null Sun 23 Dec 22:22:49 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 2o3l-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o3l-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o3l-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-3.4-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/2o3l-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-3.4-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 ============================================================ Sun 23 Dec 22:22:59 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/2o3l-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-3.4-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 147 and 0 Target number of residues in the AU: 147 Target solvent content: 0.6375 Checking the provided sequence file Detected sequence length: 85 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 170 Adjusted target solvent content: 0.58 Input MTZ file: 2o3l-3.4-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: 154 Cell parameters: 61.138 61.138 101.686 90.000 90.000 120.000 Input sequence file: 2o3l-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1360 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: 52.947 3.400 Wilson plot Bfac: 70.34 3275 reflections ( 99.79 % complete ) and 0 restraints for refining 1505 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3519 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2810 (Rfree = 0.000) for 1505 atoms. Found 10 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.16 Search for helices and strands: 0 residues in 0 chains, 1532 seeds are put forward NCS extension: 0 residues added, 1532 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.273 Round 2: 72 peptides, 14 chains. Longest chain 10 peptides. Score 0.307 Round 3: 86 peptides, 13 chains. Longest chain 15 peptides. Score 0.447 Round 4: 90 peptides, 13 chains. Longest chain 14 peptides. Score 0.474 Round 5: 93 peptides, 14 chains. Longest chain 14 peptides. Score 0.465 Taking the results from Round 4 Chains 13, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2782 restraints for refining 1236 atoms. 2487 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2900 (Rfree = 0.000) for 1236 atoms. Found 7 (9 requested) and removed 7 (4 requested) atoms. Cycle 2: After refmac, R = 0.2550 (Rfree = 0.000) for 1216 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 3: After refmac, R = 0.2388 (Rfree = 0.000) for 1206 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.2316 (Rfree = 0.000) for 1195 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 5: After refmac, R = 0.2265 (Rfree = 0.000) for 1192 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.04 Search for helices and strands: 0 residues in 0 chains, 1274 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 1285 seeds are put forward Round 1: 91 peptides, 13 chains. Longest chain 13 peptides. Score 0.481 Round 2: 108 peptides, 15 chains. Longest chain 19 peptides. Score 0.533 Round 3: 105 peptides, 14 chains. Longest chain 19 peptides. Score 0.542 Round 4: 106 peptides, 13 chains. Longest chain 18 peptides. Score 0.575 Round 5: 104 peptides, 11 chains. Longest chain 23 peptides. Score 0.615 Taking the results from Round 5 Chains 11, Residues 93, Estimated correctness of the model 33.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2698 restraints for refining 1235 atoms. 2337 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2796 (Rfree = 0.000) for 1235 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 7: After refmac, R = 0.2903 (Rfree = 0.000) for 1226 atoms. Found 5 (9 requested) and removed 17 (4 requested) atoms. Cycle 8: After refmac, R = 0.2569 (Rfree = 0.000) for 1208 atoms. Found 7 (9 requested) and removed 7 (4 requested) atoms. Cycle 9: After refmac, R = 0.2599 (Rfree = 0.000) for 1204 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.2416 (Rfree = 0.000) for 1203 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 2.98 Search for helices and strands: 0 residues in 0 chains, 1293 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 1326 seeds are put forward Round 1: 91 peptides, 16 chains. Longest chain 11 peptides. Score 0.389 Round 2: 107 peptides, 14 chains. Longest chain 13 peptides. Score 0.554 Round 3: 102 peptides, 12 chains. Longest chain 19 peptides. Score 0.578 Round 4: 100 peptides, 13 chains. Longest chain 18 peptides. Score 0.539 Round 5: 109 peptides, 13 chains. Longest chain 22 peptides. Score 0.592 Taking the results from Round 5 Chains 13, Residues 96, Estimated correctness of the model 26.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2614 restraints for refining 1236 atoms. 2231 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2587 (Rfree = 0.000) for 1236 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 12: After refmac, R = 0.2806 (Rfree = 0.000) for 1227 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 13: After refmac, R = 0.2606 (Rfree = 0.000) for 1222 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 14: After refmac, R = 0.2516 (Rfree = 0.000) for 1213 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.2239 (Rfree = 0.000) for 1213 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 2.94 Search for helices and strands: 0 residues in 0 chains, 1293 seeds are put forward NCS extension: 43 residues added (1 deleted due to clashes), 1336 seeds are put forward Round 1: 105 peptides, 18 chains. Longest chain 15 peptides. Score 0.427 Round 2: 119 peptides, 15 chains. Longest chain 18 peptides. Score 0.597 Round 3: 113 peptides, 14 chains. Longest chain 19 peptides. Score 0.589 Round 4: 118 peptides, 16 chains. Longest chain 17 peptides. Score 0.566 Round 5: 115 peptides, 13 chains. Longest chain 18 peptides. Score 0.624 Taking the results from Round 5 Chains 13, Residues 102, Estimated correctness of the model 36.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2611 restraints for refining 1236 atoms. 2216 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2467 (Rfree = 0.000) for 1236 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 17: After refmac, R = 0.2292 (Rfree = 0.000) for 1221 atoms. Found 5 (9 requested) and removed 22 (4 requested) atoms. Cycle 18: After refmac, R = 0.2412 (Rfree = 0.000) for 1198 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 19: After refmac, R = 0.3059 (Rfree = 0.000) for 1192 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 20: After refmac, R = 0.2485 (Rfree = 0.000) for 1179 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.02 Search for helices and strands: 0 residues in 0 chains, 1268 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 1293 seeds are put forward Round 1: 66 peptides, 12 chains. Longest chain 13 peptides. Score 0.329 Round 2: 81 peptides, 14 chains. Longest chain 12 peptides. Score 0.378 Round 3: 98 peptides, 17 chains. Longest chain 12 peptides. Score 0.408 Round 4: 90 peptides, 14 chains. Longest chain 13 peptides. Score 0.444 Round 5: 99 peptides, 16 chains. Longest chain 9 peptides. Score 0.446 Taking the results from Round 5 Chains 16, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2675 restraints for refining 1228 atoms. 2359 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2411 (Rfree = 0.000) for 1228 atoms. Found 8 (9 requested) and removed 10 (4 requested) atoms. Cycle 22: After refmac, R = 0.2500 (Rfree = 0.000) for 1223 atoms. Found 4 (9 requested) and removed 10 (4 requested) atoms. Cycle 23: After refmac, R = 0.2392 (Rfree = 0.000) for 1214 atoms. Found 7 (9 requested) and removed 8 (4 requested) atoms. Cycle 24: After refmac, R = 0.2757 (Rfree = 0.000) for 1207 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 25: After refmac, R = 0.2406 (Rfree = 0.000) for 1196 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.01 Search for helices and strands: 0 residues in 0 chains, 1272 seeds are put forward NCS extension: 0 residues added, 1272 seeds are put forward Round 1: 67 peptides, 12 chains. Longest chain 13 peptides. Score 0.337 Round 2: 85 peptides, 15 chains. Longest chain 13 peptides. Score 0.376 Round 3: 89 peptides, 14 chains. Longest chain 15 peptides. Score 0.437 Round 4: 93 peptides, 16 chains. Longest chain 12 peptides. Score 0.403 Round 5: 93 peptides, 16 chains. Longest chain 20 peptides. Score 0.403 Taking the results from Round 3 Chains 14, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2794 restraints for refining 1236 atoms. 2508 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2498 (Rfree = 0.000) for 1236 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 27: After refmac, R = 0.2419 (Rfree = 0.000) for 1229 atoms. Found 7 (9 requested) and removed 7 (4 requested) atoms. Cycle 28: After refmac, R = 0.2504 (Rfree = 0.000) for 1222 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 29: After refmac, R = 0.2653 (Rfree = 0.000) for 1219 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 30: After refmac, R = 0.2640 (Rfree = 0.000) for 1215 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.03 Search for helices and strands: 0 residues in 0 chains, 1288 seeds are put forward NCS extension: 0 residues added, 1288 seeds are put forward Round 1: 85 peptides, 16 chains. Longest chain 15 peptides. Score 0.343 Round 2: 82 peptides, 13 chains. Longest chain 16 peptides. Score 0.418 Round 3: 90 peptides, 15 chains. Longest chain 14 peptides. Score 0.413 Round 4: 101 peptides, 15 chains. Longest chain 15 peptides. Score 0.489 Round 5: 90 peptides, 16 chains. Longest chain 12 peptides. Score 0.381 Taking the results from Round 4 Chains 15, Residues 86, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2683 restraints for refining 1236 atoms. 2343 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2631 (Rfree = 0.000) for 1236 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 32: After refmac, R = 0.2524 (Rfree = 0.000) for 1228 atoms. Found 4 (9 requested) and removed 12 (4 requested) atoms. Cycle 33: After refmac, R = 0.2653 (Rfree = 0.000) for 1213 atoms. Found 7 (9 requested) and removed 14 (4 requested) atoms. Cycle 34: After refmac, R = 0.2618 (Rfree = 0.000) for 1199 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.2584 (Rfree = 0.000) for 1200 atoms. Found 8 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.03 Search for helices and strands: 0 residues in 0 chains, 1277 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 1295 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 6 peptides. Score 0.230 Round 2: 81 peptides, 14 chains. Longest chain 9 peptides. Score 0.378 Round 3: 84 peptides, 15 chains. Longest chain 12 peptides. Score 0.368 Round 4: 93 peptides, 16 chains. Longest chain 9 peptides. Score 0.403 Round 5: 82 peptides, 12 chains. Longest chain 13 peptides. Score 0.450 Taking the results from Round 5 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2727 restraints for refining 1236 atoms. 2422 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2858 (Rfree = 0.000) for 1236 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 37: After refmac, R = 0.2729 (Rfree = 0.000) for 1218 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 38: After refmac, R = 0.2784 (Rfree = 0.000) for 1211 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.2687 (Rfree = 0.000) for 1207 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 40: After refmac, R = 0.2785 (Rfree = 0.000) for 1198 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.20 3.77 Search for helices and strands: 0 residues in 0 chains, 1272 seeds are put forward NCS extension: 0 residues added, 1272 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 7 peptides. Score 0.218 Round 2: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.269 Round 3: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.276 Round 4: 67 peptides, 15 chains. Longest chain 7 peptides. Score 0.230 Round 5: 68 peptides, 15 chains. Longest chain 7 peptides. Score 0.238 Taking the results from Round 3 Chains 13, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2609 restraints for refining 1184 atoms. 2418 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2885 (Rfree = 0.000) for 1184 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 42: After refmac, R = 0.2770 (Rfree = 0.000) for 1170 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 43: After refmac, R = 0.2615 (Rfree = 0.000) for 1166 atoms. Found 5 (8 requested) and removed 13 (4 requested) atoms. Cycle 44: After refmac, R = 0.2829 (Rfree = 0.000) for 1154 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 45: After refmac, R = 0.2682 (Rfree = 0.000) for 1142 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.16 Search for helices and strands: 0 residues in 0 chains, 1232 seeds are put forward NCS extension: 0 residues added, 1232 seeds are put forward Round 1: 62 peptides, 14 chains. Longest chain 5 peptides. Score 0.222 Round 2: 77 peptides, 16 chains. Longest chain 7 peptides. Score 0.279 Round 3: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.334 Round 4: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.345 Round 5: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.345 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 56, 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 2o3l-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3275 reflections ( 99.79 % complete ) and 2814 restraints for refining 1236 atoms. 2602 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2564 (Rfree = 0.000) for 1236 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2668 (Rfree = 0.000) for 1227 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2684 (Rfree = 0.000) for 1221 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2612 (Rfree = 0.000) for 1216 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:50:30 GMT 2018 Job finished. TimeTaking 27.67 Used memory is bytes: 19285256