Mon 24 Dec 00:57:13 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 2pg4-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pg4-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pg4-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.8-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/2pg4-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.8-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 00:57:17 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/2pg4-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.8-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 139 and 0 Target number of residues in the AU: 139 Target solvent content: 0.6608 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: 2pg4-3.8-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: 2pg4-3.8-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 3.800 Wilson plot Bfac: 85.33 2456 reflections ( 99.47 % complete ) and 0 restraints for refining 1674 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3783 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3467 (Rfree = 0.000) for 1674 atoms. Found 3 (9 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 3.56 Search for helices and strands: 0 residues in 0 chains, 1695 seeds are put forward NCS extension: 0 residues added, 1695 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 11 peptides. Score 0.272 Round 2: 80 peptides, 15 chains. Longest chain 9 peptides. Score 0.336 Round 3: 95 peptides, 13 chains. Longest chain 15 peptides. Score 0.505 Round 4: 96 peptides, 13 chains. Longest chain 16 peptides. Score 0.512 Round 5: 103 peptides, 13 chains. Longest chain 18 peptides. Score 0.555 Taking the results from Round 5 Chains 13, Residues 90, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 3017 restraints for refining 1375 atoms. 2615 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2663 (Rfree = 0.000) for 1375 atoms. Found 2 (7 requested) and removed 13 (3 requested) atoms. Cycle 2: After refmac, R = 0.2826 (Rfree = 0.000) for 1336 atoms. Found 4 (7 requested) and removed 8 (3 requested) atoms. Cycle 3: After refmac, R = 0.2487 (Rfree = 0.000) for 1324 atoms. Found 1 (7 requested) and removed 8 (3 requested) atoms. Cycle 4: After refmac, R = 0.2545 (Rfree = 0.000) for 1308 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 5: After refmac, R = 0.2575 (Rfree = 0.000) for 1287 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.47 Search for helices and strands: 0 residues in 0 chains, 1357 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 1383 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 8 peptides. Score 0.301 Round 2: 83 peptides, 13 chains. Longest chain 12 peptides. Score 0.424 Round 3: 98 peptides, 14 chains. Longest chain 15 peptides. Score 0.496 Round 4: 88 peptides, 12 chains. Longest chain 15 peptides. Score 0.489 Round 5: 87 peptides, 13 chains. Longest chain 11 peptides. Score 0.452 Taking the results from Round 3 Chains 14, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 3020 restraints for refining 1294 atoms. 2698 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2748 (Rfree = 0.000) for 1294 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 7: After refmac, R = 0.2604 (Rfree = 0.000) for 1281 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 8: After refmac, R = 0.2578 (Rfree = 0.000) for 1271 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.2371 (Rfree = 0.000) for 1260 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.2710 (Rfree = 0.000) for 1247 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.48 Search for helices and strands: 0 residues in 0 chains, 1321 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 1351 seeds are put forward Round 1: 78 peptides, 13 chains. Longest chain 10 peptides. Score 0.387 Round 2: 82 peptides, 11 chains. Longest chain 13 peptides. Score 0.479 Round 3: 92 peptides, 12 chains. Longest chain 15 peptides. Score 0.515 Round 4: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.412 Round 5: 82 peptides, 12 chains. Longest chain 12 peptides. Score 0.448 Taking the results from Round 3 Chains 12, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 2656 restraints for refining 1232 atoms. 2348 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2534 (Rfree = 0.000) for 1232 atoms. Found 3 (6 requested) and removed 9 (3 requested) atoms. Cycle 12: After refmac, R = 0.2351 (Rfree = 0.000) for 1214 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 13: After refmac, R = 0.2181 (Rfree = 0.000) for 1202 atoms. Found 2 (6 requested) and removed 8 (3 requested) atoms. Cycle 14: After refmac, R = 0.2168 (Rfree = 0.000) for 1193 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 15: After refmac, R = 0.2240 (Rfree = 0.000) for 1187 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.48 Search for helices and strands: 0 residues in 0 chains, 1252 seeds are put forward NCS extension: 0 residues added, 1252 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 8 peptides. Score 0.285 Round 2: 96 peptides, 16 chains. Longest chain 12 peptides. Score 0.423 Round 3: 93 peptides, 15 chains. Longest chain 13 peptides. Score 0.432 Round 4: 87 peptides, 12 chains. Longest chain 22 peptides. Score 0.482 Round 5: 86 peptides, 15 chains. Longest chain 11 peptides. Score 0.382 Taking the results from Round 4 Chains 12, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 2992 restraints for refining 1323 atoms. 2704 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2909 (Rfree = 0.000) for 1323 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. Cycle 17: After refmac, R = 0.2810 (Rfree = 0.000) for 1301 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 18: After refmac, R = 0.2475 (Rfree = 0.000) for 1291 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. Cycle 19: After refmac, R = 0.2487 (Rfree = 0.000) for 1277 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.2519 (Rfree = 0.000) for 1273 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.47 Search for helices and strands: 0 residues in 0 chains, 1344 seeds are put forward NCS extension: 50 residues added (3 deleted due to clashes), 1394 seeds are put forward Round 1: 79 peptides, 17 chains. Longest chain 9 peptides. Score 0.261 Round 2: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.362 Round 3: 89 peptides, 13 chains. Longest chain 14 peptides. Score 0.466 Round 4: 89 peptides, 14 chains. Longest chain 12 peptides. Score 0.435 Round 5: 87 peptides, 13 chains. Longest chain 11 peptides. Score 0.452 Taking the results from Round 3 Chains 13, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 2906 restraints for refining 1321 atoms. 2615 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2875 (Rfree = 0.000) for 1321 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.2549 (Rfree = 0.000) for 1307 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.2418 (Rfree = 0.000) for 1296 atoms. Found 2 (7 requested) and removed 7 (3 requested) atoms. Cycle 24: After refmac, R = 0.2440 (Rfree = 0.000) for 1285 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.2176 (Rfree = 0.000) for 1271 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 1329 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 1347 seeds are put forward Round 1: 72 peptides, 17 chains. Longest chain 6 peptides. Score 0.202 Round 2: 85 peptides, 17 chains. Longest chain 8 peptides. Score 0.309 Round 3: 85 peptides, 16 chains. Longest chain 8 peptides. Score 0.342 Round 4: 85 peptides, 14 chains. Longest chain 12 peptides. Score 0.406 Round 5: 78 peptides, 12 chains. Longest chain 11 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 ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 3162 restraints for refining 1372 atoms. 2910 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2730 (Rfree = 0.000) for 1372 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 27: After refmac, R = 0.2381 (Rfree = 0.000) for 1357 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 28: After refmac, R = 0.2639 (Rfree = 0.000) for 1348 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.2409 (Rfree = 0.000) for 1341 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 30: After refmac, R = 0.2359 (Rfree = 0.000) for 1337 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 1380 seeds are put forward NCS extension: 0 residues added, 1380 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 8 peptides. Score 0.254 Round 2: 79 peptides, 16 chains. Longest chain 7 peptides. Score 0.295 Round 3: 90 peptides, 18 chains. Longest chain 7 peptides. Score 0.315 Round 4: 82 peptides, 17 chains. Longest chain 8 peptides. Score 0.285 Round 5: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.311 Taking the results from Round 3 Chains 18, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 3140 restraints for refining 1374 atoms. 2870 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2533 (Rfree = 0.000) for 1374 atoms. Found 3 (7 requested) and removed 9 (3 requested) atoms. Cycle 32: After refmac, R = 0.2633 (Rfree = 0.000) for 1353 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.2678 (Rfree = 0.000) for 1347 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 34: After refmac, R = 0.2436 (Rfree = 0.000) for 1336 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.2651 (Rfree = 0.000) for 1328 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 1381 seeds are put forward NCS extension: 0 residues added, 1381 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 6 peptides. Score 0.249 Round 2: 74 peptides, 13 chains. Longest chain 11 peptides. Score 0.356 Round 3: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.313 Round 4: 76 peptides, 15 chains. Longest chain 7 peptides. Score 0.304 Round 5: 87 peptides, 16 chains. Longest chain 10 peptides. Score 0.357 Taking the results from Round 5 Chains 16, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 2957 restraints for refining 1320 atoms. 2689 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2435 (Rfree = 0.000) for 1320 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 37: After refmac, R = 0.2422 (Rfree = 0.000) for 1314 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.2217 (Rfree = 0.000) for 1308 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 39: After refmac, R = 0.2146 (Rfree = 0.000) for 1301 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.2329 (Rfree = 0.000) for 1291 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.48 Search for helices and strands: 0 residues in 0 chains, 1334 seeds are put forward NCS extension: 0 residues added, 1334 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 7 peptides. Score 0.271 Round 2: 71 peptides, 10 chains. Longest chain 12 peptides. Score 0.434 Round 3: 73 peptides, 10 chains. Longest chain 11 peptides. Score 0.449 Round 4: 63 peptides, 10 chains. Longest chain 9 peptides. Score 0.374 Round 5: 69 peptides, 11 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 3 Chains 10, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2456 reflections ( 99.47 % complete ) and 2762 restraints for refining 1294 atoms. 2520 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2168 (Rfree = 0.000) for 1294 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 42: After refmac, R = 0.1928 (Rfree = 0.000) for 1288 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.2434 (Rfree = 0.000) for 1286 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.2194 (Rfree = 0.000) for 1283 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.2283 (Rfree = 0.000) for 1278 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 3.41 Search for helices and strands: 0 residues in 0 chains, 1311 seeds are put forward NCS extension: 0 residues added, 1311 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 9 peptides. Score 0.262 Round 2: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.315 Round 3: 77 peptides, 15 chains. Longest chain 9 peptides. Score 0.313 Round 4: 71 peptides, 12 chains. Longest chain 10 peptides. Score 0.367 Round 5: 67 peptides, 13 chains. Longest chain 8 peptides. Score 0.300 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 59, 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. 2456 reflections ( 99.47 % complete ) and 2949 restraints for refining 1310 atoms. 2725 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2644 (Rfree = 0.000) for 1310 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2434 (Rfree = 0.000) for 1295 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2449 (Rfree = 0.000) for 1285 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2513 (Rfree = 0.000) for 1278 atoms. TimeTaking 22.67