null Sun 23 Dec 22:23:10 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 2pc1-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pc1-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pc1-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-3.6-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/2pc1-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-3.6-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 22:23:19 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/2pc1-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-3.6-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 127 and 0 Target number of residues in the AU: 127 Target solvent content: 0.6325 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: 2pc1-3.6-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: 1 Cell parameters: 35.480 37.650 41.500 94.220 109.420 113.080 Input sequence file: 2pc1-3.6-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 3.601 Wilson plot Bfac: 67.51 1984 reflections ( 95.02 % complete ) and 0 restraints for refining 1788 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.2946 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2669 (Rfree = 0.000) for 1788 atoms. Found 11 (11 requested) and removed 41 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.83 Search for helices and strands: 0 residues in 0 chains, 1800 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 8 peptides. Score 0.256 Round 2: 79 peptides, 15 chains. Longest chain 9 peptides. Score 0.350 Round 3: 88 peptides, 17 chains. Longest chain 11 peptides. Score 0.355 Round 4: 88 peptides, 15 chains. Longest chain 10 peptides. Score 0.427 Round 5: 84 peptides, 14 chains. Longest chain 11 peptides. Score 0.430 Taking the results from Round 5 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1984 reflections ( 95.02 % complete ) and 3625 restraints for refining 1458 atoms. 3359 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2167 (Rfree = 0.000) for 1458 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 2: After refmac, R = 0.1793 (Rfree = 0.000) for 1436 atoms. Found 4 (9 requested) and removed 9 (4 requested) atoms. Cycle 3: After refmac, R = 0.1825 (Rfree = 0.000) for 1423 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.1649 (Rfree = 0.000) for 1420 atoms. Found 7 (9 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.1494 (Rfree = 0.000) for 1420 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.80 Search for helices and strands: 0 residues in 0 chains, 1471 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 7 peptides. Score 0.239 Round 2: 88 peptides, 17 chains. Longest chain 7 peptides. Score 0.355 Round 3: 95 peptides, 17 chains. Longest chain 11 peptides. Score 0.415 Round 4: 95 peptides, 16 chains. Longest chain 10 peptides. Score 0.449 Round 5: 84 peptides, 14 chains. Longest chain 9 peptides. Score 0.430 Taking the results from Round 4 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1984 reflections ( 95.02 % complete ) and 3269 restraints for refining 1376 atoms. 2969 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2220 (Rfree = 0.000) for 1376 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 7: After refmac, R = 0.2126 (Rfree = 0.000) for 1361 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 8: After refmac, R = 0.2120 (Rfree = 0.000) for 1344 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 9: After refmac, R = 0.2044 (Rfree = 0.000) for 1344 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.1610 (Rfree = 0.000) for 1339 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.81 Search for helices and strands: 0 residues in 0 chains, 1392 seeds are put forward Round 1: 72 peptides, 14 chains. Longest chain 7 peptides. Score 0.325 Round 2: 93 peptides, 15 chains. Longest chain 19 peptides. Score 0.467 Round 3: 94 peptides, 14 chains. Longest chain 14 peptides. Score 0.508 Round 4: 91 peptides, 13 chains. Longest chain 16 peptides. Score 0.518 Round 5: 88 peptides, 16 chains. Longest chain 14 peptides. Score 0.392 Taking the results from Round 4 Chains 13, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1984 reflections ( 95.02 % complete ) and 3134 restraints for refining 1363 atoms. 2835 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1847 (Rfree = 0.000) for 1363 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 12: After refmac, R = 0.1610 (Rfree = 0.000) for 1356 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.1687 (Rfree = 0.000) for 1346 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.1812 (Rfree = 0.000) for 1341 atoms. Found 3 (8 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.1803 (Rfree = 0.000) for 1334 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.81 Search for helices and strands: 0 residues in 0 chains, 1381 seeds are put forward Round 1: 87 peptides, 17 chains. Longest chain 9 peptides. Score 0.346 Round 2: 101 peptides, 16 chains. Longest chain 15 peptides. Score 0.495 Round 3: 102 peptides, 18 chains. Longest chain 14 peptides. Score 0.437 Round 4: 96 peptides, 16 chains. Longest chain 16 peptides. Score 0.457 Round 5: 98 peptides, 17 chains. Longest chain 11 peptides. Score 0.439 Taking the results from Round 2 Chains 16, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1984 reflections ( 95.02 % complete ) and 3087 restraints for refining 1366 atoms. 2763 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1891 (Rfree = 0.000) for 1366 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 17: After refmac, R = 0.2202 (Rfree = 0.000) for 1357 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 18: After refmac, R = 0.2139 (Rfree = 0.000) for 1352 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.2176 (Rfree = 0.000) for 1355 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.2005 (Rfree = 0.000) for 1350 atoms. Found 3 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.77 Search for helices and strands: 0 residues in 0 chains, 1379 seeds are put forward Round 1: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.352 Round 2: 86 peptides, 15 chains. Longest chain 13 peptides. Score 0.411 Round 3: 88 peptides, 15 chains. Longest chain 13 peptides. Score 0.427 Round 4: 91 peptides, 14 chains. Longest chain 13 peptides. Score 0.485 Round 5: 93 peptides, 13 chains. Longest chain 14 peptides. Score 0.533 Taking the results from Round 5 Chains 14, Residues 80, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1984 reflections ( 95.02 % complete ) and 3149 restraints for refining 1421 atoms. 2806 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1944 (Rfree = 0.000) for 1421 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 22: After refmac, R = 0.1965 (Rfree = 0.000) for 1408 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.1912 (Rfree = 0.000) for 1401 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.1733 (Rfree = 0.000) for 1396 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.1713 (Rfree = 0.000) for 1391 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.76 Search for helices and strands: 0 residues in 0 chains, 1426 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 7 peptides. Score 0.318 Round 2: 78 peptides, 13 chains. Longest chain 13 peptides. Score 0.416 Round 3: 85 peptides, 12 chains. Longest chain 14 peptides. Score 0.507 Round 4: 87 peptides, 10 chains. Longest chain 27 peptides. Score 0.586 Round 5: 85 peptides, 14 chains. Longest chain 11 peptides. Score 0.438 Taking the results from Round 4 Chains 12, Residues 77, Estimated correctness of the model 9.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1984 reflections ( 95.02 % complete ) and 3286 restraints for refining 1458 atoms. 2939 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1814 (Rfree = 0.000) for 1458 atoms. Found 5 (9 requested) and removed 17 (4 requested) atoms. Cycle 27: After refmac, R = 0.1579 (Rfree = 0.000) for 1442 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.1507 (Rfree = 0.000) for 1434 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.1441 (Rfree = 0.000) for 1430 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.1499 (Rfree = 0.000) for 1427 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.69 Search for helices and strands: 0 residues in 0 chains, 1452 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.311 Round 2: 77 peptides, 12 chains. Longest chain 12 peptides. Score 0.444 Round 3: 79 peptides, 12 chains. Longest chain 14 peptides. Score 0.460 Round 4: 78 peptides, 10 chains. Longest chain 14 peptides. Score 0.522 Round 5: 79 peptides, 9 chains. Longest chain 17 peptides. Score 0.562 Taking the results from Round 5 Chains 11, Residues 70, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1984 reflections ( 95.02 % complete ) and 3314 restraints for refining 1457 atoms. 3015 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1553 (Rfree = 0.000) for 1457 atoms. Found 6 (9 requested) and removed 12 (4 requested) atoms. Cycle 32: After refmac, R = 0.1415 (Rfree = 0.000) for 1450 atoms. Found 6 (9 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.1332 (Rfree = 0.000) for 1447 atoms. Found 7 (9 requested) and removed 8 (4 requested) atoms. Cycle 34: After refmac, R = 0.1230 (Rfree = 0.000) for 1444 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.1256 (Rfree = 0.000) for 1441 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.76 Search for helices and strands: 0 residues in 0 chains, 1493 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 10 peptides. Score 0.316 Round 2: 72 peptides, 10 chains. Longest chain 15 peptides. Score 0.475 Round 3: 71 peptides, 12 chains. Longest chain 13 peptides. Score 0.393 Round 4: 71 peptides, 9 chains. Longest chain 15 peptides. Score 0.503 Round 5: 63 peptides, 11 chains. Longest chain 10 peptides. Score 0.360 Taking the results from Round 4 Chains 10, Residues 62, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 1984 reflections ( 95.02 % complete ) and 3368 restraints for refining 1458 atoms. 3084 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1482 (Rfree = 0.000) for 1458 atoms. Found 6 (9 requested) and removed 6 (4 requested) atoms. Cycle 37: After refmac, R = 0.1411 (Rfree = 0.000) for 1455 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.1329 (Rfree = 0.000) for 1451 atoms. Found 6 (9 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.1205 (Rfree = 0.000) for 1452 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1195 (Rfree = 0.000) for 1447 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.77 Search for helices and strands: 0 residues in 0 chains, 1480 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 7 peptides. Score 0.241 Round 2: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.289 Round 3: 70 peptides, 11 chains. Longest chain 14 peptides. Score 0.422 Round 4: 69 peptides, 13 chains. Longest chain 7 peptides. Score 0.336 Round 5: 73 peptides, 11 chains. Longest chain 14 peptides. Score 0.447 Taking the results from Round 5 Chains 11, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1984 reflections ( 95.02 % complete ) and 3436 restraints for refining 1451 atoms. 3199 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1490 (Rfree = 0.000) for 1451 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 42: After refmac, R = 0.1346 (Rfree = 0.000) for 1448 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 43: After refmac, R = 0.1272 (Rfree = 0.000) for 1446 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.1222 (Rfree = 0.000) for 1443 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.1237 (Rfree = 0.000) for 1438 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.74 Search for helices and strands: 0 residues in 0 chains, 1474 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 7 peptides. Score 0.228 Round 2: 74 peptides, 15 chains. Longest chain 8 peptides. Score 0.305 Round 3: 64 peptides, 12 chains. Longest chain 9 peptides. Score 0.330 Round 4: 67 peptides, 12 chains. Longest chain 14 peptides. Score 0.357 Round 5: 65 peptides, 13 chains. Longest chain 8 peptides. Score 0.299 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 55, 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. 1984 reflections ( 95.02 % complete ) and 3585 restraints for refining 1444 atoms. 3377 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1560 (Rfree = 0.000) for 1444 atoms. Found 0 (9 requested) and removed 2 (4 requested) atoms. Cycle 47: After refmac, R = 0.1383 (Rfree = 0.000) for 1438 atoms. Found 0 (9 requested) and removed 3 (4 requested) atoms. Cycle 48: After refmac, R = 0.1284 (Rfree = 0.000) for 1434 atoms. Found 0 (9 requested) and removed 2 (4 requested) atoms. Cycle 49: After refmac, R = 0.1359 (Rfree = 0.000) for 1431 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:05 GMT 2018 Job finished. TimeTaking 28.93 Used memory is bytes: 11907648