Mon 24 Dec 00:08:40 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2nuj-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nuj-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nuj-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.6-parrot-mrncs ############### 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 00:08:44 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/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.6-parrot-mrncs/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-mrncs.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-mrncs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 0.85 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 2899 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3271 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2919 (Rfree = 0.000) for 2899 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 2.81 Search for helices and strands: 0 residues in 0 chains, 2944 seeds are put forward NCS extension: 0 residues added, 2944 seeds are put forward Round 1: 180 peptides, 29 chains. Longest chain 16 peptides. Score 0.417 Round 2: 228 peptides, 31 chains. Longest chain 17 peptides. Score 0.540 Round 3: 233 peptides, 27 chains. Longest chain 26 peptides. Score 0.603 Round 4: 232 peptides, 26 chains. Longest chain 21 peptides. Score 0.613 Round 5: 235 peptides, 28 chains. Longest chain 20 peptides. Score 0.597 Taking the results from Round 4 Chains 26, Residues 206, Estimated correctness of the model 19.7 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4766 restraints for refining 2364 atoms. 3908 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2751 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 2: After refmac, R = 0.2662 (Rfree = 0.000) for 2335 atoms. Found 10 (15 requested) and removed 7 (7 requested) atoms. Cycle 3: After refmac, R = 0.2592 (Rfree = 0.000) for 2324 atoms. Found 13 (14 requested) and removed 11 (7 requested) atoms. Cycle 4: After refmac, R = 0.2541 (Rfree = 0.000) for 2318 atoms. Found 12 (14 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.2191 (Rfree = 0.000) for 2310 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 2.86 Search for helices and strands: 0 residues in 0 chains, 2378 seeds are put forward NCS extension: 42 residues added (0 deleted due to clashes), 2420 seeds are put forward Round 1: 210 peptides, 27 chains. Longest chain 18 peptides. Score 0.540 Round 2: 233 peptides, 28 chains. Longest chain 29 peptides. Score 0.591 Round 3: 240 peptides, 24 chains. Longest chain 29 peptides. Score 0.655 Round 4: 237 peptides, 24 chains. Longest chain 29 peptides. Score 0.647 Round 5: 228 peptides, 23 chains. Longest chain 29 peptides. Score 0.637 Taking the results from Round 3 Chains 24, Residues 216, Estimated correctness of the model 34.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 5055 restraints for refining 2364 atoms. 4215 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2667 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 7: After refmac, R = 0.2519 (Rfree = 0.000) for 2349 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 8: After refmac, R = 0.2505 (Rfree = 0.000) for 2339 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 9: After refmac, R = 0.2599 (Rfree = 0.000) for 2329 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 10: After refmac, R = 0.2578 (Rfree = 0.000) for 2329 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 2.87 Search for helices and strands: 0 residues in 0 chains, 2418 seeds are put forward NCS extension: 46 residues added (8 deleted due to clashes), 2464 seeds are put forward Round 1: 200 peptides, 32 chains. Longest chain 16 peptides. Score 0.441 Round 2: 229 peptides, 28 chains. Longest chain 28 peptides. Score 0.581 Round 3: 230 peptides, 23 chains. Longest chain 28 peptides. Score 0.642 Round 4: 220 peptides, 25 chains. Longest chain 27 peptides. Score 0.593 Round 5: 222 peptides, 22 chains. Longest chain 30 peptides. Score 0.634 Taking the results from Round 3 Chains 23, Residues 207, Estimated correctness of the model 30.3 % 2 chains (46 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4609 restraints for refining 2363 atoms. 3627 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2561 (Rfree = 0.000) for 2363 atoms. Found 13 (15 requested) and removed 15 (7 requested) atoms. Cycle 12: After refmac, R = 0.2421 (Rfree = 0.000) for 2334 atoms. Found 9 (15 requested) and removed 9 (7 requested) atoms. Cycle 13: After refmac, R = 0.2338 (Rfree = 0.000) for 2327 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. Cycle 14: After refmac, R = 0.2338 (Rfree = 0.000) for 2320 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 15: After refmac, R = 0.2343 (Rfree = 0.000) for 2314 atoms. Found 11 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 2.84 Search for helices and strands: 0 residues in 0 chains, 2361 seeds are put forward NCS extension: 27 residues added (12 deleted due to clashes), 2388 seeds are put forward Round 1: 214 peptides, 25 chains. Longest chain 27 peptides. Score 0.577 Round 2: 228 peptides, 23 chains. Longest chain 29 peptides. Score 0.637 Round 3: 221 peptides, 22 chains. Longest chain 32 peptides. Score 0.632 Round 4: 224 peptides, 22 chains. Longest chain 29 peptides. Score 0.639 Round 5: 210 peptides, 23 chains. Longest chain 22 peptides. Score 0.592 Taking the results from Round 4 Chains 26, Residues 202, Estimated correctness of the model 29.3 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4770 restraints for refining 2363 atoms. 3867 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2642 (Rfree = 0.000) for 2363 atoms. Found 12 (15 requested) and removed 12 (7 requested) atoms. Cycle 17: After refmac, R = 0.2673 (Rfree = 0.000) for 2345 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 18: After refmac, R = 0.2625 (Rfree = 0.000) for 2342 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 19: After refmac, R = 0.2603 (Rfree = 0.000) for 2339 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.2331 (Rfree = 0.000) for 2333 atoms. Found 10 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 2.81 Search for helices and strands: 0 residues in 0 chains, 2379 seeds are put forward NCS extension: 54 residues added (1 deleted due to clashes), 2433 seeds are put forward Round 1: 211 peptides, 32 chains. Longest chain 14 peptides. Score 0.476 Round 2: 215 peptides, 25 chains. Longest chain 35 peptides. Score 0.580 Round 3: 223 peptides, 25 chains. Longest chain 27 peptides. Score 0.601 Round 4: 218 peptides, 29 chains. Longest chain 16 peptides. Score 0.537 Round 5: 223 peptides, 26 chains. Longest chain 31 peptides. Score 0.589 Taking the results from Round 3 Chains 26, Residues 198, Estimated correctness of the model 15.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 5010 restraints for refining 2364 atoms. 4200 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2696 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 22: After refmac, R = 0.2658 (Rfree = 0.000) for 2349 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 23: After refmac, R = 0.2534 (Rfree = 0.000) for 2348 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 24: After refmac, R = 0.2263 (Rfree = 0.000) for 2346 atoms. Found 7 (15 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.2191 (Rfree = 0.000) for 2337 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 2.85 Search for helices and strands: 0 residues in 0 chains, 2394 seeds are put forward NCS extension: 35 residues added (0 deleted due to clashes), 2429 seeds are put forward Round 1: 188 peptides, 31 chains. Longest chain 11 peptides. Score 0.415 Round 2: 215 peptides, 29 chains. Longest chain 19 peptides. Score 0.529 Round 3: 223 peptides, 31 chains. Longest chain 19 peptides. Score 0.526 Round 4: 227 peptides, 28 chains. Longest chain 26 peptides. Score 0.575 Round 5: 219 peptides, 23 chains. Longest chain 31 peptides. Score 0.615 Taking the results from Round 5 Chains 25, Residues 196, Estimated correctness of the model 20.4 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4735 restraints for refining 2364 atoms. 3883 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2891 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 27: After refmac, R = 0.2917 (Rfree = 0.000) for 2353 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 28: After refmac, R = 0.2658 (Rfree = 0.000) for 2344 atoms. Found 13 (15 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.2418 (Rfree = 0.000) for 2341 atoms. Found 4 (15 requested) and removed 10 (7 requested) atoms. Cycle 30: After refmac, R = 0.2660 (Rfree = 0.000) for 2322 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 2.77 Search for helices and strands: 0 residues in 0 chains, 2385 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2402 seeds are put forward Round 1: 189 peptides, 31 chains. Longest chain 10 peptides. Score 0.418 Round 2: 199 peptides, 27 chains. Longest chain 19 peptides. Score 0.508 Round 3: 207 peptides, 23 chains. Longest chain 24 peptides. Score 0.583 Round 4: 218 peptides, 27 chains. Longest chain 19 peptides. Score 0.563 Round 5: 207 peptides, 26 chains. Longest chain 20 peptides. Score 0.545 Taking the results from Round 3 Chains 24, Residues 184, Estimated correctness of the model 7.9 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4830 restraints for refining 2364 atoms. 4058 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2911 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 32: After refmac, R = 0.2738 (Rfree = 0.000) for 2344 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 33: After refmac, R = 0.2761 (Rfree = 0.000) for 2336 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 34: After refmac, R = 0.2752 (Rfree = 0.000) for 2334 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 35: After refmac, R = 0.2645 (Rfree = 0.000) for 2334 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 2.78 Search for helices and strands: 0 residues in 0 chains, 2418 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2442 seeds are put forward Round 1: 158 peptides, 26 chains. Longest chain 19 peptides. Score 0.387 Round 2: 193 peptides, 29 chains. Longest chain 19 peptides. Score 0.461 Round 3: 196 peptides, 27 chains. Longest chain 17 peptides. Score 0.498 Round 4: 208 peptides, 25 chains. Longest chain 32 peptides. Score 0.561 Round 5: 196 peptides, 23 chains. Longest chain 31 peptides. Score 0.553 Taking the results from Round 4 Chains 27, Residues 183, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4790 restraints for refining 2363 atoms. 3987 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2700 (Rfree = 0.000) for 2363 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 37: After refmac, R = 0.2722 (Rfree = 0.000) for 2354 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 38: After refmac, R = 0.2724 (Rfree = 0.000) for 2349 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.2647 (Rfree = 0.000) for 2347 atoms. Found 10 (15 requested) and removed 14 (7 requested) atoms. Cycle 40: After refmac, R = 0.2528 (Rfree = 0.000) for 2337 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 2.86 Search for helices and strands: 0 residues in 0 chains, 2390 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 2425 seeds are put forward Round 1: 164 peptides, 30 chains. Longest chain 12 peptides. Score 0.345 Round 2: 190 peptides, 24 chains. Longest chain 17 peptides. Score 0.522 Round 3: 205 peptides, 27 chains. Longest chain 18 peptides. Score 0.526 Round 4: 191 peptides, 26 chains. Longest chain 15 peptides. Score 0.497 Round 5: 204 peptides, 26 chains. Longest chain 17 peptides. Score 0.536 Taking the results from Round 5 Chains 27, Residues 178, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 5032 restraints for refining 2364 atoms. 4292 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2695 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 42: After refmac, R = 0.2708 (Rfree = 0.000) for 2355 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 43: After refmac, R = 0.2536 (Rfree = 0.000) for 2348 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.2626 (Rfree = 0.000) for 2347 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.2311 (Rfree = 0.000) for 2351 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 2.84 Search for helices and strands: 0 residues in 0 chains, 2417 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 2428 seeds are put forward Round 1: 166 peptides, 27 chains. Longest chain 17 peptides. Score 0.399 Round 2: 169 peptides, 26 chains. Longest chain 19 peptides. Score 0.425 Round 3: 186 peptides, 27 chains. Longest chain 17 peptides. Score 0.467 Round 4: 192 peptides, 26 chains. Longest chain 15 peptides. Score 0.500 Round 5: 181 peptides, 24 chains. Longest chain 16 peptides. Score 0.494 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 166, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 5 % 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 5194 restraints for refining 2364 atoms. 4534 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2714 (Rfree = 0.000) for 2364 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2812 (Rfree = 0.000) for 2342 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2811 (Rfree = 0.000) for 2324 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2608 (Rfree = 0.000) for 2309 atoms. TimeTaking 31.53