Sun 23 Dec 23:45:45 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 2aj7-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aj7-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aj7-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-3.6-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/2aj7-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-3.6-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 ============================================================ Sun 23 Dec 23:45:50 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/2aj7-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-3.6-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 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-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: 173 Cell parameters: 108.801 108.801 82.811 90.000 90.000 120.000 Input sequence file: 2aj7-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 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 2887 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3255 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3543 (Rfree = 0.000) for 2887 atoms. Found 18 (18 requested) and removed 64 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.81 2.92 Search for helices and strands: 0 residues in 0 chains, 2872 seeds are put forward NCS extension: 0 residues added, 2872 seeds are put forward Round 1: 162 peptides, 27 chains. Longest chain 12 peptides. Score 0.357 Round 2: 201 peptides, 24 chains. Longest chain 25 peptides. Score 0.507 Round 3: 207 peptides, 24 chains. Longest chain 23 peptides. Score 0.522 Round 4: 226 peptides, 24 chains. Longest chain 23 peptides. Score 0.568 Round 5: 221 peptides, 23 chains. Longest chain 27 peptides. Score 0.567 Taking the results from Round 4 Chains 24, Residues 202, Estimated correctness of the model 1.7 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 4792 restraints for refining 2362 atoms. 3958 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3080 (Rfree = 0.000) for 2362 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 2: After refmac, R = 0.2948 (Rfree = 0.000) for 2318 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 3: After refmac, R = 0.2742 (Rfree = 0.000) for 2290 atoms. Found 5 (14 requested) and removed 14 (7 requested) atoms. Cycle 4: After refmac, R = 0.2628 (Rfree = 0.000) for 2256 atoms. Found 8 (14 requested) and removed 11 (7 requested) atoms. Cycle 5: After refmac, R = 0.2578 (Rfree = 0.000) for 2237 atoms. Found 10 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 2.58 Search for helices and strands: 0 residues in 0 chains, 2294 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2311 seeds are put forward Round 1: 211 peptides, 28 chains. Longest chain 19 peptides. Score 0.485 Round 2: 224 peptides, 23 chains. Longest chain 25 peptides. Score 0.574 Round 3: 223 peptides, 22 chains. Longest chain 21 peptides. Score 0.583 Round 4: 218 peptides, 22 chains. Longest chain 23 peptides. Score 0.571 Round 5: 227 peptides, 25 chains. Longest chain 25 peptides. Score 0.559 Taking the results from Round 3 Chains 22, Residues 201, Estimated correctness of the model 7.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 4883 restraints for refining 2364 atoms. 4101 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2886 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 7: After refmac, R = 0.2714 (Rfree = 0.000) for 2343 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 8: After refmac, R = 0.2521 (Rfree = 0.000) for 2331 atoms. Found 14 (15 requested) and removed 12 (7 requested) atoms. Cycle 9: After refmac, R = 0.2538 (Rfree = 0.000) for 2323 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 10: After refmac, R = 0.2460 (Rfree = 0.000) for 2316 atoms. Found 9 (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, 2402 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 2415 seeds are put forward Round 1: 212 peptides, 26 chains. Longest chain 22 peptides. Score 0.511 Round 2: 224 peptides, 24 chains. Longest chain 32 peptides. Score 0.563 Round 3: 237 peptides, 22 chains. Longest chain 34 peptides. Score 0.613 Round 4: 230 peptides, 23 chains. Longest chain 27 peptides. Score 0.588 Round 5: 229 peptides, 21 chains. Longest chain 28 peptides. Score 0.607 Taking the results from Round 3 Chains 22, Residues 215, Estimated correctness of the model 19.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 4946 restraints for refining 2364 atoms. 4108 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2851 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 12: After refmac, R = 0.2854 (Rfree = 0.000) for 2340 atoms. Found 13 (15 requested) and removed 16 (7 requested) atoms. Cycle 13: After refmac, R = 0.2770 (Rfree = 0.000) for 2317 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 14: After refmac, R = 0.2794 (Rfree = 0.000) for 2298 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 15: After refmac, R = 0.2752 (Rfree = 0.000) for 2292 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 2.62 Search for helices and strands: 0 residues in 0 chains, 2373 seeds are put forward NCS extension: 31 residues added (19 deleted due to clashes), 2404 seeds are put forward Round 1: 212 peptides, 27 chains. Longest chain 32 peptides. Score 0.499 Round 2: 243 peptides, 23 chains. Longest chain 39 peptides. Score 0.616 Round 3: 237 peptides, 21 chains. Longest chain 32 peptides. Score 0.624 Round 4: 220 peptides, 21 chains. Longest chain 36 peptides. Score 0.587 Round 5: 239 peptides, 22 chains. Longest chain 41 peptides. Score 0.618 Taking the results from Round 3 Chains 24, Residues 216, Estimated correctness of the model 23.7 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 4627 restraints for refining 2364 atoms. 3663 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2916 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 17: After refmac, R = 0.2824 (Rfree = 0.000) for 2346 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 18: After refmac, R = 0.2492 (Rfree = 0.000) for 2335 atoms. Found 7 (15 requested) and removed 11 (7 requested) atoms. Cycle 19: After refmac, R = 0.2699 (Rfree = 0.000) for 2322 atoms. Found 13 (14 requested) and removed 11 (7 requested) atoms. Cycle 20: After refmac, R = 0.2664 (Rfree = 0.000) for 2322 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 2.70 Search for helices and strands: 0 residues in 0 chains, 2417 seeds are put forward NCS extension: 30 residues added (6 deleted due to clashes), 2447 seeds are put forward Round 1: 205 peptides, 26 chains. Longest chain 30 peptides. Score 0.493 Round 2: 234 peptides, 25 chains. Longest chain 27 peptides. Score 0.575 Round 3: 229 peptides, 22 chains. Longest chain 35 peptides. Score 0.596 Round 4: 213 peptides, 20 chains. Longest chain 39 peptides. Score 0.582 Round 5: 223 peptides, 22 chains. Longest chain 25 peptides. Score 0.583 Taking the results from Round 3 Chains 22, Residues 207, Estimated correctness of the model 13.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 5079 restraints for refining 2364 atoms. 4273 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3031 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 22: After refmac, R = 0.2855 (Rfree = 0.000) for 2347 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 23: After refmac, R = 0.2471 (Rfree = 0.000) for 2336 atoms. Found 5 (15 requested) and removed 11 (7 requested) atoms. Cycle 24: After refmac, R = 0.2710 (Rfree = 0.000) for 2319 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.2661 (Rfree = 0.000) for 2321 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 2.63 Search for helices and strands: 0 residues in 0 chains, 2390 seeds are put forward NCS extension: 54 residues added (0 deleted due to clashes), 2444 seeds are put forward Round 1: 228 peptides, 29 chains. Longest chain 21 peptides. Score 0.516 Round 2: 240 peptides, 24 chains. Longest chain 31 peptides. Score 0.599 Round 3: 250 peptides, 23 chains. Longest chain 29 peptides. Score 0.630 Round 4: 248 peptides, 21 chains. Longest chain 37 peptides. Score 0.646 Round 5: 233 peptides, 20 chains. Longest chain 28 peptides. Score 0.625 Taking the results from Round 4 Chains 24, Residues 227, Estimated correctness of the model 31.7 % 4 chains (86 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 4115 restraints for refining 2364 atoms. 2838 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3129 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 27: After refmac, R = 0.3116 (Rfree = 0.000) for 2327 atoms. Found 14 (15 requested) and removed 15 (7 requested) atoms. Cycle 28: After refmac, R = 0.2953 (Rfree = 0.000) for 2314 atoms. Found 9 (14 requested) and removed 11 (7 requested) atoms. Cycle 29: After refmac, R = 0.3007 (Rfree = 0.000) for 2301 atoms. Found 7 (14 requested) and removed 27 (7 requested) atoms. Cycle 30: After refmac, R = 0.2791 (Rfree = 0.000) for 2271 atoms. Found 5 (14 requested) and removed 19 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 2.67 Search for helices and strands: 0 residues in 0 chains, 2312 seeds are put forward NCS extension: 49 residues added (1 deleted due to clashes), 2361 seeds are put forward Round 1: 212 peptides, 28 chains. Longest chain 22 peptides. Score 0.487 Round 2: 211 peptides, 21 chains. Longest chain 21 peptides. Score 0.566 Round 3: 229 peptides, 23 chains. Longest chain 33 peptides. Score 0.585 Round 4: 213 peptides, 24 chains. Longest chain 20 peptides. Score 0.537 Round 5: 219 peptides, 24 chains. Longest chain 25 peptides. Score 0.551 Taking the results from Round 3 Chains 23, Residues 206, Estimated correctness of the model 8.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 5184 restraints for refining 2363 atoms. 4383 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3213 (Rfree = 0.000) for 2363 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 32: After refmac, R = 0.2867 (Rfree = 0.000) for 2339 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2830 (Rfree = 0.000) for 2319 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 34: After refmac, R = 0.2620 (Rfree = 0.000) for 2304 atoms. Found 2 (14 requested) and removed 13 (7 requested) atoms. Cycle 35: After refmac, R = 0.2847 (Rfree = 0.000) for 2284 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 2.59 Search for helices and strands: 0 residues in 0 chains, 2328 seeds are put forward NCS extension: 18 residues added (6 deleted due to clashes), 2346 seeds are put forward Round 1: 201 peptides, 28 chains. Longest chain 27 peptides. Score 0.458 Round 2: 207 peptides, 22 chains. Longest chain 42 peptides. Score 0.545 Round 3: 203 peptides, 22 chains. Longest chain 19 peptides. Score 0.535 Round 4: 203 peptides, 20 chains. Longest chain 40 peptides. Score 0.559 Round 5: 201 peptides, 21 chains. Longest chain 43 peptides. Score 0.542 Taking the results from Round 4 Chains 23, Residues 183, Estimated correctness of the model 0.0 % 2 chains (45 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 4753 restraints for refining 2363 atoms. 3866 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3065 (Rfree = 0.000) for 2363 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 37: After refmac, R = 0.2959 (Rfree = 0.000) for 2343 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 38: After refmac, R = 0.2916 (Rfree = 0.000) for 2332 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 39: After refmac, R = 0.2916 (Rfree = 0.000) for 2323 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 40: After refmac, R = 0.2752 (Rfree = 0.000) for 2309 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 2.58 Search for helices and strands: 0 residues in 0 chains, 2371 seeds are put forward NCS extension: 44 residues added (8 deleted due to clashes), 2415 seeds are put forward Round 1: 194 peptides, 26 chains. Longest chain 19 peptides. Score 0.464 Round 2: 200 peptides, 23 chains. Longest chain 21 peptides. Score 0.516 Round 3: 200 peptides, 28 chains. Longest chain 22 peptides. Score 0.455 Round 4: 215 peptides, 25 chains. Longest chain 23 peptides. Score 0.530 Round 5: 210 peptides, 24 chains. Longest chain 21 peptides. Score 0.529 Taking the results from Round 4 Chains 25, Residues 190, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6555 reflections ( 99.92 % complete ) and 5263 restraints for refining 2364 atoms. 4528 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2994 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 42: After refmac, R = 0.2899 (Rfree = 0.000) for 2353 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 43: After refmac, R = 0.2809 (Rfree = 0.000) for 2341 atoms. Found 13 (15 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.2601 (Rfree = 0.000) for 2334 atoms. Found 9 (15 requested) and removed 10 (7 requested) atoms. Cycle 45: After refmac, R = 0.2779 (Rfree = 0.000) for 2329 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 2.59 Search for helices and strands: 0 residues in 0 chains, 2386 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 2424 seeds are put forward Round 1: 187 peptides, 25 chains. Longest chain 23 peptides. Score 0.457 Round 2: 208 peptides, 25 chains. Longest chain 24 peptides. Score 0.513 Round 3: 208 peptides, 29 chains. Longest chain 21 peptides. Score 0.465 Round 4: 207 peptides, 25 chains. Longest chain 21 peptides. Score 0.510 Round 5: 212 peptides, 22 chains. Longest chain 35 peptides. Score 0.557 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 190, Estimated correctness of the model 0.0 % 2 chains (54 residues) have been docked in sequence Sequence coverage is 28 % Consider running further cycles of model building using 2aj7-3_warpNtrace.pdb as input Building loops using Loopy2018 24 chains (190 residues) following loop building 2 chains (54 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6555 reflections ( 99.92 % complete ) and 4575 restraints for refining 2364 atoms. 3617 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3181 (Rfree = 0.000) for 2364 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.3298 (Rfree = 0.000) for 2316 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.3069 (Rfree = 0.000) for 2279 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.3110 (Rfree = 0.000) for 2255 atoms. TimeTaking 45.43