Sun 23 Dec 22:22:59 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 2pg4-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pg4-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pg4-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-3.6-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/2pg4-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-3.6-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 22:23:08 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/2pg4-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-3.6-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 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-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: 90 Cell parameters: 109.840 109.840 36.760 90.000 90.000 90.000 Input sequence file: 2pg4-3.6-parrot-hancs.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 1681 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3753 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3855 (Rfree = 0.000) for 1681 atoms. Found 5 (10 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 3.41 Search for helices and strands: 0 residues in 0 chains, 1709 seeds are put forward NCS extension: 0 residues added, 1709 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 6 peptides. Score 0.230 Round 2: 90 peptides, 16 chains. Longest chain 11 peptides. Score 0.380 Round 3: 86 peptides, 15 chains. Longest chain 13 peptides. Score 0.382 Round 4: 96 peptides, 14 chains. Longest chain 18 peptides. Score 0.483 Round 5: 99 peptides, 15 chains. Longest chain 12 peptides. Score 0.473 Taking the results from Round 4 Chains 14, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3178 restraints for refining 1378 atoms. 2864 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2830 (Rfree = 0.000) for 1378 atoms. Found 3 (8 requested) and removed 11 (4 requested) atoms. Cycle 2: After refmac, R = 0.2787 (Rfree = 0.000) for 1355 atoms. Found 1 (8 requested) and removed 11 (4 requested) atoms. Cycle 3: After refmac, R = 0.2605 (Rfree = 0.000) for 1342 atoms. Found 1 (8 requested) and removed 10 (4 requested) atoms. Cycle 4: After refmac, R = 0.2555 (Rfree = 0.000) for 1329 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.2630 (Rfree = 0.000) for 1322 atoms. Found 5 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.40 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: 82 peptides, 13 chains. Longest chain 11 peptides. Score 0.416 Round 2: 96 peptides, 15 chains. Longest chain 12 peptides. Score 0.453 Round 3: 97 peptides, 13 chains. Longest chain 14 peptides. Score 0.518 Round 4: 93 peptides, 12 chains. Longest chain 16 peptides. Score 0.521 Round 5: 102 peptides, 15 chains. Longest chain 14 peptides. Score 0.493 Taking the results from Round 4 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 3261 restraints for refining 1378 atoms. 2949 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2601 (Rfree = 0.000) for 1378 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. Cycle 7: After refmac, R = 0.2499 (Rfree = 0.000) for 1359 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 8: After refmac, R = 0.2402 (Rfree = 0.000) for 1351 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 9: After refmac, R = 0.2356 (Rfree = 0.000) for 1346 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.2332 (Rfree = 0.000) for 1341 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 1402 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1421 seeds are put forward Round 1: 86 peptides, 13 chains. Longest chain 12 peptides. Score 0.445 Round 2: 96 peptides, 11 chains. Longest chain 16 peptides. Score 0.568 Round 3: 87 peptides, 10 chains. Longest chain 16 peptides. Score 0.541 Round 4: 90 peptides, 11 chains. Longest chain 17 peptides. Score 0.531 Round 5: 93 peptides, 13 chains. Longest chain 15 peptides. Score 0.492 Taking the results from Round 2 Chains 11, Residues 85, Estimated correctness of the model 1.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3078 restraints for refining 1371 atoms. 2749 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2449 (Rfree = 0.000) for 1371 atoms. Found 3 (8 requested) and removed 10 (4 requested) atoms. Cycle 12: After refmac, R = 0.2363 (Rfree = 0.000) for 1358 atoms. Found 1 (8 requested) and removed 10 (4 requested) atoms. Cycle 13: After refmac, R = 0.2341 (Rfree = 0.000) for 1349 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 14: After refmac, R = 0.2310 (Rfree = 0.000) for 1346 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2258 (Rfree = 0.000) for 1342 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 1399 seeds are put forward NCS extension: 0 residues added, 1399 seeds are put forward Round 1: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.342 Round 2: 97 peptides, 16 chains. Longest chain 9 peptides. Score 0.430 Round 3: 97 peptides, 14 chains. Longest chain 16 peptides. Score 0.489 Round 4: 92 peptides, 13 chains. Longest chain 14 peptides. Score 0.486 Round 5: 89 peptides, 11 chains. Longest chain 15 peptides. Score 0.525 Taking the results from Round 5 Chains 11, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3268 restraints for refining 1377 atoms. 2967 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2502 (Rfree = 0.000) for 1377 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 17: After refmac, R = 0.2347 (Rfree = 0.000) for 1364 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 18: After refmac, R = 0.2284 (Rfree = 0.000) for 1361 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.2240 (Rfree = 0.000) for 1355 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2249 (Rfree = 0.000) for 1351 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.34 Search for helices and strands: 0 residues in 0 chains, 1401 seeds are put forward NCS extension: 9 residues added (5 deleted due to clashes), 1410 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.262 Round 2: 86 peptides, 12 chains. Longest chain 27 peptides. Score 0.476 Round 3: 85 peptides, 11 chains. Longest chain 15 peptides. Score 0.499 Round 4: 82 peptides, 12 chains. Longest chain 12 peptides. Score 0.448 Round 5: 93 peptides, 15 chains. Longest chain 16 peptides. Score 0.432 Taking the results from Round 3 Chains 11, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3217 restraints for refining 1378 atoms. 2932 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2511 (Rfree = 0.000) for 1378 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 22: After refmac, R = 0.2426 (Rfree = 0.000) for 1368 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.2380 (Rfree = 0.000) for 1362 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.2142 (Rfree = 0.000) for 1359 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.2104 (Rfree = 0.000) for 1348 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 1397 seeds are put forward NCS extension: 0 residues added, 1397 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 6 peptides. Score 0.265 Round 2: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.362 Round 3: 98 peptides, 17 chains. Longest chain 10 peptides. Score 0.407 Round 4: 95 peptides, 15 chains. Longest chain 17 peptides. Score 0.446 Round 5: 98 peptides, 17 chains. Longest chain 10 peptides. Score 0.407 Taking the results from Round 4 Chains 15, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3231 restraints for refining 1378 atoms. 2926 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2327 (Rfree = 0.000) for 1378 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 27: After refmac, R = 0.2251 (Rfree = 0.000) for 1365 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.2022 (Rfree = 0.000) for 1363 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.1879 (Rfree = 0.000) for 1357 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2053 (Rfree = 0.000) for 1351 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 1404 seeds are put forward NCS extension: 0 residues added, 1404 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 11 peptides. Score 0.311 Round 2: 83 peptides, 15 chains. Longest chain 11 peptides. Score 0.359 Round 3: 81 peptides, 12 chains. Longest chain 13 peptides. Score 0.441 Round 4: 81 peptides, 12 chains. Longest chain 12 peptides. Score 0.441 Round 5: 84 peptides, 13 chains. Longest chain 12 peptides. Score 0.431 Taking the results from Round 4 Chains 12, Residues 69, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3095 restraints for refining 1377 atoms. 2792 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2280 (Rfree = 0.000) for 1377 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 32: After refmac, R = 0.2203 (Rfree = 0.000) for 1373 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.2274 (Rfree = 0.000) for 1368 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 34: After refmac, R = 0.2323 (Rfree = 0.000) for 1361 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.2242 (Rfree = 0.000) for 1355 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 3.33 Search for helices and strands: 0 residues in 0 chains, 1399 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 1405 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 6 peptides. Score 0.238 Round 2: 80 peptides, 15 chains. Longest chain 11 peptides. Score 0.336 Round 3: 86 peptides, 15 chains. Longest chain 10 peptides. Score 0.382 Round 4: 80 peptides, 14 chains. Longest chain 9 peptides. Score 0.369 Round 5: 83 peptides, 13 chains. Longest chain 14 peptides. Score 0.424 Taking the results from Round 5 Chains 13, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3301 restraints for refining 1378 atoms. 3034 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2406 (Rfree = 0.000) for 1378 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2167 (Rfree = 0.000) for 1369 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.2118 (Rfree = 0.000) for 1362 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.2151 (Rfree = 0.000) for 1354 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.2216 (Rfree = 0.000) for 1352 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 1412 seeds are put forward NCS extension: 0 residues added, 1412 seeds are put forward Round 1: 57 peptides, 12 chains. Longest chain 6 peptides. Score 0.251 Round 2: 73 peptides, 14 chains. Longest chain 7 peptides. Score 0.315 Round 3: 77 peptides, 13 chains. Longest chain 9 peptides. Score 0.380 Round 4: 69 peptides, 13 chains. Longest chain 8 peptides. Score 0.317 Round 5: 72 peptides, 13 chains. Longest chain 8 peptides. Score 0.341 Taking the results from Round 3 Chains 13, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2869 reflections ( 99.51 % complete ) and 3321 restraints for refining 1368 atoms. 3078 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2454 (Rfree = 0.000) for 1368 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 42: After refmac, R = 0.2312 (Rfree = 0.000) for 1363 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.2330 (Rfree = 0.000) for 1353 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.2011 (Rfree = 0.000) for 1348 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.2553 (Rfree = 0.000) for 1344 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 1403 seeds are put forward NCS extension: 0 residues added, 1403 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.225 Round 2: 55 peptides, 10 chains. Longest chain 11 peptides. Score 0.309 Round 3: 67 peptides, 13 chains. Longest chain 8 peptides. Score 0.300 Round 4: 72 peptides, 14 chains. Longest chain 10 peptides. Score 0.306 Round 5: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.313 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, 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 2pg4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2869 reflections ( 99.51 % complete ) and 3209 restraints for refining 1346 atoms. 2976 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2179 (Rfree = 0.000) for 1346 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2758 (Rfree = 0.000) for 1333 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2837 (Rfree = 0.000) for 1323 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2346 (Rfree = 0.000) for 1311 atoms. TimeTaking 28.87