Mon 24 Dec 07:28:10 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-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2nuj-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2nuj-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.2-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-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.2-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 07:28:14 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-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.2-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 337 and 0 Target number of residues in the AU: 337 Target solvent content: 0.6081 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-3.2-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-3.2-parrot-noncs.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 3.200 Wilson plot Bfac: 55.75 8166 reflections ( 97.97 % complete ) and 0 restraints for refining 2910 atoms. Observations/parameters ratio is 0.70 ------------------------------------------------------ Starting model: R = 0.3475 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3054 (Rfree = 0.000) for 2910 atoms. Found 26 (26 requested) and removed 27 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 2.63 Search for helices and strands: 0 residues in 0 chains, 2932 seeds are put forward NCS extension: 0 residues added, 2932 seeds are put forward Round 1: 179 peptides, 34 chains. Longest chain 12 peptides. Score 0.337 Round 2: 213 peptides, 38 chains. Longest chain 13 peptides. Score 0.397 Round 3: 240 peptides, 39 chains. Longest chain 17 peptides. Score 0.471 Round 4: 235 peptides, 36 chains. Longest chain 21 peptides. Score 0.496 Round 5: 235 peptides, 29 chains. Longest chain 28 peptides. Score 0.585 Taking the results from Round 5 Chains 32, Residues 206, Estimated correctness of the model 37.0 % 5 chains (72 residues) have been docked in sequence ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 4768 restraints for refining 2598 atoms. 3693 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2729 (Rfree = 0.000) for 2598 atoms. Found 16 (23 requested) and removed 18 (11 requested) atoms. Cycle 2: After refmac, R = 0.2586 (Rfree = 0.000) for 2564 atoms. Found 9 (23 requested) and removed 17 (11 requested) atoms. Cycle 3: After refmac, R = 0.2486 (Rfree = 0.000) for 2546 atoms. Found 3 (22 requested) and removed 13 (11 requested) atoms. Cycle 4: After refmac, R = 0.2488 (Rfree = 0.000) for 2527 atoms. Found 3 (22 requested) and removed 14 (11 requested) atoms. Cycle 5: After refmac, R = 0.2414 (Rfree = 0.000) for 2512 atoms. Found 7 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.07 2.61 Search for helices and strands: 0 residues in 0 chains, 2564 seeds are put forward NCS extension: 45 residues added (0 deleted due to clashes), 2609 seeds are put forward Round 1: 223 peptides, 34 chains. Longest chain 19 peptides. Score 0.486 Round 2: 252 peptides, 33 chains. Longest chain 38 peptides. Score 0.582 Round 3: 239 peptides, 29 chains. Longest chain 31 peptides. Score 0.595 Round 4: 237 peptides, 30 chains. Longest chain 39 peptides. Score 0.578 Round 5: 250 peptides, 27 chains. Longest chain 34 peptides. Score 0.645 Taking the results from Round 5 Chains 30, Residues 223, Estimated correctness of the model 52.6 % 3 chains (50 residues) have been docked in sequence ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 4537 restraints for refining 2447 atoms. 3484 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2816 (Rfree = 0.000) for 2447 atoms. Found 16 (21 requested) and removed 14 (10 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.3025 (Rfree = 0.000) for 2443 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 8: After refmac, R = 0.2885 (Rfree = 0.000) for 2442 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 9: After refmac, R = 0.2902 (Rfree = 0.000) for 2442 atoms. Found 21 (21 requested) and removed 13 (10 requested) atoms. Cycle 10: After refmac, R = 0.2566 (Rfree = 0.000) for 2441 atoms. Found 12 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 2.61 Search for helices and strands: 0 residues in 0 chains, 2493 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 2525 seeds are put forward Round 1: 226 peptides, 32 chains. Longest chain 19 peptides. Score 0.522 Round 2: 234 peptides, 27 chains. Longest chain 30 peptides. Score 0.606 Round 3: 238 peptides, 24 chains. Longest chain 28 peptides. Score 0.650 Round 4: 251 peptides, 26 chains. Longest chain 41 peptides. Score 0.658 Round 5: 252 peptides, 26 chains. Longest chain 38 peptides. Score 0.660 Taking the results from Round 5 Chains 28, Residues 226, Estimated correctness of the model 56.2 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 4405 restraints for refining 2381 atoms. 3354 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2784 (Rfree = 0.000) for 2381 atoms. Found 21 (21 requested) and removed 11 (10 requested) atoms. Cycle 12: After refmac, R = 0.2822 (Rfree = 0.000) for 2378 atoms. Found 15 (21 requested) and removed 12 (10 requested) atoms. Cycle 13: After refmac, R = 0.2659 (Rfree = 0.000) for 2376 atoms. Found 16 (21 requested) and removed 14 (10 requested) atoms. Cycle 14: After refmac, R = 0.2629 (Rfree = 0.000) for 2370 atoms. Found 14 (21 requested) and removed 10 (10 requested) atoms. Cycle 15: After refmac, R = 0.2554 (Rfree = 0.000) for 2374 atoms. Found 9 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.06 2.60 Search for helices and strands: 0 residues in 0 chains, 2426 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 2458 seeds are put forward Round 1: 225 peptides, 32 chains. Longest chain 29 peptides. Score 0.519 Round 2: 248 peptides, 26 chains. Longest chain 38 peptides. Score 0.651 Round 3: 251 peptides, 26 chains. Longest chain 38 peptides. Score 0.658 Round 4: 247 peptides, 26 chains. Longest chain 26 peptides. Score 0.649 Round 5: 252 peptides, 24 chains. Longest chain 38 peptides. Score 0.681 Taking the results from Round 5 Chains 25, Residues 228, Estimated correctness of the model 61.0 % 3 chains (59 residues) have been docked in sequence ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 4213 restraints for refining 2381 atoms. 3082 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2741 (Rfree = 0.000) for 2381 atoms. Found 19 (21 requested) and removed 17 (10 requested) atoms. Cycle 17: After refmac, R = 0.2599 (Rfree = 0.000) for 2366 atoms. Found 15 (21 requested) and removed 13 (10 requested) atoms. Cycle 18: After refmac, R = 0.2523 (Rfree = 0.000) for 2361 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. Cycle 19: After refmac, R = 0.2508 (Rfree = 0.000) for 2356 atoms. Found 9 (21 requested) and removed 11 (10 requested) atoms. Cycle 20: After refmac, R = 0.2509 (Rfree = 0.000) for 2351 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.02 2.57 Search for helices and strands: 0 residues in 0 chains, 2416 seeds are put forward NCS extension: 51 residues added (18 deleted due to clashes), 2467 seeds are put forward Round 1: 233 peptides, 26 chains. Longest chain 37 peptides. Score 0.615 Round 2: 242 peptides, 22 chains. Longest chain 35 peptides. Score 0.680 Round 3: 244 peptides, 24 chains. Longest chain 38 peptides. Score 0.664 Round 4: 253 peptides, 25 chains. Longest chain 37 peptides. Score 0.673 Round 5: 259 peptides, 22 chains. Longest chain 37 peptides. Score 0.716 Taking the results from Round 5 Chains 26, Residues 237, Estimated correctness of the model 68.5 % 4 chains (35 residues) have been docked in sequence Building loops using Loopy2018 26 chains (237 residues) following loop building 4 chains (35 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 4390 restraints for refining 2381 atoms. 3320 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3123 (Rfree = 0.000) for 2381 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 22: After refmac, R = 0.2634 (Rfree = 0.000) for 2374 atoms. Found 14 (21 requested) and removed 12 (10 requested) atoms. Cycle 23: After refmac, R = 0.2502 (Rfree = 0.000) for 2373 atoms. Found 6 (20 requested) and removed 12 (10 requested) atoms. Cycle 24: After refmac, R = 0.2448 (Rfree = 0.000) for 2364 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.2636 (Rfree = 0.000) for 2356 atoms. Found 19 (19 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.02 2.57 Search for helices and strands: 0 residues in 0 chains, 2417 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 2442 seeds are put forward Round 1: 239 peptides, 23 chains. Longest chain 32 peptides. Score 0.663 Round 2: 244 peptides, 20 chains. Longest chain 69 peptides. Score 0.705 Round 3: 240 peptides, 23 chains. Longest chain 50 peptides. Score 0.665 Round 4: 248 peptides, 19 chains. Longest chain 72 peptides. Score 0.723 Round 5: 244 peptides, 19 chains. Longest chain 58 peptides. Score 0.715 Taking the results from Round 4 Chains 20, Residues 229, Estimated correctness of the model 69.9 % 5 chains (135 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 98 B and 102 B 19 chains (232 residues) following loop building 4 chains (138 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3779 restraints for refining 2486 atoms. 2325 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2723 (Rfree = 0.000) for 2486 atoms. Found 20 (20 requested) and removed 20 (11 requested) atoms. Cycle 27: After refmac, R = 0.2635 (Rfree = 0.000) for 2474 atoms. Found 19 (19 requested) and removed 19 (11 requested) atoms. Cycle 28: After refmac, R = 0.2418 (Rfree = 0.000) for 2467 atoms. Found 8 (19 requested) and removed 11 (11 requested) atoms. Cycle 29: After refmac, R = 0.2398 (Rfree = 0.000) for 2459 atoms. Found 12 (18 requested) and removed 13 (11 requested) atoms. Cycle 30: After refmac, R = 0.2252 (Rfree = 0.000) for 2453 atoms. Found 6 (18 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 2.61 Search for helices and strands: 0 residues in 0 chains, 2519 seeds are put forward NCS extension: 20 residues added (8 deleted due to clashes), 2539 seeds are put forward Round 1: 248 peptides, 31 chains. Longest chain 59 peptides. Score 0.595 Round 2: 264 peptides, 24 chains. Longest chain 61 peptides. Score 0.706 Round 3: 251 peptides, 22 chains. Longest chain 61 peptides. Score 0.700 Round 4: 260 peptides, 22 chains. Longest chain 62 peptides. Score 0.718 Round 5: 269 peptides, 20 chains. Longest chain 65 peptides. Score 0.752 Taking the results from Round 5 Chains 23, Residues 249, Estimated correctness of the model 75.4 % 8 chains (153 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 B and 93 B Built loop between residues 104 B and 109 B 19 chains (252 residues) following loop building 6 chains (160 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3340 restraints for refining 2413 atoms. 1784 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2958 (Rfree = 0.000) for 2413 atoms. Found 17 (17 requested) and removed 22 (10 requested) atoms. Cycle 32: After refmac, R = 0.2609 (Rfree = 0.000) for 2392 atoms. Found 16 (16 requested) and removed 14 (10 requested) atoms. Cycle 33: After refmac, R = 0.2484 (Rfree = 0.000) for 2387 atoms. Found 12 (16 requested) and removed 10 (10 requested) atoms. Cycle 34: After refmac, R = 0.2403 (Rfree = 0.000) for 2387 atoms. Found 5 (16 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.2365 (Rfree = 0.000) for 2379 atoms. Found 6 (15 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.05 2.59 Search for helices and strands: 0 residues in 0 chains, 2432 seeds are put forward NCS extension: 59 residues added (3 deleted due to clashes), 2491 seeds are put forward Round 1: 244 peptides, 21 chains. Longest chain 51 peptides. Score 0.695 Round 2: 252 peptides, 15 chains. Longest chain 72 peptides. Score 0.767 Round 3: 254 peptides, 22 chains. Longest chain 49 peptides. Score 0.706 Round 4: 252 peptides, 22 chains. Longest chain 55 peptides. Score 0.702 Round 5: 244 peptides, 18 chains. Longest chain 63 peptides. Score 0.725 Taking the results from Round 2 Chains 18, Residues 237, Estimated correctness of the model 78.1 % 3 chains (134 residues) have been docked in sequence Building loops using Loopy2018 18 chains (237 residues) following loop building 3 chains (134 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3564 restraints for refining 2380 atoms. 2091 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2658 (Rfree = 0.000) for 2380 atoms. Found 15 (15 requested) and removed 15 (10 requested) atoms. Cycle 37: After refmac, R = 0.2458 (Rfree = 0.000) for 2375 atoms. Found 11 (14 requested) and removed 12 (10 requested) atoms. Cycle 38: After refmac, R = 0.2711 (Rfree = 0.000) for 2372 atoms. Found 14 (14 requested) and removed 13 (10 requested) atoms. Cycle 39: After refmac, R = 0.2421 (Rfree = 0.000) for 2370 atoms. Found 8 (13 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.2262 (Rfree = 0.000) for 2363 atoms. Found 6 (13 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.05 2.59 Search for helices and strands: 0 residues in 0 chains, 2424 seeds are put forward NCS extension: 59 residues added (9 deleted due to clashes), 2483 seeds are put forward Round 1: 243 peptides, 22 chains. Longest chain 51 peptides. Score 0.683 Round 2: 256 peptides, 15 chains. Longest chain 69 peptides. Score 0.774 Round 3: 252 peptides, 19 chains. Longest chain 69 peptides. Score 0.731 Round 4: 244 peptides, 21 chains. Longest chain 51 peptides. Score 0.695 Round 5: 248 peptides, 21 chains. Longest chain 51 peptides. Score 0.703 Taking the results from Round 2 Chains 15, Residues 241, Estimated correctness of the model 79.3 % 3 chains (144 residues) have been docked in sequence Building loops using Loopy2018 15 chains (241 residues) following loop building 3 chains (144 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3482 restraints for refining 2380 atoms. 1961 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2761 (Rfree = 0.000) for 2380 atoms. Found 13 (13 requested) and removed 19 (10 requested) atoms. Cycle 42: After refmac, R = 0.2390 (Rfree = 0.000) for 2366 atoms. Found 12 (12 requested) and removed 12 (10 requested) atoms. Cycle 43: After refmac, R = 0.2379 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.2425 (Rfree = 0.000) for 2359 atoms. Found 11 (11 requested) and removed 11 (10 requested) atoms. Cycle 45: After refmac, R = 0.2437 (Rfree = 0.000) for 2357 atoms. Found 11 (11 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.00 2.55 Search for helices and strands: 0 residues in 0 chains, 2427 seeds are put forward NCS extension: 13 residues added (10 deleted due to clashes), 2440 seeds are put forward Round 1: 244 peptides, 23 chains. Longest chain 49 peptides. Score 0.674 Round 2: 261 peptides, 18 chains. Longest chain 68 peptides. Score 0.756 Round 3: 260 peptides, 17 chains. Longest chain 70 peptides. Score 0.763 Round 4: 268 peptides, 16 chains. Longest chain 68 peptides. Score 0.784 Round 5: 260 peptides, 14 chains. Longest chain 68 peptides. Score 0.788 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 246, Estimated correctness of the model 81.6 % 4 chains (180 residues) have been docked in sequence Sequence coverage is 72 % Consider running further cycles of model building using 2nuj-3_warpNtrace.pdb as input Building loops using Loopy2018 14 chains (246 residues) following loop building 4 chains (180 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8166 reflections ( 97.97 % complete ) and 3298 restraints for refining 2417 atoms. 1609 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2553 (Rfree = 0.000) for 2417 atoms. Found 0 (10 requested) and removed 6 (10 requested) atoms. Cycle 47: After refmac, R = 0.2353 (Rfree = 0.000) for 2402 atoms. Found 0 (10 requested) and removed 2 (10 requested) atoms. Cycle 48: After refmac, R = 0.2433 (Rfree = 0.000) for 2395 atoms. Found 0 (10 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2380 (Rfree = 0.000) for 2376 atoms. TimeTaking 35.43