Mon 24 Dec 00:26:39 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pg4-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pg4-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pg4-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.6-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:26:43 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.6-parrot-mrncs/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 141 and 0 Target number of residues in the AU: 141 Target solvent content: 0.6559 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: 2pg4-3.6-parrot-mrncs.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: 2pg4-3.6-parrot-mrncs.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 3.600 Wilson plot Bfac: 81.13 2869 reflections ( 99.51 % complete ) and 0 restraints for refining 1688 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3729 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3421 (Rfree = 0.000) for 1688 atoms. Found 9 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 1729 seeds are put forward NCS extension: 0 residues added, 1729 seeds are put forward Round 1: 72 peptides, 14 chains. Longest chain 11 peptides. Score 0.306 Round 2: 95 peptides, 16 chains. Longest chain 16 peptides. Score 0.416 Round 3: 100 peptides, 14 chains. Longest chain 21 peptides. Score 0.509 Round 4: 96 peptides, 14 chains. Longest chain 15 peptides. Score 0.483 Round 5: 89 peptides, 14 chains. Longest chain 14 peptides. Score 0.435 Taking the results from Round 3 Chains 14, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3221 restraints for refining 1377 atoms. 2891 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2984 (Rfree = 0.000) for 1377 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 2: After refmac, R = 0.2945 (Rfree = 0.000) for 1343 atoms. Found 0 (8 requested) and removed 7 (4 requested) atoms. Cycle 3: After refmac, R = 0.2776 (Rfree = 0.000) for 1312 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. Cycle 4: After refmac, R = 0.2705 (Rfree = 0.000) for 1293 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. Cycle 5: After refmac, R = 0.2752 (Rfree = 0.000) for 1277 atoms. Found 0 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 1332 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 1358 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 8 peptides. Score 0.287 Round 2: 98 peptides, 18 chains. Longest chain 12 peptides. Score 0.376 Round 3: 96 peptides, 15 chains. Longest chain 13 peptides. Score 0.453 Round 4: 99 peptides, 16 chains. Longest chain 15 peptides. Score 0.444 Round 5: 93 peptides, 14 chains. Longest chain 14 peptides. Score 0.463 Taking the results from Round 5 Chains 14, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3061 restraints for refining 1327 atoms. 2759 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2826 (Rfree = 0.000) for 1327 atoms. Found 2 (8 requested) and removed 10 (4 requested) atoms. Cycle 7: After refmac, R = 0.2484 (Rfree = 0.000) for 1310 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 8: After refmac, R = 0.2523 (Rfree = 0.000) for 1299 atoms. Found 3 (8 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.2448 (Rfree = 0.000) for 1290 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2301 (Rfree = 0.000) for 1283 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.33 Search for helices and strands: 0 residues in 0 chains, 1363 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1378 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 11 peptides. Score 0.320 Round 2: 91 peptides, 13 chains. Longest chain 13 peptides. Score 0.479 Round 3: 98 peptides, 14 chains. Longest chain 14 peptides. Score 0.496 Round 4: 98 peptides, 14 chains. Longest chain 16 peptides. Score 0.496 Round 5: 93 peptides, 12 chains. Longest chain 20 peptides. Score 0.521 Taking the results from Round 5 Chains 12, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 2956 restraints for refining 1342 atoms. 2644 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2659 (Rfree = 0.000) for 1342 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. Cycle 12: After refmac, R = 0.2267 (Rfree = 0.000) for 1327 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 13: After refmac, R = 0.2402 (Rfree = 0.000) for 1318 atoms. Found 3 (8 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.2236 (Rfree = 0.000) for 1308 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.2215 (Rfree = 0.000) for 1302 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.51 3.33 Search for helices and strands: 0 residues in 0 chains, 1370 seeds are put forward NCS extension: 0 residues added, 1370 seeds are put forward Round 1: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.389 Round 2: 96 peptides, 14 chains. Longest chain 13 peptides. Score 0.483 Round 3: 91 peptides, 12 chains. Longest chain 17 peptides. Score 0.509 Round 4: 96 peptides, 12 chains. Longest chain 15 peptides. Score 0.540 Round 5: 101 peptides, 14 chains. Longest chain 13 peptides. Score 0.515 Taking the results from Round 4 Chains 12, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 2890 restraints for refining 1346 atoms. 2566 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2488 (Rfree = 0.000) for 1346 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. Cycle 17: After refmac, R = 0.2497 (Rfree = 0.000) for 1336 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 18: After refmac, R = 0.2385 (Rfree = 0.000) for 1328 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2202 (Rfree = 0.000) for 1323 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.2016 (Rfree = 0.000) for 1319 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.33 Search for helices and strands: 0 residues in 0 chains, 1358 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 1384 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.334 Round 2: 91 peptides, 13 chains. Longest chain 14 peptides. Score 0.479 Round 3: 95 peptides, 12 chains. Longest chain 14 peptides. Score 0.534 Round 4: 98 peptides, 14 chains. Longest chain 14 peptides. Score 0.496 Round 5: 95 peptides, 15 chains. Longest chain 10 peptides. Score 0.446 Taking the results from Round 3 Chains 12, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3043 restraints for refining 1378 atoms. 2723 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2515 (Rfree = 0.000) for 1378 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 22: After refmac, R = 0.2343 (Rfree = 0.000) for 1370 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.2361 (Rfree = 0.000) for 1364 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.2505 (Rfree = 0.000) for 1354 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2473 (Rfree = 0.000) for 1351 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.41 Search for helices and strands: 0 residues in 0 chains, 1398 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1413 seeds are put forward Round 1: 73 peptides, 14 chains. Longest chain 12 peptides. Score 0.315 Round 2: 86 peptides, 12 chains. Longest chain 13 peptides. Score 0.476 Round 3: 89 peptides, 15 chains. Longest chain 11 peptides. Score 0.404 Round 4: 89 peptides, 15 chains. Longest chain 14 peptides. Score 0.404 Round 5: 95 peptides, 15 chains. Longest chain 10 peptides. Score 0.446 Taking the results from Round 2 Chains 12, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3149 restraints for refining 1378 atoms. 2865 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2591 (Rfree = 0.000) for 1378 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 27: After refmac, R = 0.2637 (Rfree = 0.000) for 1370 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. Cycle 28: After refmac, R = 0.2543 (Rfree = 0.000) for 1367 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. Cycle 29: After refmac, R = 0.2149 (Rfree = 0.000) for 1356 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.2084 (Rfree = 0.000) for 1349 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 1398 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1413 seeds are put forward Round 1: 61 peptides, 11 chains. Longest chain 10 peptides. Score 0.322 Round 2: 82 peptides, 13 chains. Longest chain 10 peptides. Score 0.416 Round 3: 80 peptides, 11 chains. Longest chain 13 peptides. Score 0.466 Round 4: 87 peptides, 11 chains. Longest chain 18 peptides. Score 0.512 Round 5: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.406 Taking the results from Round 4 Chains 11, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3156 restraints for refining 1378 atoms. 2863 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2344 (Rfree = 0.000) for 1378 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.2283 (Rfree = 0.000) for 1370 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.2349 (Rfree = 0.000) for 1368 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.2406 (Rfree = 0.000) for 1367 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.2205 (Rfree = 0.000) for 1363 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 1413 seeds are put forward NCS extension: 0 residues added, 1413 seeds are put forward Round 1: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.344 Round 2: 90 peptides, 15 chains. Longest chain 11 peptides. Score 0.411 Round 3: 90 peptides, 17 chains. Longest chain 12 peptides. Score 0.348 Round 4: 94 peptides, 14 chains. Longest chain 17 peptides. Score 0.469 Round 5: 93 peptides, 16 chains. Longest chain 9 peptides. Score 0.401 Taking the results from Round 4 Chains 14, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3021 restraints for refining 1376 atoms. 2715 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2664 (Rfree = 0.000) for 1376 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 37: After refmac, R = 0.2460 (Rfree = 0.000) for 1368 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.2345 (Rfree = 0.000) for 1365 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.2082 (Rfree = 0.000) for 1359 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.2208 (Rfree = 0.000) for 1353 atoms. Found 1 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 1390 seeds are put forward NCS extension: 0 residues added, 1390 seeds are put forward Round 1: 66 peptides, 13 chains. Longest chain 7 peptides. Score 0.292 Round 2: 80 peptides, 14 chains. Longest chain 9 peptides. Score 0.369 Round 3: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.315 Round 4: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.333 Round 5: 78 peptides, 12 chains. Longest chain 14 peptides. Score 0.420 Taking the results from Round 5 Chains 12, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3096 restraints for refining 1378 atoms. 2844 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2217 (Rfree = 0.000) for 1378 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 42: After refmac, R = 0.2181 (Rfree = 0.000) for 1373 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.2033 (Rfree = 0.000) for 1367 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.1965 (Rfree = 0.000) for 1362 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.2065 (Rfree = 0.000) for 1354 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.32 Search for helices and strands: 0 residues in 0 chains, 1402 seeds are put forward NCS extension: 0 residues added, 1402 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.296 Round 2: 89 peptides, 16 chains. Longest chain 8 peptides. Score 0.372 Round 3: 78 peptides, 14 chains. Longest chain 8 peptides. Score 0.354 Round 4: 78 peptides, 14 chains. Longest chain 7 peptides. Score 0.354 Round 5: 78 peptides, 14 chains. Longest chain 8 peptides. Score 0.354 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 73, 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. 2869 reflections ( 99.51 % complete ) and 3070 restraints for refining 1377 atoms. 2794 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1979 (Rfree = 0.000) for 1377 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2074 (Rfree = 0.000) for 1371 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1993 (Rfree = 0.000) for 1364 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2040 (Rfree = 0.000) for 1359 atoms. TimeTaking 26.45