Sun 23 Dec 22:22:55 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 1o6a-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1o6a-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1o6a-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-3.4-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/1o6a-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-3.4-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 22:23:04 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/1o6a-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-3.4-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 139 and 0 Target number of residues in the AU: 139 Target solvent content: 0.6506 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-3.4-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: 61.652 61.652 113.295 90.000 90.000 90.000 Input sequence file: 1o6a-3.4-parrot-hancs.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 3.400 Wilson plot Bfac: 78.56 3317 reflections ( 99.88 % complete ) and 0 restraints for refining 1705 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.4202 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4292 (Rfree = 0.000) for 1705 atoms. Found 11 (12 requested) and removed 23 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 1721 seeds are put forward NCS extension: 0 residues added, 1721 seeds are put forward Round 1: 90 peptides, 17 chains. Longest chain 12 peptides. Score 0.352 Round 2: 97 peptides, 13 chains. Longest chain 15 peptides. Score 0.525 Round 3: 102 peptides, 13 chains. Longest chain 17 peptides. Score 0.556 Round 4: 98 peptides, 13 chains. Longest chain 17 peptides. Score 0.532 Round 5: 91 peptides, 13 chains. Longest chain 12 peptides. Score 0.486 Taking the results from Round 3 Chains 14, Residues 89, Estimated correctness of the model 13.7 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 3071 restraints for refining 1396 atoms. 2676 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3908 (Rfree = 0.000) for 1396 atoms. Found 8 (10 requested) and removed 24 (5 requested) atoms. Cycle 2: After refmac, R = 0.3741 (Rfree = 0.000) for 1356 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. Cycle 3: After refmac, R = 0.3621 (Rfree = 0.000) for 1339 atoms. Found 8 (10 requested) and removed 12 (5 requested) atoms. Cycle 4: After refmac, R = 0.3527 (Rfree = 0.000) for 1324 atoms. Found 10 (10 requested) and removed 22 (5 requested) atoms. Cycle 5: After refmac, R = 0.3462 (Rfree = 0.000) for 1306 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.39 Search for helices and strands: 0 residues in 0 chains, 1348 seeds are put forward NCS extension: 0 residues added, 1348 seeds are put forward Round 1: 89 peptides, 15 chains. Longest chain 15 peptides. Score 0.409 Round 2: 108 peptides, 14 chains. Longest chain 14 peptides. Score 0.565 Round 3: 100 peptides, 12 chains. Longest chain 18 peptides. Score 0.572 Round 4: 93 peptides, 13 chains. Longest chain 18 peptides. Score 0.499 Round 5: 99 peptides, 11 chains. Longest chain 28 peptides. Score 0.593 Taking the results from Round 5 Chains 11, Residues 88, Estimated correctness of the model 26.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 3075 restraints for refining 1345 atoms. 2734 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3691 (Rfree = 0.000) for 1345 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 7: After refmac, R = 0.3354 (Rfree = 0.000) for 1329 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 8: After refmac, R = 0.3337 (Rfree = 0.000) for 1310 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 9: After refmac, R = 0.3272 (Rfree = 0.000) for 1303 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 10: After refmac, R = 0.3262 (Rfree = 0.000) for 1297 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 1335 seeds are put forward NCS extension: 32 residues added (6 deleted due to clashes), 1367 seeds are put forward Round 1: 88 peptides, 16 chains. Longest chain 9 peptides. Score 0.369 Round 2: 107 peptides, 15 chains. Longest chain 12 peptides. Score 0.532 Round 3: 106 peptides, 14 chains. Longest chain 16 peptides. Score 0.553 Round 4: 106 peptides, 14 chains. Longest chain 18 peptides. Score 0.553 Round 5: 102 peptides, 14 chains. Longest chain 15 peptides. Score 0.529 Taking the results from Round 4 Chains 14, Residues 92, Estimated correctness of the model 12.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 2935 restraints for refining 1346 atoms. 2581 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3489 (Rfree = 0.000) for 1346 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 12: After refmac, R = 0.3176 (Rfree = 0.000) for 1314 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 13: After refmac, R = 0.2989 (Rfree = 0.000) for 1298 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 14: After refmac, R = 0.2985 (Rfree = 0.000) for 1294 atoms. Found 8 (9 requested) and removed 17 (4 requested) atoms. Cycle 15: After refmac, R = 0.2928 (Rfree = 0.000) for 1281 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.35 Search for helices and strands: 0 residues in 0 chains, 1335 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 1372 seeds are put forward Round 1: 85 peptides, 15 chains. Longest chain 11 peptides. Score 0.379 Round 2: 91 peptides, 15 chains. Longest chain 10 peptides. Score 0.424 Round 3: 110 peptides, 18 chains. Longest chain 14 peptides. Score 0.466 Round 4: 97 peptides, 16 chains. Longest chain 10 peptides. Score 0.436 Round 5: 110 peptides, 16 chains. Longest chain 13 peptides. Score 0.523 Taking the results from Round 5 Chains 16, Residues 94, Estimated correctness of the model 1.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 3120 restraints for refining 1384 atoms. 2760 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3363 (Rfree = 0.000) for 1384 atoms. Found 6 (10 requested) and removed 33 (5 requested) atoms. Cycle 17: After refmac, R = 0.3171 (Rfree = 0.000) for 1346 atoms. Found 5 (10 requested) and removed 17 (5 requested) atoms. Cycle 18: After refmac, R = 0.2983 (Rfree = 0.000) for 1329 atoms. Found 6 (10 requested) and removed 10 (5 requested) atoms. Cycle 19: After refmac, R = 0.3041 (Rfree = 0.000) for 1319 atoms. Found 4 (10 requested) and removed 12 (5 requested) atoms. Cycle 20: After refmac, R = 0.2936 (Rfree = 0.000) for 1306 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.34 Search for helices and strands: 0 residues in 0 chains, 1345 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1359 seeds are put forward Round 1: 89 peptides, 16 chains. Longest chain 10 peptides. Score 0.377 Round 2: 98 peptides, 15 chains. Longest chain 11 peptides. Score 0.473 Round 3: 97 peptides, 17 chains. Longest chain 11 peptides. Score 0.405 Round 4: 93 peptides, 15 chains. Longest chain 11 peptides. Score 0.438 Round 5: 100 peptides, 14 chains. Longest chain 14 peptides. Score 0.516 Taking the results from Round 5 Chains 14, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 3012 restraints for refining 1377 atoms. 2682 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3247 (Rfree = 0.000) for 1377 atoms. Found 10 (10 requested) and removed 25 (5 requested) atoms. Cycle 22: After refmac, R = 0.3013 (Rfree = 0.000) for 1349 atoms. Found 9 (10 requested) and removed 12 (5 requested) atoms. Cycle 23: After refmac, R = 0.3098 (Rfree = 0.000) for 1342 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 24: After refmac, R = 0.2997 (Rfree = 0.000) for 1339 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.2990 (Rfree = 0.000) for 1332 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 1361 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1376 seeds are put forward Round 1: 83 peptides, 16 chains. Longest chain 11 peptides. Score 0.330 Round 2: 78 peptides, 13 chains. Longest chain 10 peptides. Score 0.392 Round 3: 94 peptides, 16 chains. Longest chain 13 peptides. Score 0.414 Round 4: 94 peptides, 14 chains. Longest chain 15 peptides. Score 0.476 Round 5: 89 peptides, 13 chains. Longest chain 18 peptides. Score 0.472 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 ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 2994 restraints for refining 1368 atoms. 2688 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3262 (Rfree = 0.000) for 1368 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 27: After refmac, R = 0.3074 (Rfree = 0.000) for 1350 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 28: After refmac, R = 0.2809 (Rfree = 0.000) for 1343 atoms. Found 7 (10 requested) and removed 12 (5 requested) atoms. Cycle 29: After refmac, R = 0.3064 (Rfree = 0.000) for 1332 atoms. Found 6 (10 requested) and removed 9 (5 requested) atoms. Cycle 30: After refmac, R = 0.2721 (Rfree = 0.000) for 1327 atoms. Found 6 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 1360 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 1380 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 8 peptides. Score 0.274 Round 2: 90 peptides, 15 chains. Longest chain 14 peptides. Score 0.416 Round 3: 98 peptides, 16 chains. Longest chain 13 peptides. Score 0.443 Round 4: 97 peptides, 14 chains. Longest chain 14 peptides. Score 0.496 Round 5: 103 peptides, 15 chains. Longest chain 12 peptides. Score 0.506 Taking the results from Round 5 Chains 15, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 3060 restraints for refining 1372 atoms. 2723 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3251 (Rfree = 0.000) for 1372 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 32: After refmac, R = 0.2938 (Rfree = 0.000) for 1354 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 33: After refmac, R = 0.2774 (Rfree = 0.000) for 1347 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 34: After refmac, R = 0.2685 (Rfree = 0.000) for 1345 atoms. Found 9 (10 requested) and removed 21 (5 requested) atoms. Cycle 35: After refmac, R = 0.2613 (Rfree = 0.000) for 1330 atoms. Found 6 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.35 Search for helices and strands: 0 residues in 0 chains, 1368 seeds are put forward NCS extension: 10 residues added (1 deleted due to clashes), 1378 seeds are put forward Round 1: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.348 Round 2: 84 peptides, 14 chains. Longest chain 20 peptides. Score 0.404 Round 3: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.377 Round 4: 95 peptides, 13 chains. Longest chain 28 peptides. Score 0.512 Round 5: 87 peptides, 15 chains. Longest chain 11 peptides. Score 0.394 Taking the results from Round 4 Chains 13, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 3096 restraints for refining 1374 atoms. 2781 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3429 (Rfree = 0.000) for 1374 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 37: After refmac, R = 0.3097 (Rfree = 0.000) for 1353 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 38: After refmac, R = 0.2899 (Rfree = 0.000) for 1350 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.2808 (Rfree = 0.000) for 1343 atoms. Found 8 (10 requested) and removed 12 (5 requested) atoms. Cycle 40: After refmac, R = 0.2652 (Rfree = 0.000) for 1337 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.30 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: 82 peptides, 15 chains. Longest chain 16 peptides. Score 0.356 Round 2: 97 peptides, 17 chains. Longest chain 13 peptides. Score 0.405 Round 3: 96 peptides, 15 chains. Longest chain 20 peptides. Score 0.459 Round 4: 96 peptides, 16 chains. Longest chain 12 peptides. Score 0.429 Round 5: 89 peptides, 14 chains. Longest chain 22 peptides. Score 0.441 Taking the results from Round 3 Chains 15, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 3158 restraints for refining 1386 atoms. 2849 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3398 (Rfree = 0.000) for 1386 atoms. Found 10 (10 requested) and removed 26 (5 requested) atoms. Cycle 42: After refmac, R = 0.3027 (Rfree = 0.000) for 1364 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 43: After refmac, R = 0.2969 (Rfree = 0.000) for 1361 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.2937 (Rfree = 0.000) for 1361 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 45: After refmac, R = 0.3051 (Rfree = 0.000) for 1360 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 3.37 Search for helices and strands: 0 residues in 0 chains, 1387 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 1410 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.264 Round 2: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.387 Round 3: 77 peptides, 12 chains. Longest chain 15 peptides. Score 0.417 Round 4: 78 peptides, 12 chains. Longest chain 11 peptides. Score 0.425 Round 5: 72 peptides, 10 chains. Longest chain 17 peptides. Score 0.447 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 62, 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. 3317 reflections ( 99.88 % complete ) and 3269 restraints for refining 1396 atoms. 3031 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3219 (Rfree = 0.000) for 1396 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.3185 (Rfree = 0.000) for 1386 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2738 (Rfree = 0.000) for 1379 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2741 (Rfree = 0.000) for 1372 atoms. TimeTaking 28