null Sun 23 Dec 22:22:56 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 2pg4-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pg4-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pg4-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-3.4-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/2pg4-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-3.4-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 22:23:06 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/2pg4-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-3.4-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 146 and 0 Target number of residues in the AU: 146 Target solvent content: 0.6437 Checking the provided sequence file Detected sequence length: 95 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 190 Adjusted target solvent content: 0.54 Input MTZ file: 2pg4-3.4-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: 90 Cell parameters: 109.840 109.840 36.760 90.000 90.000 90.000 Input sequence file: 2pg4-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1520 target number of atoms Had to go as low as 0.70 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: 77.669 3.400 Wilson plot Bfac: 73.96 3374 reflections ( 99.59 % complete ) and 0 restraints for refining 1684 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3710 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3374 (Rfree = 0.000) for 1684 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 1725 seeds are put forward NCS extension: 0 residues added, 1725 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 9 peptides. Score 0.313 Round 2: 101 peptides, 16 chains. Longest chain 15 peptides. Score 0.457 Round 3: 118 peptides, 19 chains. Longest chain 21 peptides. Score 0.484 Round 4: 109 peptides, 15 chains. Longest chain 20 peptides. Score 0.537 Round 5: 118 peptides, 15 chains. Longest chain 14 peptides. Score 0.589 Taking the results from Round 5 Chains 15, Residues 103, Estimated correctness of the model 25.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 3119 restraints for refining 1381 atoms. 2722 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2818 (Rfree = 0.000) for 1381 atoms. Found 4 (10 requested) and removed 14 (5 requested) atoms. Cycle 2: After refmac, R = 0.2782 (Rfree = 0.000) for 1349 atoms. Found 5 (10 requested) and removed 16 (5 requested) atoms. Cycle 3: After refmac, R = 0.2624 (Rfree = 0.000) for 1326 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2445 (Rfree = 0.000) for 1305 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2828 (Rfree = 0.000) for 1290 atoms. Found 4 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 1362 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1380 seeds are put forward Round 1: 82 peptides, 15 chains. Longest chain 12 peptides. Score 0.352 Round 2: 106 peptides, 16 chains. Longest chain 13 peptides. Score 0.490 Round 3: 107 peptides, 14 chains. Longest chain 17 peptides. Score 0.552 Round 4: 114 peptides, 14 chains. Longest chain 27 peptides. Score 0.592 Round 5: 108 peptides, 13 chains. Longest chain 27 peptides. Score 0.584 Taking the results from Round 4 Chains 14, Residues 100, Estimated correctness of the model 26.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 2853 restraints for refining 1321 atoms. 2467 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2739 (Rfree = 0.000) for 1321 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 7: After refmac, R = 0.3251 (Rfree = 0.000) for 1309 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 8: After refmac, R = 0.2548 (Rfree = 0.000) for 1295 atoms. Found 5 (9 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.2280 (Rfree = 0.000) for 1289 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.2189 (Rfree = 0.000) for 1282 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 1351 seeds are put forward NCS extension: 38 residues added (3 deleted due to clashes), 1389 seeds are put forward Round 1: 105 peptides, 19 chains. Longest chain 14 peptides. Score 0.396 Round 2: 109 peptides, 16 chains. Longest chain 20 peptides. Score 0.510 Round 3: 99 peptides, 13 chains. Longest chain 17 peptides. Score 0.531 Round 4: 104 peptides, 12 chains. Longest chain 22 peptides. Score 0.587 Round 5: 104 peptides, 16 chains. Longest chain 17 peptides. Score 0.477 Taking the results from Round 4 Chains 12, Residues 92, Estimated correctness of the model 24.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 2991 restraints for refining 1316 atoms. 2635 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2828 (Rfree = 0.000) for 1316 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 12: After refmac, R = 0.2457 (Rfree = 0.000) for 1310 atoms. Found 1 (9 requested) and removed 7 (4 requested) atoms. Cycle 13: After refmac, R = 0.2453 (Rfree = 0.000) for 1302 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2393 (Rfree = 0.000) for 1296 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.2329 (Rfree = 0.000) for 1291 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 1349 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 1377 seeds are put forward Round 1: 99 peptides, 17 chains. Longest chain 22 peptides. Score 0.414 Round 2: 113 peptides, 16 chains. Longest chain 22 peptides. Score 0.534 Round 3: 113 peptides, 15 chains. Longest chain 24 peptides. Score 0.560 Round 4: 107 peptides, 15 chains. Longest chain 16 peptides. Score 0.525 Round 5: 103 peptides, 11 chains. Longest chain 21 peptides. Score 0.607 Taking the results from Round 5 Chains 11, Residues 92, Estimated correctness of the model 30.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 3022 restraints for refining 1366 atoms. 2665 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2592 (Rfree = 0.000) for 1366 atoms. Found 6 (10 requested) and removed 12 (5 requested) atoms. Cycle 17: After refmac, R = 0.2309 (Rfree = 0.000) for 1356 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 18: After refmac, R = 0.2360 (Rfree = 0.000) for 1348 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2186 (Rfree = 0.000) for 1342 atoms. Found 0 (10 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.2250 (Rfree = 0.000) for 1334 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 1402 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 1434 seeds are put forward Round 1: 97 peptides, 16 chains. Longest chain 19 peptides. Score 0.430 Round 2: 112 peptides, 15 chains. Longest chain 19 peptides. Score 0.555 Round 3: 111 peptides, 15 chains. Longest chain 18 peptides. Score 0.549 Round 4: 119 peptides, 15 chains. Longest chain 19 peptides. Score 0.594 Round 5: 118 peptides, 17 chains. Longest chain 20 peptides. Score 0.538 Taking the results from Round 4 Chains 15, Residues 104, Estimated correctness of the model 26.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 3081 restraints for refining 1382 atoms. 2680 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2663 (Rfree = 0.000) for 1382 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. Cycle 22: After refmac, R = 0.2390 (Rfree = 0.000) for 1376 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.2377 (Rfree = 0.000) for 1369 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 24: After refmac, R = 0.2387 (Rfree = 0.000) for 1365 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2285 (Rfree = 0.000) for 1362 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 1421 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1442 seeds are put forward Round 1: 96 peptides, 15 chains. Longest chain 16 peptides. Score 0.453 Round 2: 118 peptides, 17 chains. Longest chain 17 peptides. Score 0.538 Round 3: 102 peptides, 14 chains. Longest chain 16 peptides. Score 0.521 Round 4: 108 peptides, 13 chains. Longest chain 17 peptides. Score 0.584 Round 5: 98 peptides, 12 chains. Longest chain 21 peptides. Score 0.552 Taking the results from Round 4 Chains 13, Residues 95, Estimated correctness of the model 23.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 3080 restraints for refining 1382 atoms. 2713 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2732 (Rfree = 0.000) for 1382 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. Cycle 27: After refmac, R = 0.2620 (Rfree = 0.000) for 1372 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.2545 (Rfree = 0.000) for 1366 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.2542 (Rfree = 0.000) for 1359 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2714 (Rfree = 0.000) for 1356 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 1412 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 1439 seeds are put forward Round 1: 86 peptides, 17 chains. Longest chain 12 peptides. Score 0.317 Round 2: 106 peptides, 19 chains. Longest chain 12 peptides. Score 0.403 Round 3: 98 peptides, 13 chains. Longest chain 15 peptides. Score 0.524 Round 4: 102 peptides, 15 chains. Longest chain 20 peptides. Score 0.493 Round 5: 105 peptides, 15 chains. Longest chain 13 peptides. Score 0.512 Taking the results from Round 3 Chains 13, Residues 85, Estimated correctness of the model 1.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 3212 restraints for refining 1382 atoms. 2885 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2590 (Rfree = 0.000) for 1382 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.2308 (Rfree = 0.000) for 1379 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 33: After refmac, R = 0.2246 (Rfree = 0.000) for 1376 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2222 (Rfree = 0.000) for 1372 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2215 (Rfree = 0.000) for 1367 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 1413 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1427 seeds are put forward Round 1: 85 peptides, 14 chains. Longest chain 12 peptides. Score 0.406 Round 2: 93 peptides, 13 chains. Longest chain 16 peptides. Score 0.492 Round 3: 99 peptides, 15 chains. Longest chain 13 peptides. Score 0.473 Round 4: 98 peptides, 14 chains. Longest chain 13 peptides. Score 0.496 Round 5: 97 peptides, 15 chains. Longest chain 13 peptides. Score 0.460 Taking the results from Round 4 Chains 14, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 3160 restraints for refining 1382 atoms. 2838 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2522 (Rfree = 0.000) for 1382 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. Cycle 37: After refmac, R = 0.2423 (Rfree = 0.000) for 1376 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 38: After refmac, R = 0.2393 (Rfree = 0.000) for 1371 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2340 (Rfree = 0.000) for 1370 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2318 (Rfree = 0.000) for 1368 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 1408 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 1420 seeds are put forward Round 1: 88 peptides, 14 chains. Longest chain 15 peptides. Score 0.428 Round 2: 88 peptides, 14 chains. Longest chain 13 peptides. Score 0.428 Round 3: 96 peptides, 13 chains. Longest chain 15 peptides. Score 0.512 Round 4: 99 peptides, 14 chains. Longest chain 13 peptides. Score 0.502 Round 5: 100 peptides, 15 chains. Longest chain 16 peptides. Score 0.480 Taking the results from Round 3 Chains 13, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 3143 restraints for refining 1364 atoms. 2824 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2532 (Rfree = 0.000) for 1364 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 42: After refmac, R = 0.2474 (Rfree = 0.000) for 1358 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.2682 (Rfree = 0.000) for 1352 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2687 (Rfree = 0.000) for 1353 atoms. Found 4 (10 requested) and removed 12 (5 requested) atoms. Cycle 45: After refmac, R = 0.2413 (Rfree = 0.000) for 1339 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.22 Search for helices and strands: 0 residues in 0 chains, 1380 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 1395 seeds are put forward Round 1: 83 peptides, 17 chains. Longest chain 9 peptides. Score 0.293 Round 2: 81 peptides, 14 chains. Longest chain 10 peptides. Score 0.377 Round 3: 82 peptides, 14 chains. Longest chain 10 peptides. Score 0.384 Round 4: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.354 Round 5: 67 peptides, 12 chains. Longest chain 8 peptides. Score 0.336 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 68, 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 2pg4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3374 reflections ( 99.59 % complete ) and 3127 restraints for refining 1350 atoms. 2869 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2490 (Rfree = 0.000) for 1350 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2333 (Rfree = 0.000) for 1345 atoms. Found 0 (10 requested) and removed 2 (5 requested) atoms. Cycle 48: After refmac, R = 0.2394 (Rfree = 0.000) for 1342 atoms. Found 0 (10 requested) and removed 1 (5 requested) atoms. Cycle 49: After refmac, R = 0.2596 (Rfree = 0.000) for 1340 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:41 GMT 2018 Job finished. TimeTaking 29.76 Used memory is bytes: 7797160