null Sun 23 Dec 22:22:52 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 2pc1-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pc1-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pc1-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-3.8-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/2pc1-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-3.8-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 ============================================================ Sun 23 Dec 22:23:00 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/2pc1-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-3.8-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 123 and 0 Target number of residues in the AU: 123 Target solvent content: 0.6440 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 201 Adjusted target solvent content: 0.42 Input MTZ file: 2pc1-3.8-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: 1 Cell parameters: 35.480 37.650 41.500 94.220 109.420 113.080 Input sequence file: 2pc1-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1608 target number of atoms Had to go as low as 0.65 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: 25.956 3.801 Wilson plot Bfac: 72.97 1684 reflections ( 94.39 % complete ) and 0 restraints for refining 1783 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.2963 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2608 (Rfree = 0.000) for 1783 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.91 Search for helices and strands: 0 residues in 0 chains, 1793 seeds are put forward Round 1: 49 peptides, 10 chains. Longest chain 8 peptides. Score 0.266 Round 2: 69 peptides, 14 chains. Longest chain 8 peptides. Score 0.297 Round 3: 70 peptides, 13 chains. Longest chain 11 peptides. Score 0.346 Round 4: 73 peptides, 13 chains. Longest chain 11 peptides. Score 0.372 Round 5: 72 peptides, 13 chains. Longest chain 12 peptides. Score 0.364 Taking the results from Round 4 Chains 13, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1684 reflections ( 94.39 % complete ) and 3529 restraints for refining 1455 atoms. 3302 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.1734 (Rfree = 0.000) for 1455 atoms. Found 5 (7 requested) and removed 7 (3 requested) atoms. Cycle 2: After refmac, R = 0.1476 (Rfree = 0.000) for 1444 atoms. Found 2 (7 requested) and removed 7 (3 requested) atoms. Cycle 3: After refmac, R = 0.1573 (Rfree = 0.000) for 1437 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 4: After refmac, R = 0.1370 (Rfree = 0.000) for 1429 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 5: After refmac, R = 0.1309 (Rfree = 0.000) for 1422 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 4.02 Search for helices and strands: 0 residues in 0 chains, 1469 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 7 peptides. Score 0.228 Round 2: 79 peptides, 15 chains. Longest chain 10 peptides. Score 0.350 Round 3: 66 peptides, 12 chains. Longest chain 13 peptides. Score 0.348 Round 4: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.325 Round 5: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.381 Taking the results from Round 5 Chains 13, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1684 reflections ( 94.39 % complete ) and 3538 restraints for refining 1425 atoms. 3307 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1708 (Rfree = 0.000) for 1425 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 7: After refmac, R = 0.1681 (Rfree = 0.000) for 1417 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 8: After refmac, R = 0.1594 (Rfree = 0.000) for 1411 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 9: After refmac, R = 0.1549 (Rfree = 0.000) for 1410 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.1420 (Rfree = 0.000) for 1408 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 4.04 Search for helices and strands: 0 residues in 0 chains, 1455 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.233 Round 2: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.375 Round 3: 67 peptides, 12 chains. Longest chain 10 peptides. Score 0.357 Round 4: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.314 Round 5: 71 peptides, 12 chains. Longest chain 11 peptides. Score 0.393 Taking the results from Round 5 Chains 12, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1684 reflections ( 94.39 % complete ) and 3506 restraints for refining 1419 atoms. 3282 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1776 (Rfree = 0.000) for 1419 atoms. Found 6 (7 requested) and removed 13 (3 requested) atoms. Cycle 12: After refmac, R = 0.1542 (Rfree = 0.000) for 1407 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.1456 (Rfree = 0.000) for 1406 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 14: After refmac, R = 0.1499 (Rfree = 0.000) for 1404 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.1374 (Rfree = 0.000) for 1401 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 4.05 Search for helices and strands: 0 residues in 0 chains, 1439 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 7 peptides. Score 0.278 Round 2: 69 peptides, 14 chains. Longest chain 7 peptides. Score 0.297 Round 3: 57 peptides, 11 chains. Longest chain 11 peptides. Score 0.304 Round 4: 59 peptides, 10 chains. Longest chain 12 peptides. Score 0.364 Round 5: 58 peptides, 9 chains. Longest chain 14 peptides. Score 0.395 Taking the results from Round 5 Chains 9, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1684 reflections ( 94.39 % complete ) and 3581 restraints for refining 1419 atoms. 3394 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1596 (Rfree = 0.000) for 1419 atoms. Found 6 (7 requested) and removed 11 (3 requested) atoms. Cycle 17: After refmac, R = 0.1464 (Rfree = 0.000) for 1409 atoms. Found 4 (7 requested) and removed 8 (3 requested) atoms. Cycle 18: After refmac, R = 0.1319 (Rfree = 0.000) for 1402 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 19: After refmac, R = 0.1425 (Rfree = 0.000) for 1395 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.1196 (Rfree = 0.000) for 1388 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 4.00 Search for helices and strands: 0 residues in 0 chains, 1428 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 6 peptides. Score 0.231 Round 2: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.280 Round 3: 66 peptides, 11 chains. Longest chain 10 peptides. Score 0.387 Round 4: 76 peptides, 13 chains. Longest chain 11 peptides. Score 0.399 Round 5: 76 peptides, 13 chains. Longest chain 11 peptides. Score 0.399 Taking the results from Round 5 Chains 13, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1684 reflections ( 94.39 % complete ) and 3457 restraints for refining 1411 atoms. 3218 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1552 (Rfree = 0.000) for 1411 atoms. Found 6 (7 requested) and removed 27 (3 requested) atoms. Cycle 22: After refmac, R = 0.1392 (Rfree = 0.000) for 1383 atoms. Found 3 (7 requested) and removed 10 (3 requested) atoms. Cycle 23: After refmac, R = 0.1499 (Rfree = 0.000) for 1372 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 24: After refmac, R = 0.1267 (Rfree = 0.000) for 1372 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.1425 (Rfree = 0.000) for 1369 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 4.05 Search for helices and strands: 0 residues in 0 chains, 1416 seeds are put forward Round 1: 63 peptides, 15 chains. Longest chain 5 peptides. Score 0.198 Round 2: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.280 Round 3: 57 peptides, 10 chains. Longest chain 14 peptides. Score 0.345 Round 4: 62 peptides, 10 chains. Longest chain 14 peptides. Score 0.391 Round 5: 60 peptides, 10 chains. Longest chain 14 peptides. Score 0.373 Taking the results from Round 4 Chains 10, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1684 reflections ( 94.39 % complete ) and 3554 restraints for refining 1420 atoms. 3356 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1666 (Rfree = 0.000) for 1420 atoms. Found 6 (7 requested) and removed 7 (3 requested) atoms. Cycle 27: After refmac, R = 0.1793 (Rfree = 0.000) for 1410 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 28: After refmac, R = 0.1535 (Rfree = 0.000) for 1401 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.1695 (Rfree = 0.000) for 1401 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1295 (Rfree = 0.000) for 1402 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.99 Search for helices and strands: 0 residues in 0 chains, 1443 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 6 peptides. Score 0.238 Round 2: 69 peptides, 12 chains. Longest chain 12 peptides. Score 0.375 Round 3: 67 peptides, 12 chains. Longest chain 10 peptides. Score 0.357 Round 4: 73 peptides, 13 chains. Longest chain 11 peptides. Score 0.372 Round 5: 85 peptides, 16 chains. Longest chain 12 peptides. Score 0.366 Taking the results from Round 2 Chains 12, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1684 reflections ( 94.39 % complete ) and 3343 restraints for refining 1381 atoms. 3127 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1871 (Rfree = 0.000) for 1381 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 32: After refmac, R = 0.1660 (Rfree = 0.000) for 1376 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. Cycle 33: After refmac, R = 0.1545 (Rfree = 0.000) for 1371 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.1620 (Rfree = 0.000) for 1367 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.1845 (Rfree = 0.000) for 1362 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.62 4.03 Search for helices and strands: 0 residues in 0 chains, 1412 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 9 peptides. Score 0.260 Round 2: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.379 Round 3: 66 peptides, 12 chains. Longest chain 11 peptides. Score 0.348 Round 4: 68 peptides, 13 chains. Longest chain 11 peptides. Score 0.327 Round 5: 77 peptides, 14 chains. Longest chain 11 peptides. Score 0.370 Taking the results from Round 2 Chains 14, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1684 reflections ( 94.39 % complete ) and 3181 restraints for refining 1364 atoms. 2939 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1915 (Rfree = 0.000) for 1364 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 37: After refmac, R = 0.1447 (Rfree = 0.000) for 1359 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.1466 (Rfree = 0.000) for 1354 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.1299 (Rfree = 0.000) for 1352 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.1400 (Rfree = 0.000) for 1348 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 4.00 Search for helices and strands: 0 residues in 0 chains, 1395 seeds are put forward Round 1: 57 peptides, 11 chains. Longest chain 10 peptides. Score 0.304 Round 2: 59 peptides, 11 chains. Longest chain 10 peptides. Score 0.323 Round 3: 59 peptides, 11 chains. Longest chain 11 peptides. Score 0.323 Round 4: 61 peptides, 11 chains. Longest chain 11 peptides. Score 0.342 Round 5: 60 peptides, 12 chains. Longest chain 11 peptides. Score 0.291 Taking the results from Round 4 Chains 11, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1684 reflections ( 94.39 % complete ) and 3328 restraints for refining 1361 atoms. 3139 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2152 (Rfree = 0.000) for 1361 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.1895 (Rfree = 0.000) for 1364 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.1986 (Rfree = 0.000) for 1363 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.1756 (Rfree = 0.000) for 1362 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.1116 (Rfree = 0.000) for 1358 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 4.00 Search for helices and strands: 0 residues in 0 chains, 1395 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 8 peptides. Score 0.260 Round 2: 75 peptides, 13 chains. Longest chain 10 peptides. Score 0.390 Round 3: 70 peptides, 14 chains. Longest chain 10 peptides. Score 0.306 Round 4: 72 peptides, 12 chains. Longest chain 11 peptides. Score 0.402 Round 5: 71 peptides, 14 chains. Longest chain 11 peptides. Score 0.316 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 60, 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 2pc1-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1684 reflections ( 94.39 % complete ) and 3270 restraints for refining 1357 atoms. 3042 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1882 (Rfree = 0.000) for 1357 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1403 (Rfree = 0.000) for 1353 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1380 (Rfree = 0.000) for 1345 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1228 (Rfree = 0.000) for 1341 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:49:44 GMT 2018 Job finished. TimeTaking 26.87 Used memory is bytes: 3703432