null Mon 24 Dec 07:27:13 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 2o08-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o08-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o08-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-4.0-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/2o08-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-4.0-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 07:27:16 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/2o08-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-4.0-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 333 and 0 Target number of residues in the AU: 333 Target solvent content: 0.6691 Checking the provided sequence file Detected sequence length: 188 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 376 Adjusted target solvent content: 0.63 Input MTZ file: 2o08-4.0-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: 20 Cell parameters: 87.690 166.470 74.630 90.000 90.000 90.000 Input sequence file: 2o08-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3008 target number of atoms Had to go as low as 0.95 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: 83.235 4.000 Wilson plot Bfac: 91.80 4727 reflections ( 97.24 % complete ) and 0 restraints for refining 3316 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3519 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3587 (Rfree = 0.000) for 3316 atoms. Found 15 (15 requested) and removed 182 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.98 3.33 Search for helices and strands: 0 residues in 0 chains, 3178 seeds are put forward NCS extension: 0 residues added, 3178 seeds are put forward Round 1: 117 peptides, 25 chains. Longest chain 8 peptides. Score 0.236 Round 2: 144 peptides, 26 chains. Longest chain 14 peptides. Score 0.317 Round 3: 161 peptides, 25 chains. Longest chain 14 peptides. Score 0.387 Round 4: 175 peptides, 26 chains. Longest chain 13 peptides. Score 0.416 Round 5: 171 peptides, 27 chains. Longest chain 15 peptides. Score 0.390 Taking the results from Round 4 Chains 26, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6435 restraints for refining 2716 atoms. 5865 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3206 (Rfree = 0.000) for 2716 atoms. Found 12 (12 requested) and removed 43 (6 requested) atoms. Cycle 2: After refmac, R = 0.2914 (Rfree = 0.000) for 2637 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. Cycle 3: After refmac, R = 0.2607 (Rfree = 0.000) for 2599 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 4: After refmac, R = 0.2503 (Rfree = 0.000) for 2578 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 5: After refmac, R = 0.2427 (Rfree = 0.000) for 2569 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.11 Search for helices and strands: 0 residues in 0 chains, 2703 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2722 seeds are put forward Round 1: 168 peptides, 31 chains. Longest chain 11 peptides. Score 0.325 Round 2: 179 peptides, 28 chains. Longest chain 12 peptides. Score 0.401 Round 3: 182 peptides, 25 chains. Longest chain 14 peptides. Score 0.450 Round 4: 188 peptides, 26 chains. Longest chain 13 peptides. Score 0.454 Round 5: 179 peptides, 24 chains. Longest chain 13 peptides. Score 0.455 Taking the results from Round 5 Chains 24, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6329 restraints for refining 2717 atoms. 5733 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2945 (Rfree = 0.000) for 2717 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 7: After refmac, R = 0.2640 (Rfree = 0.000) for 2683 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 8: After refmac, R = 0.2379 (Rfree = 0.000) for 2654 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 9: After refmac, R = 0.2687 (Rfree = 0.000) for 2636 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 10: After refmac, R = 0.2369 (Rfree = 0.000) for 2612 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.12 Search for helices and strands: 0 residues in 0 chains, 2710 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2727 seeds are put forward Round 1: 170 peptides, 28 chains. Longest chain 13 peptides. Score 0.373 Round 2: 181 peptides, 27 chains. Longest chain 13 peptides. Score 0.421 Round 3: 177 peptides, 23 chains. Longest chain 17 peptides. Score 0.462 Round 4: 180 peptides, 25 chains. Longest chain 15 peptides. Score 0.444 Round 5: 175 peptides, 23 chains. Longest chain 15 peptides. Score 0.456 Taking the results from Round 3 Chains 23, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6177 restraints for refining 2706 atoms. 5584 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2786 (Rfree = 0.000) for 2706 atoms. Found 12 (12 requested) and removed 33 (6 requested) atoms. Cycle 12: After refmac, R = 0.2332 (Rfree = 0.000) for 2654 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 13: After refmac, R = 0.2208 (Rfree = 0.000) for 2633 atoms. Found 12 (12 requested) and removed 42 (6 requested) atoms. Cycle 14: After refmac, R = 0.2372 (Rfree = 0.000) for 2596 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 15: After refmac, R = 0.2226 (Rfree = 0.000) for 2589 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.80 3.18 Search for helices and strands: 0 residues in 0 chains, 2693 seeds are put forward NCS extension: 0 residues added, 2693 seeds are put forward Round 1: 160 peptides, 30 chains. Longest chain 10 peptides. Score 0.313 Round 2: 172 peptides, 24 chains. Longest chain 25 peptides. Score 0.434 Round 3: 187 peptides, 27 chains. Longest chain 17 peptides. Score 0.438 Round 4: 194 peptides, 26 chains. Longest chain 15 peptides. Score 0.471 Round 5: 187 peptides, 19 chains. Longest chain 33 peptides. Score 0.540 Taking the results from Round 5 Chains 20, Residues 168, Estimated correctness of the model 0.0 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 5720 restraints for refining 2717 atoms. 4927 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2743 (Rfree = 0.000) for 2717 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 17: After refmac, R = 0.2899 (Rfree = 0.000) for 2692 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 18: After refmac, R = 0.2888 (Rfree = 0.000) for 2685 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 19: After refmac, R = 0.2215 (Rfree = 0.000) for 2675 atoms. Found 9 (12 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.2302 (Rfree = 0.000) for 2674 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.78 3.17 Search for helices and strands: 0 residues in 0 chains, 2759 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 2794 seeds are put forward Round 1: 171 peptides, 32 chains. Longest chain 9 peptides. Score 0.321 Round 2: 192 peptides, 29 chains. Longest chain 15 peptides. Score 0.427 Round 3: 192 peptides, 28 chains. Longest chain 21 peptides. Score 0.440 Round 4: 194 peptides, 26 chains. Longest chain 20 peptides. Score 0.471 Round 5: 201 peptides, 31 chains. Longest chain 14 peptides. Score 0.427 Taking the results from Round 4 Chains 28, Residues 168, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6060 restraints for refining 2716 atoms. 5350 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2587 (Rfree = 0.000) for 2716 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 22: After refmac, R = 0.2397 (Rfree = 0.000) for 2689 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 23: After refmac, R = 0.2510 (Rfree = 0.000) for 2673 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 24: After refmac, R = 0.2020 (Rfree = 0.000) for 2659 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.1898 (Rfree = 0.000) for 2654 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.80 3.18 Search for helices and strands: 0 residues in 0 chains, 2714 seeds are put forward NCS extension: 0 residues added, 2714 seeds are put forward Round 1: 165 peptides, 29 chains. Longest chain 10 peptides. Score 0.343 Round 2: 193 peptides, 29 chains. Longest chain 13 peptides. Score 0.430 Round 3: 183 peptides, 24 chains. Longest chain 17 peptides. Score 0.466 Round 4: 183 peptides, 23 chains. Longest chain 17 peptides. Score 0.479 Round 5: 193 peptides, 25 chains. Longest chain 18 peptides. Score 0.481 Taking the results from Round 5 Chains 25, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6149 restraints for refining 2715 atoms. 5502 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2526 (Rfree = 0.000) for 2715 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 27: After refmac, R = 0.2421 (Rfree = 0.000) for 2701 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.2829 (Rfree = 0.000) for 2701 atoms. Found 10 (12 requested) and removed 11 (6 requested) atoms. Cycle 29: After refmac, R = 0.2711 (Rfree = 0.000) for 2699 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.2587 (Rfree = 0.000) for 2698 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.80 3.18 Search for helices and strands: 0 residues in 0 chains, 2793 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 2819 seeds are put forward Round 1: 139 peptides, 26 chains. Longest chain 10 peptides. Score 0.300 Round 2: 169 peptides, 27 chains. Longest chain 15 peptides. Score 0.384 Round 3: 169 peptides, 26 chains. Longest chain 13 peptides. Score 0.398 Round 4: 175 peptides, 27 chains. Longest chain 12 peptides. Score 0.403 Round 5: 179 peptides, 29 chains. Longest chain 12 peptides. Score 0.388 Taking the results from Round 4 Chains 27, Residues 148, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6255 restraints for refining 2717 atoms. 5666 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2644 (Rfree = 0.000) for 2717 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 32: After refmac, R = 0.2508 (Rfree = 0.000) for 2665 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.2470 (Rfree = 0.000) for 2627 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. Cycle 34: After refmac, R = 0.2466 (Rfree = 0.000) for 2598 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.2338 (Rfree = 0.000) for 2592 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.86 3.23 Search for helices and strands: 0 residues in 0 chains, 2686 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2700 seeds are put forward Round 1: 145 peptides, 30 chains. Longest chain 8 peptides. Score 0.261 Round 2: 172 peptides, 29 chains. Longest chain 19 peptides. Score 0.366 Round 3: 182 peptides, 30 chains. Longest chain 12 peptides. Score 0.383 Round 4: 193 peptides, 28 chains. Longest chain 22 peptides. Score 0.443 Round 5: 189 peptides, 28 chains. Longest chain 17 peptides. Score 0.431 Taking the results from Round 4 Chains 28, Residues 165, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 5761 restraints for refining 2661 atoms. 5064 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2498 (Rfree = 0.000) for 2661 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 37: After refmac, R = 0.2556 (Rfree = 0.000) for 2633 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 38: After refmac, R = 0.2293 (Rfree = 0.000) for 2606 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.2305 (Rfree = 0.000) for 2588 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 40: After refmac, R = 0.2277 (Rfree = 0.000) for 2575 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 3.17 Search for helices and strands: 0 residues in 0 chains, 2696 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 2717 seeds are put forward Round 1: 154 peptides, 32 chains. Longest chain 9 peptides. Score 0.263 Round 2: 177 peptides, 28 chains. Longest chain 14 peptides. Score 0.395 Round 3: 171 peptides, 27 chains. Longest chain 19 peptides. Score 0.390 Round 4: 182 peptides, 29 chains. Longest chain 19 peptides. Score 0.397 Round 5: 179 peptides, 29 chains. Longest chain 14 peptides. Score 0.388 Taking the results from Round 4 Chains 29, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6008 restraints for refining 2658 atoms. 5425 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2520 (Rfree = 0.000) for 2658 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 42: After refmac, R = 0.2288 (Rfree = 0.000) for 2629 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.2255 (Rfree = 0.000) for 2612 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 44: After refmac, R = 0.2167 (Rfree = 0.000) for 2604 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 45: After refmac, R = 0.2156 (Rfree = 0.000) for 2592 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.16 Search for helices and strands: 0 residues in 0 chains, 2654 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 2675 seeds are put forward Round 1: 138 peptides, 30 chains. Longest chain 8 peptides. Score 0.236 Round 2: 145 peptides, 25 chains. Longest chain 11 peptides. Score 0.336 Round 3: 147 peptides, 24 chains. Longest chain 12 peptides. Score 0.357 Round 4: 164 peptides, 27 chains. Longest chain 13 peptides. Score 0.368 Round 5: 164 peptides, 27 chains. Longest chain 19 peptides. Score 0.368 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 137, 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 2o08-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4727 reflections ( 97.24 % complete ) and 5981 restraints for refining 2638 atoms. 5460 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2373 (Rfree = 0.000) for 2638 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2363 (Rfree = 0.000) for 2613 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2173 (Rfree = 0.000) for 2599 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1903 (Rfree = 0.000) for 2590 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 07:58:44 GMT 2018 Job finished. TimeTaking 31.53 Used memory is bytes: 10677016