Mon 24 Dec 00:51:02 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-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nuj-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nuj-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-4.0-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-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-4.0-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 00:51:07 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-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-4.0-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 306 and 0 Target number of residues in the AU: 306 Target solvent content: 0.6441 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-4.0-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-4.0-parrot-mrncs.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 4.001 Wilson plot Bfac: 74.31 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4253 reflections ( 97.23 % complete ) and 0 restraints for refining 2899 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3534 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2751 (Rfree = 0.000) for 2899 atoms. Found 12 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.05 Search for helices and strands: 0 residues in 0 chains, 2941 seeds are put forward NCS extension: 0 residues added, 2941 seeds are put forward Round 1: 148 peptides, 27 chains. Longest chain 12 peptides. Score 0.333 Round 2: 191 peptides, 30 chains. Longest chain 16 peptides. Score 0.440 Round 3: 197 peptides, 29 chains. Longest chain 18 peptides. Score 0.474 Round 4: 201 peptides, 29 chains. Longest chain 17 peptides. Score 0.486 Round 5: 201 peptides, 25 chains. Longest chain 21 peptides. Score 0.541 Taking the results from Round 5 Chains 25, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5199 restraints for refining 2355 atoms. 4520 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2755 (Rfree = 0.000) for 2355 atoms. Found 8 (11 requested) and removed 5 (5 requested) atoms. Cycle 2: After refmac, R = 0.2630 (Rfree = 0.000) for 2334 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 3: After refmac, R = 0.2562 (Rfree = 0.000) for 2317 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 4: After refmac, R = 0.2514 (Rfree = 0.000) for 2309 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.2467 (Rfree = 0.000) for 2303 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.11 Search for helices and strands: 0 residues in 0 chains, 2363 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2381 seeds are put forward Round 1: 168 peptides, 28 chains. Longest chain 14 peptides. Score 0.391 Round 2: 204 peptides, 27 chains. Longest chain 21 peptides. Score 0.523 Round 3: 215 peptides, 29 chains. Longest chain 18 peptides. Score 0.529 Round 4: 205 peptides, 26 chains. Longest chain 16 peptides. Score 0.539 Round 5: 204 peptides, 27 chains. Longest chain 16 peptides. Score 0.523 Taking the results from Round 4 Chains 26, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5206 restraints for refining 2355 atoms. 4516 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2664 (Rfree = 0.000) for 2355 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 7: After refmac, R = 0.2517 (Rfree = 0.000) for 2337 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 8: After refmac, R = 0.2479 (Rfree = 0.000) for 2333 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 9: After refmac, R = 0.2460 (Rfree = 0.000) for 2328 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.2425 (Rfree = 0.000) for 2323 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 3.11 Search for helices and strands: 0 residues in 0 chains, 2373 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2392 seeds are put forward Round 1: 162 peptides, 29 chains. Longest chain 10 peptides. Score 0.354 Round 2: 185 peptides, 28 chains. Longest chain 16 peptides. Score 0.449 Round 3: 180 peptides, 23 chains. Longest chain 19 peptides. Score 0.505 Round 4: 185 peptides, 27 chains. Longest chain 15 peptides. Score 0.464 Round 5: 182 peptides, 23 chains. Longest chain 16 peptides. Score 0.511 Taking the results from Round 5 Chains 23, Residues 159, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5252 restraints for refining 2355 atoms. 4612 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2589 (Rfree = 0.000) for 2355 atoms. Found 8 (11 requested) and removed 5 (5 requested) atoms. Cycle 12: After refmac, R = 0.2494 (Rfree = 0.000) for 2342 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 13: After refmac, R = 0.2402 (Rfree = 0.000) for 2338 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.2369 (Rfree = 0.000) for 2331 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 15: After refmac, R = 0.2339 (Rfree = 0.000) for 2326 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.08 Search for helices and strands: 0 residues in 0 chains, 2385 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 2397 seeds are put forward Round 1: 178 peptides, 31 chains. Longest chain 13 peptides. Score 0.380 Round 2: 188 peptides, 26 chains. Longest chain 19 peptides. Score 0.488 Round 3: 199 peptides, 32 chains. Longest chain 14 peptides. Score 0.437 Round 4: 185 peptides, 23 chains. Longest chain 16 peptides. Score 0.520 Round 5: 207 peptides, 27 chains. Longest chain 17 peptides. Score 0.532 Taking the results from Round 5 Chains 27, Residues 180, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5178 restraints for refining 2354 atoms. 4429 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2579 (Rfree = 0.000) for 2354 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 17: After refmac, R = 0.2468 (Rfree = 0.000) for 2341 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 18: After refmac, R = 0.2384 (Rfree = 0.000) for 2333 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.2333 (Rfree = 0.000) for 2328 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2372 (Rfree = 0.000) for 2324 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.15 Search for helices and strands: 0 residues in 0 chains, 2380 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 2401 seeds are put forward Round 1: 170 peptides, 28 chains. Longest chain 14 peptides. Score 0.398 Round 2: 173 peptides, 24 chains. Longest chain 16 peptides. Score 0.468 Round 3: 173 peptides, 21 chains. Longest chain 17 peptides. Score 0.512 Round 4: 175 peptides, 24 chains. Longest chain 19 peptides. Score 0.475 Round 5: 178 peptides, 22 chains. Longest chain 19 peptides. Score 0.513 Taking the results from Round 5 Chains 22, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5472 restraints for refining 2354 atoms. 4870 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2759 (Rfree = 0.000) for 2354 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 22: After refmac, R = 0.2561 (Rfree = 0.000) for 2354 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 23: After refmac, R = 0.2483 (Rfree = 0.000) for 2352 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 24: After refmac, R = 0.2451 (Rfree = 0.000) for 2346 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2415 (Rfree = 0.000) for 2341 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 3.09 Search for helices and strands: 0 residues in 0 chains, 2400 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2415 seeds are put forward Round 1: 160 peptides, 32 chains. Longest chain 9 peptides. Score 0.298 Round 2: 183 peptides, 28 chains. Longest chain 13 peptides. Score 0.442 Round 3: 176 peptides, 27 chains. Longest chain 14 peptides. Score 0.434 Round 4: 187 peptides, 27 chains. Longest chain 16 peptides. Score 0.470 Round 5: 182 peptides, 26 chains. Longest chain 14 peptides. Score 0.468 Taking the results from Round 4 Chains 27, Residues 160, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5245 restraints for refining 2355 atoms. 4608 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2738 (Rfree = 0.000) for 2355 atoms. Found 7 (11 requested) and removed 9 (5 requested) atoms. Cycle 27: After refmac, R = 0.2594 (Rfree = 0.000) for 2343 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.2558 (Rfree = 0.000) for 2337 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.2508 (Rfree = 0.000) for 2334 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.2495 (Rfree = 0.000) for 2326 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 3.12 Search for helices and strands: 0 residues in 0 chains, 2385 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2411 seeds are put forward Round 1: 159 peptides, 29 chains. Longest chain 12 peptides. Score 0.342 Round 2: 157 peptides, 26 chains. Longest chain 10 peptides. Score 0.383 Round 3: 187 peptides, 28 chains. Longest chain 15 peptides. Score 0.456 Round 4: 168 peptides, 28 chains. Longest chain 16 peptides. Score 0.391 Round 5: 171 peptides, 25 chains. Longest chain 12 peptides. Score 0.447 Taking the results from Round 3 Chains 28, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5456 restraints for refining 2355 atoms. 4848 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2553 (Rfree = 0.000) for 2355 atoms. Found 9 (11 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.2460 (Rfree = 0.000) for 2340 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.2539 (Rfree = 0.000) for 2331 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2443 (Rfree = 0.000) for 2327 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2431 (Rfree = 0.000) for 2323 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.13 Search for helices and strands: 0 residues in 0 chains, 2369 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2381 seeds are put forward Round 1: 149 peptides, 26 chains. Longest chain 21 peptides. Score 0.354 Round 2: 171 peptides, 27 chains. Longest chain 13 peptides. Score 0.417 Round 3: 158 peptides, 25 chains. Longest chain 19 peptides. Score 0.402 Round 4: 162 peptides, 25 chains. Longest chain 12 peptides. Score 0.416 Round 5: 156 peptides, 27 chains. Longest chain 11 peptides. Score 0.363 Taking the results from Round 2 Chains 27, Residues 144, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5497 restraints for refining 2355 atoms. 4933 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2728 (Rfree = 0.000) for 2355 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 37: After refmac, R = 0.2646 (Rfree = 0.000) for 2352 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.2625 (Rfree = 0.000) for 2349 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. Cycle 39: After refmac, R = 0.2571 (Rfree = 0.000) for 2344 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2574 (Rfree = 0.000) for 2343 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.10 Search for helices and strands: 0 residues in 0 chains, 2397 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 2416 seeds are put forward Round 1: 138 peptides, 26 chains. Longest chain 10 peptides. Score 0.312 Round 2: 169 peptides, 28 chains. Longest chain 12 peptides. Score 0.394 Round 3: 154 peptides, 23 chains. Longest chain 16 peptides. Score 0.420 Round 4: 155 peptides, 24 chains. Longest chain 12 peptides. Score 0.407 Round 5: 146 peptides, 21 chains. Longest chain 16 peptides. Score 0.423 Taking the results from Round 5 Chains 21, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5615 restraints for refining 2355 atoms. 5136 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2747 (Rfree = 0.000) for 2355 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 42: After refmac, R = 0.2622 (Rfree = 0.000) for 2361 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 43: After refmac, R = 0.2566 (Rfree = 0.000) for 2354 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2530 (Rfree = 0.000) for 2352 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2547 (Rfree = 0.000) for 2348 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.13 Search for helices and strands: 0 residues in 0 chains, 2401 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2416 seeds are put forward Round 1: 124 peptides, 24 chains. Longest chain 9 peptides. Score 0.290 Round 2: 131 peptides, 23 chains. Longest chain 10 peptides. Score 0.335 Round 3: 130 peptides, 20 chains. Longest chain 13 peptides. Score 0.382 Round 4: 132 peptides, 19 chains. Longest chain 20 peptides. Score 0.406 Round 5: 141 peptides, 22 chains. Longest chain 15 peptides. Score 0.389 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 113, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2nuj-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4253 reflections ( 97.23 % complete ) and 5649 restraints for refining 2355 atoms. 5181 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2682 (Rfree = 0.000) for 2355 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2610 (Rfree = 0.000) for 2347 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2621 (Rfree = 0.000) for 2341 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2596 (Rfree = 0.000) for 2336 atoms. TimeTaking 35.7