null Mon 24 Dec 08:01:25 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1o6a-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1o6a-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1o6a-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.6-parrot-noncs ############### 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 08:01:29 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/noncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.6-parrot-noncs/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 136 and 0 Target number of residues in the AU: 136 Target solvent content: 0.6582 Checking the provided sequence file Detected sequence length: 96 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 192 Adjusted target solvent content: 0.52 Input MTZ file: 1o6a-3.6-parrot-noncs.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: 61.652 61.652 113.295 90.000 90.000 90.000 Input sequence file: 1o6a-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 1536 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 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: 41.713 3.601 Wilson plot Bfac: 83.20 2821 reflections ( 99.86 % complete ) and 0 restraints for refining 1694 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.4289 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4218 (Rfree = 0.000) for 1694 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 1713 seeds are put forward NCS extension: 0 residues added, 1713 seeds are put forward Round 1: 79 peptides, 16 chains. Longest chain 8 peptides. Score 0.298 Round 2: 91 peptides, 16 chains. Longest chain 12 peptides. Score 0.392 Round 3: 99 peptides, 13 chains. Longest chain 19 peptides. Score 0.538 Round 4: 105 peptides, 15 chains. Longest chain 15 peptides. Score 0.519 Round 5: 105 peptides, 12 chains. Longest chain 18 peptides. Score 0.601 Taking the results from Round 5 Chains 12, Residues 93, Estimated correctness of the model 15.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3103 restraints for refining 1354 atoms. 2743 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3662 (Rfree = 0.000) for 1354 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 2: After refmac, R = 0.3483 (Rfree = 0.000) for 1321 atoms. Found 6 (8 requested) and removed 14 (4 requested) atoms. Cycle 3: After refmac, R = 0.3770 (Rfree = 0.000) for 1299 atoms. Found 7 (8 requested) and removed 17 (4 requested) atoms. Cycle 4: After refmac, R = 0.3219 (Rfree = 0.000) for 1280 atoms. Found 5 (8 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.3152 (Rfree = 0.000) for 1273 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 1309 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 1334 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 11 peptides. Score 0.327 Round 2: 91 peptides, 14 chains. Longest chain 13 peptides. Score 0.455 Round 3: 98 peptides, 15 chains. Longest chain 12 peptides. Score 0.473 Round 4: 111 peptides, 18 chains. Longest chain 11 peptides. Score 0.473 Round 5: 96 peptides, 15 chains. Longest chain 14 peptides. Score 0.459 Taking the results from Round 4 Chains 18, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3230 restraints for refining 1380 atoms. 2876 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3242 (Rfree = 0.000) for 1380 atoms. Found 5 (8 requested) and removed 32 (4 requested) atoms. Cycle 7: After refmac, R = 0.3141 (Rfree = 0.000) for 1337 atoms. Found 5 (8 requested) and removed 14 (4 requested) atoms. Cycle 8: After refmac, R = 0.2956 (Rfree = 0.000) for 1326 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 9: After refmac, R = 0.2822 (Rfree = 0.000) for 1317 atoms. Found 1 (8 requested) and removed 9 (4 requested) atoms. Cycle 10: After refmac, R = 0.3013 (Rfree = 0.000) for 1308 atoms. Found 6 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 1341 seeds are put forward NCS extension: 0 residues added, 1341 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 11 peptides. Score 0.316 Round 2: 104 peptides, 19 chains. Longest chain 12 peptides. Score 0.393 Round 3: 98 peptides, 18 chains. Longest chain 12 peptides. Score 0.380 Round 4: 98 peptides, 13 chains. Longest chain 21 peptides. Score 0.532 Round 5: 104 peptides, 16 chains. Longest chain 17 peptides. Score 0.484 Taking the results from Round 4 Chains 13, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3172 restraints for refining 1391 atoms. 2845 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3264 (Rfree = 0.000) for 1391 atoms. Found 6 (8 requested) and removed 23 (4 requested) atoms. Cycle 12: After refmac, R = 0.3041 (Rfree = 0.000) for 1364 atoms. Found 3 (8 requested) and removed 11 (4 requested) atoms. Cycle 13: After refmac, R = 0.3063 (Rfree = 0.000) for 1351 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. Cycle 14: After refmac, R = 0.3123 (Rfree = 0.000) for 1346 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.2981 (Rfree = 0.000) for 1338 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.53 Search for helices and strands: 0 residues in 0 chains, 1377 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 1400 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 9 peptides. Score 0.306 Round 2: 99 peptides, 17 chains. Longest chain 10 peptides. Score 0.419 Round 3: 97 peptides, 17 chains. Longest chain 11 peptides. Score 0.405 Round 4: 104 peptides, 15 chains. Longest chain 16 peptides. Score 0.513 Round 5: 105 peptides, 18 chains. Longest chain 10 peptides. Score 0.431 Taking the results from Round 4 Chains 15, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3232 restraints for refining 1393 atoms. 2891 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3248 (Rfree = 0.000) for 1393 atoms. Found 6 (8 requested) and removed 17 (4 requested) atoms. Cycle 17: After refmac, R = 0.3134 (Rfree = 0.000) for 1368 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 18: After refmac, R = 0.3042 (Rfree = 0.000) for 1352 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 19: After refmac, R = 0.3185 (Rfree = 0.000) for 1344 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 20: After refmac, R = 0.2821 (Rfree = 0.000) for 1342 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.52 Search for helices and strands: 0 residues in 0 chains, 1376 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 1405 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.251 Round 2: 73 peptides, 13 chains. Longest chain 8 peptides. Score 0.353 Round 3: 81 peptides, 14 chains. Longest chain 9 peptides. Score 0.381 Round 4: 75 peptides, 13 chains. Longest chain 10 peptides. Score 0.368 Round 5: 81 peptides, 11 chains. Longest chain 12 peptides. Score 0.479 Taking the results from Round 5 Chains 11, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3223 restraints for refining 1383 atoms. 2954 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3168 (Rfree = 0.000) for 1383 atoms. Found 4 (8 requested) and removed 15 (4 requested) atoms. Cycle 22: After refmac, R = 0.2792 (Rfree = 0.000) for 1362 atoms. Found 1 (8 requested) and removed 11 (4 requested) atoms. Cycle 23: After refmac, R = 0.2749 (Rfree = 0.000) for 1348 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 24: After refmac, R = 0.2834 (Rfree = 0.000) for 1345 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.2892 (Rfree = 0.000) for 1339 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.40 Search for helices and strands: 0 residues in 0 chains, 1377 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1395 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 10 peptides. Score 0.306 Round 2: 96 peptides, 15 chains. Longest chain 11 peptides. Score 0.459 Round 3: 89 peptides, 15 chains. Longest chain 10 peptides. Score 0.409 Round 4: 90 peptides, 15 chains. Longest chain 10 peptides. Score 0.416 Round 5: 88 peptides, 14 chains. Longest chain 9 peptides. Score 0.434 Taking the results from Round 2 Chains 15, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3099 restraints for refining 1369 atoms. 2790 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3194 (Rfree = 0.000) for 1369 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 27: After refmac, R = 0.2953 (Rfree = 0.000) for 1352 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 28: After refmac, R = 0.3089 (Rfree = 0.000) for 1346 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 29: After refmac, R = 0.2948 (Rfree = 0.000) for 1339 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 30: After refmac, R = 0.2999 (Rfree = 0.000) for 1336 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.44 Search for helices and strands: 0 residues in 0 chains, 1389 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 1402 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.255 Round 2: 83 peptides, 15 chains. Longest chain 9 peptides. Score 0.364 Round 3: 88 peptides, 13 chains. Longest chain 11 peptides. Score 0.465 Round 4: 84 peptides, 12 chains. Longest chain 10 peptides. Score 0.468 Round 5: 90 peptides, 15 chains. Longest chain 11 peptides. Score 0.416 Taking the results from Round 4 Chains 12, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3241 restraints for refining 1393 atoms. 2965 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2971 (Rfree = 0.000) for 1393 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 32: After refmac, R = 0.3071 (Rfree = 0.000) for 1380 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 33: After refmac, R = 0.2775 (Rfree = 0.000) for 1375 atoms. Found 6 (8 requested) and removed 10 (4 requested) atoms. Cycle 34: After refmac, R = 0.2984 (Rfree = 0.000) for 1369 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.2917 (Rfree = 0.000) for 1368 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 1401 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1404 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.251 Round 2: 70 peptides, 12 chains. Longest chain 10 peptides. Score 0.363 Round 3: 70 peptides, 11 chains. Longest chain 11 peptides. Score 0.398 Round 4: 79 peptides, 13 chains. Longest chain 11 peptides. Score 0.399 Round 5: 73 peptides, 10 chains. Longest chain 15 peptides. Score 0.454 Taking the results from Round 5 Chains 10, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3154 restraints for refining 1390 atoms. 2912 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3222 (Rfree = 0.000) for 1390 atoms. Found 6 (8 requested) and removed 13 (4 requested) atoms. Cycle 37: After refmac, R = 0.2957 (Rfree = 0.000) for 1375 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.3021 (Rfree = 0.000) for 1372 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.3079 (Rfree = 0.000) for 1371 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 40: After refmac, R = 0.2765 (Rfree = 0.000) for 1370 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 1412 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 1425 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.208 Round 2: 63 peptides, 12 chains. Longest chain 8 peptides. Score 0.306 Round 3: 66 peptides, 12 chains. Longest chain 8 peptides. Score 0.331 Round 4: 70 peptides, 13 chains. Longest chain 10 peptides. Score 0.328 Round 5: 78 peptides, 14 chains. Longest chain 11 peptides. Score 0.358 Taking the results from Round 5 Chains 14, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3217 restraints for refining 1392 atoms. 2975 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3004 (Rfree = 0.000) for 1392 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 42: After refmac, R = 0.3012 (Rfree = 0.000) for 1383 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 43: After refmac, R = 0.2994 (Rfree = 0.000) for 1379 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 44: After refmac, R = 0.2981 (Rfree = 0.000) for 1370 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 45: After refmac, R = 0.2995 (Rfree = 0.000) for 1364 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.38 Search for helices and strands: 0 residues in 0 chains, 1400 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1403 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 6 peptides. Score 0.251 Round 2: 78 peptides, 14 chains. Longest chain 12 peptides. Score 0.358 Round 3: 74 peptides, 15 chains. Longest chain 12 peptides. Score 0.291 Round 4: 74 peptides, 15 chains. Longest chain 8 peptides. Score 0.291 Round 5: 79 peptides, 16 chains. Longest chain 11 peptides. Score 0.298 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 64, 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 1o6a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2821 reflections ( 99.86 % complete ) and 3163 restraints for refining 1386 atoms. 2921 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2836 (Rfree = 0.000) for 1386 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2773 (Rfree = 0.000) for 1378 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2734 (Rfree = 0.000) for 1369 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2884 (Rfree = 0.000) for 1359 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:22:19 GMT 2018 Job finished. TimeTaking 20.91 Used memory is bytes: 6852536