325 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 4: After refmac, R = 0.2741 (Rfree = 0.000) for 2313 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Cycle 5: After refmac, R = 0.2698 (Rfree = 0.000) for 2309 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 2.78 Search for helices and strands: 0 residues in 0 chains, 2380 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 2407 seeds are put forward Round 1: 190 peptides, 34 chains. Longest chain 12 peptides. Score 0.377 Round 2: 228 peptides, 34 chains. Longest chain 19 peptides. Score 0.501 Round 3: 225 peptides, 29 chains. Longest chain 21 peptides. Score 0.557 Round 4: 233 peptides, 29 chains. Longest chain 24 peptides. Score 0.579 Round 5: 217 peptides, 27 chains. Longest chain 22 peptides. Score 0.560 Taking the results from Round 4 Chains 29, Residues 204, Estimated correctness of the model 6.3 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4750 restraints for refining 2364 atoms. 3922 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2720 (Rfree = 0.000) for 2364 atoms. Found 14 (15 requested) and removed 16 (7 requested) atoms. Cycle 7: After refmac, R = 0.2616 (Rfree = 0.000) for 2346 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 8: After refmac, R = 0.2498 (Rfree = 0.000) for 2339 atoms. Found 11 (15 requested) and removed 9 (7 requested) atoms. Cycle 9: After refmac, R = 0.2522 (Rfree = 0.000) for 2338 atoms. Found 14 (14 requested) and removed 7 (7 requested) atoms. Cycle 10: After refmac, R = 0.2511 (Rfree = 0.000) for 2340 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 2.84 Search for helices and strands: 0 residues in 0 chains, 2370 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2396 seeds are put forward Round 1: 194 peptides, 32 chains. Longest chain 16 peptides. Score 0.421 Round 2: 217 peptides, 30 chains. Longest chain 19 peptides. Score 0.521 Round 3: 227 peptides, 32 chains. Longest chain 19 peptides. Score 0.525 Round 4: 227 peptides, 31 chains. Longest chain 17 peptides. Score 0.537 Round 5: 227 peptides, 28 chains. Longest chain 24 peptides. Score 0.575 Taking the results from Round 5 Chains 29, Residues 199, Estimated correctness of the model 4.6 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4636 restraints for refining 2363 atoms. 3756 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2888 (Rfree = 0.000) for 2363 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 12: After refmac, R = 0.2710 (Rfree = 0.000) for 2342 atoms. Found 12 (15 requested) and removed 8 (7 requested) atoms. Cycle 13: After refmac, R = 0.2578 (Rfree = 0.000) for 2327 atoms. Found 11 (15 requested) and removed 9 (7 requested) atoms. Cycle 14: After refmac, R = 0.2574 (Rfree = 0.000) for 2322 atoms. Found 11 (14 requested) and removed 10 (7 requested) atoms. Cycle 15: After refmac, R = 0.2279 (Rfree = 0.000) for 2317 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 2.83 Search for helices and strands: 0 residues in 0 chains, 2351 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 2381 seeds are put forward Round 1: 188 peptides, 33 chains. Longest chain 14 peptides. Score 0.385 Round 2: 208 peptides, 30 chains. Longest chain 15 peptides. Score 0.494 Round 3: 213 peptides, 33 chains. Longest chain 17 peptides. Score 0.468 Round 4: 202 peptides, 28 chains. Longest chain 19 peptides. Score 0.503 Round 5: 211 peptides, 27 chains. Longest chain 27 peptides. Score 0.543 Taking the results from Round 5 Chains 27, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 5043 restraints for refining 2364 atoms. 4334 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2593 (Rfree = 0.000) for 2364 atoms. Found 11 (15 requested) and removed 11 (7 requested) atoms. Cycle 17: After refmac, R = 0.2731 (Rfree = 0.000) for 2350 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 18: After refmac, R = 0.2562 (Rfree = 0.000) for 2342 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 19: After refmac, R = 0.2598 (Rfree = 0.000) for 2342 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 20: After refmac, R = 0.2238 (Rfree = 0.000) for 2335 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 2.86 Search for helices and strands: 0 residues in 0 chains, 2392 seeds are put forward NCS extension: 39 residues added (3 deleted due to clashes), 2431 seeds are put forward Round 1: 174 peptides, 32 chains. Longest chain 10 peptides. Score 0.350 Round 2: 199 peptides, 31 chains. Longest chain 17 peptides. Score 0.452 Round 3: 214 peptides, 32 chains. Longest chain 21 peptides. Score 0.485 Round 4: 221 peptides, 33 chains. Longest chain 13 peptides. Score 0.493 Round 5: 190 peptides, 28 chains. Longest chain 12 peptides. Score 0.465 Taking the results from Round 4 Chains 33, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 5082 restraints for refining 2363 atoms. 4363 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2730 (Rfree = 0.000) for 2363 atoms. Found 14 (15 requested) and removed 10 (7 requested) atoms. Cycle 22: After refmac, R = 0.2774 (Rfree = 0.000) for 2357 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 23: After refmac, R = 0.2652 (Rfree = 0.000) for 2344 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 24: After refmac, R = 0.2683 (Rfree = 0.000) for 2340 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 25: After refmac, R = 0.2604 (Rfree = 0.000) for 2341 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 2.80 Search for helices and strands: 0 residues in 0 chains, 2430 seeds are put forward NCS extension: 0 residues added, 2430 seeds are put forward Round 1: 173 peptides, 31 chains. Longest chain 12 peptides. Score 0.362 Round 2: 190 peptides, 29 chains. Longest chain 14 peptides. Score 0.451 Round 3: 191 peptides, 28 chains. Longest chain 13 peptides. Score 0.469 Round 4: 179 peptides, 23 chains. Longest chain 22 peptides. Score 0.502 Round 5: 179 peptides, 26 chains. Longest chain 15 peptides. Score 0.459 Taking the results from Round 4 Chains 23, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 5227 restraints for refining 2364 atoms. 4626 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2782 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 27: After refmac, R = 0.2617 (Rfree = 0.000) for 2354 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 28: After refmac, R = 0.2635 (Rfree = 0.000) for 2349 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 29: After refmac, R = 0.2517 (Rfree = 0.000) for 2342 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.2494 (Rfree = 0.000) for 2344 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 2.86 Search for helices and strands: 0 residues in 0 chains, 2395 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 2420 seeds are put forward Round 1: 164 peptides, 29 chains. Longest chain 15 peptides. Score 0.361 Round 2: 193 peptides, 31 chains. Longest chain 17 peptides. Score 0.432 Round 3: 190 peptides, 32 chains. Longest chain 16 peptides. Score 0.407 Round 4: 193 peptides, 27 chains. Longest chain 22 peptides. Score 0.489 Round 5: 183 peptides, 26 chains. Longest chain 15 peptides. Score 0.472 Taking the results from Round 4 Chains 27, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 5253 restraints for refining 2364 atoms. 4616 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2728 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 32: After refmac, R = 0.2782 (Rfree = 0.000) for 2354 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 33: After refmac, R = 0.2449 (Rfree = 0.000) for 2358 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.2479 (Rfree = 0.000) for 2358 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 35: After refmac, R = 0.2541 (Rfree = 0.000) for 2356 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 2.85 Search for helices and strands: 0 residues in 0 chains, 2440 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2454 seeds are put forward Round 1: 162 peptides, 32 chains. Longest chain 11 peptides. Score 0.305 Round 2: 179 peptides, 28 chains. Longest chain 17 peptides. Score 0.429 Round 3: 192 peptides, 28 chains. Longest chain 18 peptides. Score 0.472 Round 4: 172 peptides, 24 chains. Longest chain 22 peptides. Score 0.465 Round 5: 192 peptides, 28 chains. Longest chain 19 peptides. Score 0.472 Taking the results from Round 5 Chains 29, Residues 164, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 5124 restraints for refining 2364 atoms. 4460 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2580 (Rfree = 0.000) for 2364 atoms. Found 12 (15 requested) and removed 7 (7 requested) atoms. Cycle 37: After refmac, R = 0.2615 (Rfree = 0.000) for 2359 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 38: After refmac, R = 0.2564 (Rfree = 0.000) for 2362 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.2389 (Rfree = 0.000) for 2359 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 40: After refmac, R = 0.2444 (Rfree = 0.000) for 2362 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 2.80 Search for helices and strands: 0 residues in 0 chains, 2427 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 2460 seeds are put forward Round 1: 164 peptides, 31 chains. Longest chain 11 peptides. Score 0.329 Round 2: 182 peptides, 28 chains. Longest chain 13 peptides. Score 0.439 Round 3: 181 peptides, 27 chains. Longest chain 14 peptides. Score 0.451 Round 4: 192 peptides, 27 chains. Longest chain 13 peptides. Score 0.486 Round 5: 185 peptides, 25 chains. Longest chain 21 peptides. Score 0.492 Taking the results from Round 5 Chains 25, Residues 160, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 5135 restraints for refining 2364 atoms. 4520 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2613 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 42: After refmac, R = 0.2569 (Rfree = 0.000) for 2350 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 43: After refmac, R = 0.2471 (Rfree = 0.000) for 2347 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.2317 (Rfree = 0.000) for 2351 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.2256 (Rfree = 0.000) for 2354 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 2.85 Search for helices and strands: 0 residues in 0 chains, 2414 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2431 seeds are put forward Round 1: 165 peptides, 34 chains. Longest chain 13 peptides. Score 0.285 Round 2: 183 peptides, 31 chains. Longest chain 16 peptides. Score 0.398 Round 3: 174 peptides, 30 chains. Longest chain 14 peptides. Score 0.381 Round 4: 181 peptides, 31 chains. Longest chain 15 peptides. Score 0.391 Round 5: 168 peptides, 27 chains. Longest chain 14 peptides. Score 0.406 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 141, 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 2nuj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5780 reflections ( 97.59 % complete ) and 5242 restraints for refining 2363 atoms. 4705 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2579 (Rfree = 0.000) for 2363 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2557 (Rfree = 0.000) for 2337 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2549 (Rfree = 0.000) for 2321 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2150 (Rfree = 0.000) for 2306 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... TimeTaking 31.42