Sun 23 Dec 22:22:59 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 1vr3-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr3-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr3-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-3.6-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/1vr3-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-3.6-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 22:23:09 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/1vr3-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-3.6-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 234 and 0 Target number of residues in the AU: 234 Target solvent content: 0.6456 Checking the provided sequence file Detected sequence length: 191 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 191 Adjusted target solvent content: 0.71 Input MTZ file: 1vr3-3.6-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: 92 Cell parameters: 79.137 79.137 114.115 90.000 90.000 90.000 Input sequence file: 1vr3-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1528 target number of atoms Had to go as low as 1.10 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 Loops will be built when appropriate and at the last cycle Resolution range: 65.030 3.600 Wilson plot Bfac: 74.70 4544 reflections ( 99.69 % complete ) and 0 restraints for refining 1707 atoms. Observations/parameters ratio is 0.67 ------------------------------------------------------ Starting model: R = 0.3437 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3094 (Rfree = 0.000) for 1707 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 2.59 Search for helices and strands: 0 residues in 0 chains, 1744 seeds are put forward Round 1: 131 peptides, 17 chains. Longest chain 15 peptides. Score 0.488 Round 2: 132 peptides, 13 chains. Longest chain 16 peptides. Score 0.566 Round 3: 131 peptides, 14 chains. Longest chain 20 peptides. Score 0.544 Round 4: 140 peptides, 15 chains. Longest chain 17 peptides. Score 0.560 Round 5: 141 peptides, 13 chains. Longest chain 34 peptides. Score 0.599 Taking the results from Round 5 Chains 13, Residues 128, Estimated correctness of the model 14.3 % 1 chains (33 residues) have been docked in sequence ------------------------------------------------------ 4544 reflections ( 99.69 % complete ) and 2752 restraints for refining 1463 atoms. 2100 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2688 (Rfree = 0.000) for 1463 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 2: After refmac, R = 0.2495 (Rfree = 0.000) for 1434 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 3: After refmac, R = 0.2366 (Rfree = 0.000) for 1430 atoms. Found 7 (9 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.2309 (Rfree = 0.000) for 1425 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 5: After refmac, R = 0.2257 (Rfree = 0.000) for 1424 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 2.61 Search for helices and strands: 0 residues in 0 chains, 1479 seeds are put forward Round 1: 148 peptides, 14 chains. Longest chain 19 peptides. Score 0.606 Round 2: 141 peptides, 13 chains. Longest chain 22 peptides. Score 0.599 Round 3: 142 peptides, 13 chains. Longest chain 30 peptides. Score 0.602 Round 4: 145 peptides, 13 chains. Longest chain 39 peptides. Score 0.612 Round 5: 142 peptides, 14 chains. Longest chain 28 peptides. Score 0.585 Taking the results from Round 4 Chains 15, Residues 132, Estimated correctness of the model 19.3 % 3 chains (48 residues) have been docked in sequence ------------------------------------------------------ 4544 reflections ( 99.69 % complete ) and 2597 restraints for refining 1462 atoms. 1851 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2735 (Rfree = 0.000) for 1462 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 7: After refmac, R = 0.2572 (Rfree = 0.000) for 1438 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. Cycle 8: After refmac, R = 0.2441 (Rfree = 0.000) for 1432 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 9: After refmac, R = 0.2404 (Rfree = 0.000) for 1427 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.2331 (Rfree = 0.000) for 1422 atoms. Found 4 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 2.55 Search for helices and strands: 0 residues in 0 chains, 1451 seeds are put forward Round 1: 132 peptides, 12 chains. Longest chain 21 peptides. Score 0.584 Round 2: 144 peptides, 12 chains. Longest chain 33 peptides. Score 0.625 Round 3: 148 peptides, 12 chains. Longest chain 37 peptides. Score 0.638 Round 4: 139 peptides, 11 chains. Longest chain 46 peptides. Score 0.625 Round 5: 135 peptides, 16 chains. Longest chain 22 peptides. Score 0.523 Taking the results from Round 3 Chains 14, Residues 136, Estimated correctness of the model 28.9 % 2 chains (46 residues) have been docked in sequence ------------------------------------------------------ 4544 reflections ( 99.69 % complete ) and 2348 restraints for refining 1386 atoms. 1625 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2747 (Rfree = 0.000) for 1386 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 12: After refmac, R = 0.2549 (Rfree = 0.000) for 1363 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 13: After refmac, R = 0.2436 (Rfree = 0.000) for 1363 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2360 (Rfree = 0.000) for 1359 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.2257 (Rfree = 0.000) for 1362 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 2.66 Search for helices and strands: 0 residues in 0 chains, 1414 seeds are put forward Round 1: 139 peptides, 12 chains. Longest chain 38 peptides. Score 0.609 Round 2: 136 peptides, 12 chains. Longest chain 29 peptides. Score 0.598 Round 3: 143 peptides, 10 chains. Longest chain 45 peptides. Score 0.654 Round 4: 145 peptides, 10 chains. Longest chain 49 peptides. Score 0.661 Round 5: 142 peptides, 12 chains. Longest chain 49 peptides. Score 0.619 Taking the results from Round 4 Chains 10, Residues 135, Estimated correctness of the model 37.0 % 1 chains (48 residues) have been docked in sequence ------------------------------------------------------ 4544 reflections ( 99.69 % complete ) and 2356 restraints for refining 1404 atoms. 1599 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2738 (Rfree = 0.000) for 1404 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 17: After refmac, R = 0.2535 (Rfree = 0.000) for 1387 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 18: After refmac, R = 0.2376 (Rfree = 0.000) for 1379 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2290 (Rfree = 0.000) for 1375 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2229 (Rfree = 0.000) for 1372 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 2.66 Search for helices and strands: 0 residues in 0 chains, 1416 seeds are put forward Round 1: 128 peptides, 16 chains. Longest chain 21 peptides. Score 0.495 Round 2: 142 peptides, 14 chains. Longest chain 23 peptides. Score 0.585 Round 3: 140 peptides, 12 chains. Longest chain 33 peptides. Score 0.612 Round 4: 136 peptides, 13 chains. Longest chain 35 peptides. Score 0.581 Round 5: 139 peptides, 11 chains. Longest chain 36 peptides. Score 0.625 Taking the results from Round 5 Chains 11, Residues 128, Estimated correctness of the model 24.2 % 2 chains (60 residues) have been docked in sequence ------------------------------------------------------ 4544 reflections ( 99.69 % complete ) and 2264 restraints for refining 1400 atoms. 1476 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2677 (Rfree = 0.000) for 1400 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 22: After refmac, R = 0.2428 (Rfree = 0.000) for 1371 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.2272 (Rfree = 0.000) for 1368 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. Cycle 24: After refmac, R = 0.2137 (Rfree = 0.000) for 1365 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.2052 (Rfree = 0.000) for 1357 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 2.52 Search for helices and strands: 0 residues in 0 chains, 1406 seeds are put forward Round 1: 126 peptides, 15 chains. Longest chain 19 peptides. Score 0.506 Round 2: 133 peptides, 13 chains. Longest chain 30 peptides. Score 0.570 Round 3: 140 peptides, 14 chains. Longest chain 24 peptides. Score 0.578 Round 4: 138 peptides, 15 chains. Longest chain 26 peptides. Score 0.553 Round 5: 140 peptides, 9 chains. Longest chain 37 peptides. Score 0.661 Taking the results from Round 5 Chains 9, Residues 131, Estimated correctness of the model 37.0 % 1 chains (36 residues) have been docked in sequence ------------------------------------------------------ 4544 reflections ( 99.69 % complete ) and 2544 restraints for refining 1412 atoms. 1845 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2667 (Rfree = 0.000) for 1412 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 27: After refmac, R = 0.2453 (Rfree = 0.000) for 1401 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.2335 (Rfree = 0.000) for 1396 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 29: After refmac, R = 0.2198 (Rfree = 0.000) for 1395 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2133 (Rfree = 0.000) for 1392 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 2.54 Search for helices and strands: 0 residues in 0 chains, 1438 seeds are put forward Round 1: 124 peptides, 12 chains. Longest chain 22 peptides. Score 0.554 Round 2: 130 peptides, 13 chains. Longest chain 18 peptides. Score 0.559 Round 3: 147 peptides, 12 chains. Longest chain 21 peptides. Score 0.635 Round 4: 145 peptides, 13 chains. Longest chain 30 peptides. Score 0.612 Round 5: 144 peptides, 12 chains. Longest chain 31 peptides. Score 0.625 Taking the results from Round 3 Chains 14, Residues 135, Estimated correctness of the model 27.8 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 4544 reflections ( 99.69 % complete ) and 2441 restraints for refining 1396 atoms. 1719 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2462 (Rfree = 0.000) for 1396 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.2305 (Rfree = 0.000) for 1394 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.2466 (Rfree = 0.000) for 1391 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 34: After refmac, R = 0.2301 (Rfree = 0.000) for 1377 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.2200 (Rfree = 0.000) for 1375 atoms. Found 4 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 2.57 Search for helices and strands: 0 residues in 0 chains, 1420 seeds are put forward Round 1: 138 peptides, 13 chains. Longest chain 47 peptides. Score 0.588 Round 2: 140 peptides, 10 chains. Longest chain 32 peptides. Score 0.645 Round 3: 140 peptides, 14 chains. Longest chain 30 peptides. Score 0.578 Round 4: 139 peptides, 11 chains. Longest chain 30 peptides. Score 0.625 Round 5: 129 peptides, 12 chains. Longest chain 35 peptides. Score 0.573 Taking the results from Round 2 Chains 10, Residues 130, Estimated correctness of the model 31.4 % 1 chains (31 residues) have been docked in sequence ------------------------------------------------------ 4544 reflections ( 99.69 % complete ) and 2535 restraints for refining 1386 atoms. 1877 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2524 (Rfree = 0.000) for 1386 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 37: After refmac, R = 0.2375 (Rfree = 0.000) for 1376 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.2258 (Rfree = 0.000) for 1375 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.2215 (Rfree = 0.000) for 1374 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 40: After refmac, R = 0.2188 (Rfree = 0.000) for 1367 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 2.66 Search for helices and strands: 0 residues in 0 chains, 1399 seeds are put forward Round 1: 136 peptides, 15 chains. Longest chain 28 peptides. Score 0.545 Round 2: 144 peptides, 12 chains. Longest chain 26 peptides. Score 0.625 Round 3: 139 peptides, 13 chains. Longest chain 29 peptides. Score 0.592 Round 4: 143 peptides, 17 chains. Longest chain 18 peptides. Score 0.536 Round 5: 150 peptides, 12 chains. Longest chain 30 peptides. Score 0.645 Taking the results from Round 5 Chains 12, Residues 138, Estimated correctness of the model 31.4 % 2 chains (51 residues) have been docked in sequence ------------------------------------------------------ 4544 reflections ( 99.69 % complete ) and 2303 restraints for refining 1386 atoms. 1510 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2680 (Rfree = 0.000) for 1386 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 42: After refmac, R = 0.2490 (Rfree = 0.000) for 1378 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 43: After refmac, R = 0.2534 (Rfree = 0.000) for 1368 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 44: After refmac, R = 0.2111 (Rfree = 0.000) for 1352 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 45: After refmac, R = 0.2016 (Rfree = 0.000) for 1346 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 2.55 Search for helices and strands: 0 residues in 0 chains, 1385 seeds are put forward Round 1: 123 peptides, 13 chains. Longest chain 21 peptides. Score 0.532 Round 2: 131 peptides, 10 chains. Longest chain 34 peptides. Score 0.615 Round 3: 134 peptides, 10 chains. Longest chain 25 peptides. Score 0.625 Round 4: 139 peptides, 9 chains. Longest chain 28 peptides. Score 0.658 Round 5: 138 peptides, 9 chains. Longest chain 26 peptides. Score 0.655 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 130, Estimated correctness of the model 35.9 % 3 chains (67 residues) have been docked in sequence Sequence coverage is 51 % Consider running further cycles of model building using 1vr3-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 83 A and 95 A 8 chains (141 residues) following loop building 2 chains (78 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4544 reflections ( 99.69 % complete ) and 2224 restraints for refining 1444 atoms. 1282 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2663 (Rfree = 0.000) for 1444 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2326 (Rfree = 0.000) for 1433 atoms. Found 0 (9 requested) and removed 3 (4 requested) atoms. Cycle 48: After refmac, R = 0.2154 (Rfree = 0.000) for 1427 atoms. Found 0 (9 requested) and removed 1 (4 requested) atoms. Cycle 49: After refmac, R = 0.2063 (Rfree = 0.000) for 1423 atoms. TimeTaking 33.37