Mon 24 Dec 08:08:06 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 2ozj-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ozj-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ozj-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.8-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/2ozj-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.8-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 08:08:11 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/2ozj-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.8-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: 0.6579 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 228 Adjusted target solvent content: 0.43 Input MTZ file: 2ozj-3.8-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: 20 Cell parameters: 40.940 69.810 150.550 90.000 90.000 90.000 Input sequence file: 2ozj-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 1824 target number of atoms Had to go as low as 0.60 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: 75.275 3.800 Wilson plot Bfac: 83.46 Failed to save intermediate PDB 2297 reflections ( 99.14 % complete ) and 0 restraints for refining 2016 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3396 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3304 (Rfree = 0.000) for 2016 atoms. Found 10 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.88 4.26 Search for helices and strands: 0 residues in 0 chains, 2036 seeds are put forward NCS extension: 0 residues added, 2036 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 8 peptides. Score 0.247 Round 2: 92 peptides, 15 chains. Longest chain 12 peptides. Score 0.431 Round 3: 102 peptides, 16 chains. Longest chain 11 peptides. Score 0.471 Round 4: 111 peptides, 18 chains. Longest chain 11 peptides. Score 0.473 Round 5: 116 peptides, 16 chains. Longest chain 15 peptides. Score 0.560 Taking the results from Round 5 Chains 17, Residues 100, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3730 restraints for refining 1649 atoms. 3301 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2626 (Rfree = 0.000) for 1649 atoms. Found 6 (9 requested) and removed 15 (4 requested) atoms. Cycle 2: After refmac, R = 0.2658 (Rfree = 0.000) for 1606 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 3: After refmac, R = 0.2645 (Rfree = 0.000) for 1595 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 4: After refmac, R = 0.2623 (Rfree = 0.000) for 1571 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.2547 (Rfree = 0.000) for 1559 atoms. Found 6 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.91 Search for helices and strands: 0 residues in 0 chains, 1577 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1594 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 10 peptides. Score 0.324 Round 2: 108 peptides, 18 chains. Longest chain 13 peptides. Score 0.452 Round 3: 97 peptides, 16 chains. Longest chain 15 peptides. Score 0.436 Round 4: 96 peptides, 13 chains. Longest chain 15 peptides. Score 0.519 Round 5: 119 peptides, 17 chains. Longest chain 14 peptides. Score 0.551 Taking the results from Round 5 Chains 17, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3615 restraints for refining 1548 atoms. 3224 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2424 (Rfree = 0.000) for 1548 atoms. Found 7 (8 requested) and removed 13 (4 requested) atoms. Cycle 7: After refmac, R = 0.2609 (Rfree = 0.000) for 1534 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 8: After refmac, R = 0.2311 (Rfree = 0.000) for 1527 atoms. Found 5 (8 requested) and removed 10 (4 requested) atoms. Cycle 9: After refmac, R = 0.2316 (Rfree = 0.000) for 1513 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 10: After refmac, R = 0.2295 (Rfree = 0.000) for 1506 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.93 Search for helices and strands: 0 residues in 0 chains, 1543 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1562 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.269 Round 2: 103 peptides, 19 chains. Longest chain 11 peptides. Score 0.386 Round 3: 94 peptides, 16 chains. Longest chain 11 peptides. Score 0.414 Round 4: 92 peptides, 17 chains. Longest chain 12 peptides. Score 0.367 Round 5: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.350 Taking the results from Round 3 Chains 16, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3737 restraints for refining 1537 atoms. 3441 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2520 (Rfree = 0.000) for 1537 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. Cycle 12: After refmac, R = 0.2665 (Rfree = 0.000) for 1507 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 13: After refmac, R = 0.2651 (Rfree = 0.000) for 1495 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 14: After refmac, R = 0.2605 (Rfree = 0.000) for 1481 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 15: After refmac, R = 0.2065 (Rfree = 0.000) for 1479 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.98 Search for helices and strands: 0 residues in 0 chains, 1533 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 1540 seeds are put forward Round 1: 50 peptides, 10 chains. Longest chain 8 peptides. Score 0.266 Round 2: 58 peptides, 11 chains. Longest chain 7 peptides. Score 0.300 Round 3: 84 peptides, 15 chains. Longest chain 10 peptides. Score 0.371 Round 4: 86 peptides, 15 chains. Longest chain 14 peptides. Score 0.387 Round 5: 90 peptides, 15 chains. Longest chain 11 peptides. Score 0.416 Taking the results from Round 5 Chains 15, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3475 restraints for refining 1466 atoms. 3190 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2487 (Rfree = 0.000) for 1466 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 17: After refmac, R = 0.2400 (Rfree = 0.000) for 1455 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 18: After refmac, R = 0.2530 (Rfree = 0.000) for 1450 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 19: After refmac, R = 0.2231 (Rfree = 0.000) for 1440 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.2348 (Rfree = 0.000) for 1433 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 4.01 Search for helices and strands: 0 residues in 0 chains, 1485 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 1492 seeds are put forward Round 1: 71 peptides, 16 chains. Longest chain 8 peptides. Score 0.230 Round 2: 79 peptides, 15 chains. Longest chain 9 peptides. Score 0.332 Round 3: 86 peptides, 16 chains. Longest chain 8 peptides. Score 0.354 Round 4: 90 peptides, 17 chains. Longest chain 10 peptides. Score 0.352 Round 5: 81 peptides, 13 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 5 Chains 13, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3564 restraints for refining 1532 atoms. 3305 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2756 (Rfree = 0.000) for 1532 atoms. Found 6 (8 requested) and removed 11 (4 requested) atoms. Cycle 22: After refmac, R = 0.2349 (Rfree = 0.000) for 1509 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 23: After refmac, R = 0.2068 (Rfree = 0.000) for 1499 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2526 (Rfree = 0.000) for 1492 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.2230 (Rfree = 0.000) for 1480 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.95 Search for helices and strands: 0 residues in 0 chains, 1530 seeds are put forward NCS extension: 0 residues added, 1530 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 5 peptides. Score 0.206 Round 2: 63 peptides, 14 chains. Longest chain 6 peptides. Score 0.232 Round 3: 70 peptides, 14 chains. Longest chain 10 peptides. Score 0.293 Round 4: 73 peptides, 15 chains. Longest chain 7 peptides. Score 0.283 Round 5: 76 peptides, 16 chains. Longest chain 7 peptides. Score 0.273 Taking the results from Round 3 Chains 14, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3182 restraints for refining 1375 atoms. 2972 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2617 (Rfree = 0.000) for 1375 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 27: After refmac, R = 0.2486 (Rfree = 0.000) for 1362 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 28: After refmac, R = 0.2360 (Rfree = 0.000) for 1356 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.2624 (Rfree = 0.000) for 1357 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.2333 (Rfree = 0.000) for 1354 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 4.06 Search for helices and strands: 0 residues in 0 chains, 1396 seeds are put forward NCS extension: 0 residues added, 1396 seeds are put forward Round 1: 67 peptides, 16 chains. Longest chain 7 peptides. Score 0.194 Round 2: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.399 Round 3: 93 peptides, 18 chains. Longest chain 9 peptides. Score 0.342 Round 4: 80 peptides, 14 chains. Longest chain 10 peptides. Score 0.374 Round 5: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.322 Taking the results from Round 2 Chains 16, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 2954 restraints for refining 1337 atoms. 2666 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2349 (Rfree = 0.000) for 1337 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 32: After refmac, R = 0.2429 (Rfree = 0.000) for 1327 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.2326 (Rfree = 0.000) for 1323 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 34: After refmac, R = 0.2359 (Rfree = 0.000) for 1325 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 35: After refmac, R = 0.2162 (Rfree = 0.000) for 1321 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 1368 seeds are put forward NCS extension: 0 residues added, 1368 seeds are put forward Round 1: 58 peptides, 14 chains. Longest chain 5 peptides. Score 0.186 Round 2: 70 peptides, 14 chains. Longest chain 8 peptides. Score 0.293 Round 3: 76 peptides, 13 chains. Longest chain 11 peptides. Score 0.376 Round 4: 76 peptides, 15 chains. Longest chain 9 peptides. Score 0.307 Round 5: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.309 Taking the results from Round 3 Chains 13, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 2811 restraints for refining 1289 atoms. 2572 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2347 (Rfree = 0.000) for 1289 atoms. Found 6 (7 requested) and removed 7 (3 requested) atoms. Cycle 37: After refmac, R = 0.2337 (Rfree = 0.000) for 1278 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 38: After refmac, R = 0.2370 (Rfree = 0.000) for 1280 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 39: After refmac, R = 0.2399 (Rfree = 0.000) for 1276 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.2298 (Rfree = 0.000) for 1270 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.93 Search for helices and strands: 0 residues in 0 chains, 1313 seeds are put forward NCS extension: 0 residues added, 1313 seeds are put forward Round 1: 53 peptides, 12 chains. Longest chain 6 peptides. Score 0.216 Round 2: 53 peptides, 9 chains. Longest chain 11 peptides. Score 0.332 Round 3: 64 peptides, 11 chains. Longest chain 9 peptides. Score 0.350 Round 4: 72 peptides, 11 chains. Longest chain 13 peptides. Score 0.413 Round 5: 69 peptides, 13 chains. Longest chain 9 peptides. Score 0.320 Taking the results from Round 4 Chains 11, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 2616 restraints for refining 1229 atoms. 2383 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2494 (Rfree = 0.000) for 1229 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 42: After refmac, R = 0.2265 (Rfree = 0.000) for 1226 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 43: After refmac, R = 0.2245 (Rfree = 0.000) for 1223 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.2178 (Rfree = 0.000) for 1223 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.1819 (Rfree = 0.000) for 1223 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 3.99 Search for helices and strands: 0 residues in 0 chains, 1258 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1280 seeds are put forward Round 1: 34 peptides, 8 chains. Longest chain 5 peptides. Score 0.190 Round 2: 38 peptides, 8 chains. Longest chain 7 peptides. Score 0.233 Round 3: 46 peptides, 10 chains. Longest chain 7 peptides. Score 0.228 Round 4: 51 peptides, 10 chains. Longest chain 10 peptides. Score 0.276 Round 5: 49 peptides, 9 chains. Longest chain 10 peptides. Score 0.297 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 40, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2ozj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2297 reflections ( 99.14 % complete ) and 2678 restraints for refining 1222 atoms. 2504 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2338 (Rfree = 0.000) for 1222 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2438 (Rfree = 0.000) for 1217 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2309 (Rfree = 0.000) for 1209 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2332 (Rfree = 0.000) for 1203 atoms. TimeTaking 22.63