null Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2opl-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2opl-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2opl-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2opl-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-3.8-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:06 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/hancs/ArpWArp/wArpResults/WorkingDir/2opl-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-3.8-parrot-hancs/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 239 and 0 Target number of residues in the AU: 239 Target solvent content: 0.6536 Checking the provided sequence file Detected sequence length: 187 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 374 Adjusted target solvent content: 0.46 Input MTZ file: 2opl-3.8-parrot-hancs.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: 19 Cell parameters: 47.200 82.950 95.370 90.000 90.000 90.000 Input sequence file: 2opl-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2992 target number of atoms Had to go as low as 0.75 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: 62.588 3.801 Wilson plot Bfac: 79.76 3962 reflections ( 99.30 % complete ) and 0 restraints for refining 3321 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3348 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3055 (Rfree = 0.000) for 3321 atoms. Found 12 (18 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.83 Search for helices and strands: 0 residues in 0 chains, 3393 seeds are put forward NCS extension: 0 residues added, 3393 seeds are put forward Round 1: 136 peptides, 28 chains. Longest chain 8 peptides. Score 0.288 Round 2: 172 peptides, 29 chains. Longest chain 12 peptides. Score 0.429 Round 3: 185 peptides, 27 chains. Longest chain 13 peptides. Score 0.514 Round 4: 204 peptides, 25 chains. Longest chain 19 peptides. Score 0.609 Round 5: 200 peptides, 28 chains. Longest chain 19 peptides. Score 0.552 Taking the results from Round 4 Chains 25, Residues 179, Estimated correctness of the model 2.9 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6041 restraints for refining 2706 atoms. 5324 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2395 (Rfree = 0.000) for 2706 atoms. Found 7 (14 requested) and removed 16 (7 requested) atoms. Cycle 2: After refmac, R = 0.2162 (Rfree = 0.000) for 2660 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Cycle 3: After refmac, R = 0.1958 (Rfree = 0.000) for 2647 atoms. Found 1 (14 requested) and removed 10 (7 requested) atoms. Cycle 4: After refmac, R = 0.1923 (Rfree = 0.000) for 2637 atoms. Found 1 (14 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.1967 (Rfree = 0.000) for 2625 atoms. Found 6 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.76 Search for helices and strands: 0 residues in 0 chains, 2720 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2743 seeds are put forward Round 1: 169 peptides, 32 chains. Longest chain 9 peptides. Score 0.362 Round 2: 189 peptides, 29 chains. Longest chain 18 peptides. Score 0.496 Round 3: 177 peptides, 28 chains. Longest chain 13 peptides. Score 0.467 Round 4: 194 peptides, 30 chains. Longest chain 18 peptides. Score 0.498 Round 5: 185 peptides, 27 chains. Longest chain 18 peptides. Score 0.514 Taking the results from Round 5 Chains 28, Residues 158, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6230 restraints for refining 2706 atoms. 5567 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2125 (Rfree = 0.000) for 2706 atoms. Found 10 (14 requested) and removed 14 (7 requested) atoms. Cycle 7: After refmac, R = 0.1869 (Rfree = 0.000) for 2693 atoms. Found 8 (14 requested) and removed 11 (7 requested) atoms. Cycle 8: After refmac, R = 0.1763 (Rfree = 0.000) for 2687 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. Cycle 9: After refmac, R = 0.1667 (Rfree = 0.000) for 2681 atoms. Found 3 (14 requested) and removed 10 (7 requested) atoms. Cycle 10: After refmac, R = 0.1623 (Rfree = 0.000) for 2672 atoms. Found 0 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.80 Search for helices and strands: 0 residues in 0 chains, 2738 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2751 seeds are put forward Round 1: 182 peptides, 31 chains. Longest chain 16 peptides. Score 0.435 Round 2: 184 peptides, 29 chains. Longest chain 14 peptides. Score 0.477 Round 3: 188 peptides, 32 chains. Longest chain 11 peptides. Score 0.442 Round 4: 182 peptides, 26 chains. Longest chain 18 peptides. Score 0.519 Round 5: 193 peptides, 31 chains. Longest chain 16 peptides. Score 0.478 Taking the results from Round 4 Chains 26, Residues 156, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6230 restraints for refining 2706 atoms. 5582 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1997 (Rfree = 0.000) for 2706 atoms. Found 7 (14 requested) and removed 19 (7 requested) atoms. Cycle 12: After refmac, R = 0.1985 (Rfree = 0.000) for 2677 atoms. Found 10 (14 requested) and removed 11 (7 requested) atoms. Cycle 13: After refmac, R = 0.1892 (Rfree = 0.000) for 2669 atoms. Found 9 (14 requested) and removed 13 (7 requested) atoms. Cycle 14: After refmac, R = 0.1671 (Rfree = 0.000) for 2653 atoms. Found 4 (14 requested) and removed 13 (7 requested) atoms. Cycle 15: After refmac, R = 0.1676 (Rfree = 0.000) for 2642 atoms. Found 9 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.69 Search for helices and strands: 0 residues in 0 chains, 2732 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2751 seeds are put forward Round 1: 133 peptides, 25 chains. Longest chain 11 peptides. Score 0.333 Round 2: 159 peptides, 24 chains. Longest chain 12 peptides. Score 0.465 Round 3: 168 peptides, 25 chains. Longest chain 11 peptides. Score 0.483 Round 4: 155 peptides, 22 chains. Longest chain 11 peptides. Score 0.484 Round 5: 165 peptides, 25 chains. Longest chain 11 peptides. Score 0.471 Taking the results from Round 4 Chains 23, Residues 133, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6394 restraints for refining 2705 atoms. 5860 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2532 (Rfree = 0.000) for 2705 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 17: After refmac, R = 0.2180 (Rfree = 0.000) for 2664 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 18: After refmac, R = 0.2072 (Rfree = 0.000) for 2646 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 19: After refmac, R = 0.1554 (Rfree = 0.000) for 2640 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.1531 (Rfree = 0.000) for 2630 atoms. Found 5 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.84 Search for helices and strands: 0 residues in 0 chains, 2711 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2723 seeds are put forward Round 1: 132 peptides, 27 chains. Longest chain 8 peptides. Score 0.289 Round 2: 161 peptides, 26 chains. Longest chain 14 peptides. Score 0.437 Round 3: 159 peptides, 25 chains. Longest chain 13 peptides. Score 0.447 Round 4: 157 peptides, 26 chains. Longest chain 13 peptides. Score 0.420 Round 5: 149 peptides, 24 chains. Longest chain 10 peptides. Score 0.423 Taking the results from Round 3 Chains 25, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6267 restraints for refining 2658 atoms. 5756 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2388 (Rfree = 0.000) for 2658 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 22: After refmac, R = 0.2305 (Rfree = 0.000) for 2640 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 23: After refmac, R = 0.2219 (Rfree = 0.000) for 2625 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 24: After refmac, R = 0.2110 (Rfree = 0.000) for 2617 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.2241 (Rfree = 0.000) for 2616 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2707 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2722 seeds are put forward Round 1: 133 peptides, 27 chains. Longest chain 10 peptides. Score 0.293 Round 2: 139 peptides, 25 chains. Longest chain 9 peptides. Score 0.361 Round 3: 152 peptides, 26 chains. Longest chain 13 peptides. Score 0.399 Round 4: 158 peptides, 27 chains. Longest chain 11 peptides. Score 0.406 Round 5: 153 peptides, 24 chains. Longest chain 14 peptides. Score 0.440 Taking the results from Round 5 Chains 24, Residues 129, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6272 restraints for refining 2652 atoms. 5763 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2180 (Rfree = 0.000) for 2652 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 27: After refmac, R = 0.2245 (Rfree = 0.000) for 2634 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 28: After refmac, R = 0.2173 (Rfree = 0.000) for 2620 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 29: After refmac, R = 0.1582 (Rfree = 0.000) for 2613 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. Cycle 30: After refmac, R = 0.1737 (Rfree = 0.000) for 2608 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.71 Search for helices and strands: 0 residues in 0 chains, 2687 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2708 seeds are put forward Round 1: 139 peptides, 30 chains. Longest chain 9 peptides. Score 0.262 Round 2: 149 peptides, 29 chains. Longest chain 8 peptides. Score 0.329 Round 3: 146 peptides, 26 chains. Longest chain 9 peptides. Score 0.373 Round 4: 154 peptides, 26 chains. Longest chain 10 peptides. Score 0.408 Round 5: 157 peptides, 27 chains. Longest chain 10 peptides. Score 0.402 Taking the results from Round 4 Chains 26, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6453 restraints for refining 2706 atoms. 5967 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2486 (Rfree = 0.000) for 2706 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 32: After refmac, R = 0.2198 (Rfree = 0.000) for 2677 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 33: After refmac, R = 0.2079 (Rfree = 0.000) for 2663 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 34: After refmac, R = 0.2173 (Rfree = 0.000) for 2653 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 35: After refmac, R = 0.2216 (Rfree = 0.000) for 2649 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2750 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 2758 seeds are put forward Round 1: 119 peptides, 27 chains. Longest chain 8 peptides. Score 0.224 Round 2: 123 peptides, 24 chains. Longest chain 9 peptides. Score 0.306 Round 3: 135 peptides, 23 chains. Longest chain 10 peptides. Score 0.382 Round 4: 139 peptides, 24 chains. Longest chain 10 peptides. Score 0.380 Round 5: 150 peptides, 26 chains. Longest chain 11 peptides. Score 0.391 Taking the results from Round 5 Chains 26, Residues 124, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6251 restraints for refining 2697 atoms. 5762 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2014 (Rfree = 0.000) for 2697 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 37: After refmac, R = 0.1746 (Rfree = 0.000) for 2667 atoms. Found 10 (14 requested) and removed 10 (7 requested) atoms. Cycle 38: After refmac, R = 0.1390 (Rfree = 0.000) for 2659 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. Cycle 39: After refmac, R = 0.1292 (Rfree = 0.000) for 2649 atoms. Found 2 (14 requested) and removed 11 (7 requested) atoms. Cycle 40: After refmac, R = 0.1263 (Rfree = 0.000) for 2640 atoms. Found 0 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2688 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2701 seeds are put forward Round 1: 83 peptides, 16 chains. Longest chain 9 peptides. Score 0.278 Round 2: 88 peptides, 17 chains. Longest chain 8 peptides. Score 0.281 Round 3: 92 peptides, 16 chains. Longest chain 9 peptides. Score 0.324 Round 4: 97 peptides, 17 chains. Longest chain 10 peptides. Score 0.327 Round 5: 93 peptides, 16 chains. Longest chain 9 peptides. Score 0.329 Taking the results from Round 5 Chains 16, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3962 reflections ( 99.30 % complete ) and 6503 restraints for refining 2658 atoms. 6211 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2291 (Rfree = 0.000) for 2658 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 42: After refmac, R = 0.1801 (Rfree = 0.000) for 2647 atoms. Found 4 (14 requested) and removed 15 (7 requested) atoms. Cycle 43: After refmac, R = 0.1497 (Rfree = 0.000) for 2631 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.1313 (Rfree = 0.000) for 2623 atoms. Found 0 (14 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.1308 (Rfree = 0.000) for 2612 atoms. Found 1 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.79 Search for helices and strands: 0 residues in 0 chains, 2677 seeds are put forward NCS extension: 0 residues added, 2677 seeds are put forward Round 1: 89 peptides, 18 chains. Longest chain 9 peptides. Score 0.264 Round 2: 104 peptides, 21 chains. Longest chain 9 peptides. Score 0.275 Round 3: 95 peptides, 18 chains. Longest chain 10 peptides. Score 0.295 Round 4: 103 peptides, 18 chains. Longest chain 10 peptides. Score 0.335 Round 5: 101 peptides, 18 chains. Longest chain 10 peptides. Score 0.325 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 85, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2opl-3_warpNtrace.pdb as input Building loops using Loopy2018 18 chains (85 residues) following loop building 2 chains (11 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3962 reflections ( 99.30 % complete ) and 6237 restraints for refining 2626 atoms. 5892 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1977 (Rfree = 0.000) for 2626 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1987 (Rfree = 0.000) for 2606 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1569 (Rfree = 0.000) for 2597 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1404 (Rfree = 0.000) for 2588 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:16:33 GMT 2018 Job finished. TimeTaking 48.61 Used memory is bytes: 13489400