Sun 23 Dec 23:47:43 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 2prx-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prx-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prx-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-3.2-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/2prx-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-3.2-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 ============================================================ Sun 23 Dec 23:47:47 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/2prx-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-3.2-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 223 and 0 Target number of residues in the AU: 223 Target solvent content: 0.5895 Checking the provided sequence file Detected sequence length: 160 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 320 Adjusted target solvent content: 0.41 Input MTZ file: 2prx-3.2-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: 144 Cell parameters: 38.520 38.520 171.590 90.000 90.000 120.000 Input sequence file: 2prx-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2560 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: 28.816 3.201 Wilson plot Bfac: 47.95 4648 reflections ( 99.64 % complete ) and 0 restraints for refining 2819 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3167 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3013 (Rfree = 0.000) for 2819 atoms. Found 21 (25 requested) and removed 59 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.00 3.39 Search for helices and strands: 0 residues in 0 chains, 2805 seeds are put forward NCS extension: 0 residues added, 2805 seeds are put forward Round 1: 70 peptides, 16 chains. Longest chain 6 peptides. Score 0.210 Round 2: 95 peptides, 21 chains. Longest chain 7 peptides. Score 0.240 Round 3: 98 peptides, 18 chains. Longest chain 16 peptides. Score 0.336 Round 4: 89 peptides, 19 chains. Longest chain 9 peptides. Score 0.254 Round 5: 96 peptides, 19 chains. Longest chain 12 peptides. Score 0.298 Taking the results from Round 3 Chains 18, Residues 80, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 5428 restraints for refining 2337 atoms. 5112 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2538 (Rfree = 0.000) for 2337 atoms. Found 12 (20 requested) and removed 24 (10 requested) atoms. Cycle 2: After refmac, R = 0.2576 (Rfree = 0.000) for 2306 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 3: After refmac, R = 0.2701 (Rfree = 0.000) for 2295 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 4: After refmac, R = 0.1802 (Rfree = 0.000) for 2281 atoms. Found 8 (20 requested) and removed 15 (10 requested) atoms. Cycle 5: After refmac, R = 0.1964 (Rfree = 0.000) for 2270 atoms. Found 19 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.93 3.31 Search for helices and strands: 0 residues in 0 chains, 2330 seeds are put forward NCS extension: 0 residues added, 2330 seeds are put forward Round 1: 89 peptides, 21 chains. Longest chain 5 peptides. Score 0.200 Round 2: 104 peptides, 23 chains. Longest chain 8 peptides. Score 0.244 Round 3: 111 peptides, 23 chains. Longest chain 8 peptides. Score 0.287 Round 4: 108 peptides, 22 chains. Longest chain 9 peptides. Score 0.295 Round 5: 107 peptides, 21 chains. Longest chain 10 peptides. Score 0.314 Taking the results from Round 5 Chains 21, Residues 86, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 4889 restraints for refining 2135 atoms. 4552 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1983 (Rfree = 0.000) for 2135 atoms. Found 16 (19 requested) and removed 15 (9 requested) atoms. Cycle 7: After refmac, R = 0.1736 (Rfree = 0.000) for 2128 atoms. Found 9 (19 requested) and removed 13 (9 requested) atoms. Cycle 8: After refmac, R = 0.1691 (Rfree = 0.000) for 2121 atoms. Found 14 (19 requested) and removed 11 (9 requested) atoms. Cycle 9: After refmac, R = 0.1551 (Rfree = 0.000) for 2122 atoms. Found 17 (19 requested) and removed 11 (9 requested) atoms. Cycle 10: After refmac, R = 0.1650 (Rfree = 0.000) for 2122 atoms. Found 18 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.92 3.30 Search for helices and strands: 0 residues in 0 chains, 2173 seeds are put forward NCS extension: 0 residues added, 2173 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 7 peptides. Score 0.236 Round 2: 126 peptides, 26 chains. Longest chain 9 peptides. Score 0.302 Round 3: 137 peptides, 25 chains. Longest chain 9 peptides. Score 0.388 Round 4: 137 peptides, 23 chains. Longest chain 12 peptides. Score 0.434 Round 5: 133 peptides, 21 chains. Longest chain 13 peptides. Score 0.458 Taking the results from Round 5 Chains 21, Residues 112, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 4810 restraints for refining 2216 atoms. 4363 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1714 (Rfree = 0.000) for 2216 atoms. Found 19 (19 requested) and removed 10 (9 requested) atoms. Cycle 12: After refmac, R = 0.1546 (Rfree = 0.000) for 2221 atoms. Found 13 (19 requested) and removed 26 (9 requested) atoms. Cycle 13: After refmac, R = 0.1577 (Rfree = 0.000) for 2204 atoms. Found 19 (19 requested) and removed 9 (9 requested) atoms. Cycle 14: After refmac, R = 0.1539 (Rfree = 0.000) for 2212 atoms. Found 18 (19 requested) and removed 16 (9 requested) atoms. Cycle 15: After refmac, R = 0.2022 (Rfree = 0.000) for 2213 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.85 3.22 Search for helices and strands: 0 residues in 0 chains, 2262 seeds are put forward NCS extension: 0 residues added, 2262 seeds are put forward Round 1: 102 peptides, 21 chains. Longest chain 9 peptides. Score 0.283 Round 2: 129 peptides, 24 chains. Longest chain 11 peptides. Score 0.367 Round 3: 124 peptides, 21 chains. Longest chain 12 peptides. Score 0.410 Round 4: 123 peptides, 19 chains. Longest chain 16 peptides. Score 0.451 Round 5: 124 peptides, 20 chains. Longest chain 12 peptides. Score 0.434 Taking the results from Round 4 Chains 21, Residues 104, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 4777 restraints for refining 2264 atoms. 4325 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1739 (Rfree = 0.000) for 2264 atoms. Found 17 (20 requested) and removed 24 (10 requested) atoms. Cycle 17: After refmac, R = 0.1450 (Rfree = 0.000) for 2255 atoms. Found 12 (20 requested) and removed 13 (10 requested) atoms. Cycle 18: After refmac, R = 0.1358 (Rfree = 0.000) for 2254 atoms. Found 8 (20 requested) and removed 14 (10 requested) atoms. Cycle 19: After refmac, R = 0.1281 (Rfree = 0.000) for 2244 atoms. Found 9 (20 requested) and removed 12 (10 requested) atoms. Cycle 20: After refmac, R = 0.1261 (Rfree = 0.000) for 2239 atoms. Found 6 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.97 3.35 Search for helices and strands: 0 residues in 0 chains, 2269 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2287 seeds are put forward Round 1: 125 peptides, 27 chains. Longest chain 7 peptides. Score 0.272 Round 2: 138 peptides, 25 chains. Longest chain 14 peptides. Score 0.393 Round 3: 138 peptides, 20 chains. Longest chain 14 peptides. Score 0.504 Round 4: 134 peptides, 23 chains. Longest chain 11 peptides. Score 0.418 Round 5: 139 peptides, 20 chains. Longest chain 15 peptides. Score 0.509 Taking the results from Round 5 Chains 21, Residues 119, Estimated correctness of the model 14.1 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 5143 restraints for refining 2337 atoms. 4639 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1697 (Rfree = 0.000) for 2337 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 22: After refmac, R = 0.1546 (Rfree = 0.000) for 2334 atoms. Found 9 (20 requested) and removed 12 (10 requested) atoms. Cycle 23: After refmac, R = 0.1440 (Rfree = 0.000) for 2329 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. Cycle 24: After refmac, R = 0.1892 (Rfree = 0.000) for 2324 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 25: After refmac, R = 0.1413 (Rfree = 0.000) for 2323 atoms. Found 10 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.91 3.28 Search for helices and strands: 0 residues in 0 chains, 2359 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2375 seeds are put forward Round 1: 122 peptides, 27 chains. Longest chain 7 peptides. Score 0.254 Round 2: 152 peptides, 27 chains. Longest chain 18 peptides. Score 0.423 Round 3: 147 peptides, 26 chains. Longest chain 12 peptides. Score 0.419 Round 4: 152 peptides, 23 chains. Longest chain 18 peptides. Score 0.508 Round 5: 142 peptides, 23 chains. Longest chain 12 peptides. Score 0.459 Taking the results from Round 4 Chains 23, Residues 129, Estimated correctness of the model 13.8 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 5111 restraints for refining 2336 atoms. 4578 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1610 (Rfree = 0.000) for 2336 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 27: After refmac, R = 0.1479 (Rfree = 0.000) for 2336 atoms. Found 9 (20 requested) and removed 11 (10 requested) atoms. Cycle 28: After refmac, R = 0.1444 (Rfree = 0.000) for 2330 atoms. Found 9 (20 requested) and removed 12 (10 requested) atoms. Cycle 29: After refmac, R = 0.1321 (Rfree = 0.000) for 2324 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.1285 (Rfree = 0.000) for 2319 atoms. Found 8 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.93 3.31 Search for helices and strands: 0 residues in 0 chains, 2358 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2378 seeds are put forward Round 1: 121 peptides, 25 chains. Longest chain 8 peptides. Score 0.297 Round 2: 142 peptides, 24 chains. Longest chain 14 peptides. Score 0.437 Round 3: 144 peptides, 27 chains. Longest chain 9 peptides. Score 0.380 Round 4: 134 peptides, 22 chains. Longest chain 15 peptides. Score 0.440 Round 5: 138 peptides, 23 chains. Longest chain 16 peptides. Score 0.439 Taking the results from Round 4 Chains 22, Residues 112, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 5173 restraints for refining 2337 atoms. 4715 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1479 (Rfree = 0.000) for 2337 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 32: After refmac, R = 0.1374 (Rfree = 0.000) for 2339 atoms. Found 10 (21 requested) and removed 11 (10 requested) atoms. Cycle 33: After refmac, R = 0.1292 (Rfree = 0.000) for 2334 atoms. Found 8 (20 requested) and removed 10 (10 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1254 (Rfree = 0.000) for 2329 atoms. Found 3 (20 requested) and removed 13 (10 requested) atoms. Cycle 35: After refmac, R = 0.1256 (Rfree = 0.000) for 2318 atoms. Found 10 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.93 3.31 Search for helices and strands: 0 residues in 0 chains, 2351 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2374 seeds are put forward Round 1: 120 peptides, 25 chains. Longest chain 8 peptides. Score 0.291 Round 2: 133 peptides, 23 chains. Longest chain 11 peptides. Score 0.412 Round 3: 132 peptides, 24 chains. Longest chain 13 peptides. Score 0.384 Round 4: 135 peptides, 22 chains. Longest chain 10 peptides. Score 0.446 Round 5: 149 peptides, 24 chains. Longest chain 10 peptides. Score 0.473 Taking the results from Round 5 Chains 24, Residues 125, Estimated correctness of the model 2.3 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 5118 restraints for refining 2337 atoms. 4623 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1538 (Rfree = 0.000) for 2337 atoms. Found 16 (20 requested) and removed 11 (10 requested) atoms. Cycle 37: After refmac, R = 0.1433 (Rfree = 0.000) for 2339 atoms. Found 8 (21 requested) and removed 11 (10 requested) atoms. Cycle 38: After refmac, R = 0.1341 (Rfree = 0.000) for 2335 atoms. Found 8 (20 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.1312 (Rfree = 0.000) for 2333 atoms. Found 3 (20 requested) and removed 11 (10 requested) atoms. Cycle 40: After refmac, R = 0.1280 (Rfree = 0.000) for 2322 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.93 3.31 Search for helices and strands: 0 residues in 0 chains, 2339 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2350 seeds are put forward Round 1: 123 peptides, 25 chains. Longest chain 12 peptides. Score 0.309 Round 2: 109 peptides, 18 chains. Longest chain 11 peptides. Score 0.400 Round 3: 115 peptides, 18 chains. Longest chain 13 peptides. Score 0.432 Round 4: 117 peptides, 20 chains. Longest chain 13 peptides. Score 0.396 Round 5: 119 peptides, 18 chains. Longest chain 13 peptides. Score 0.453 Taking the results from Round 5 Chains 18, Residues 101, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 5411 restraints for refining 2337 atoms. 5010 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1437 (Rfree = 0.000) for 2337 atoms. Found 20 (20 requested) and removed 10 (10 requested) atoms. Cycle 42: After refmac, R = 0.1334 (Rfree = 0.000) for 2347 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.1336 (Rfree = 0.000) for 2343 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.1289 (Rfree = 0.000) for 2337 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.1262 (Rfree = 0.000) for 2333 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.96 3.34 Search for helices and strands: 0 residues in 0 chains, 2358 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 2376 seeds are put forward Round 1: 91 peptides, 19 chains. Longest chain 11 peptides. Score 0.267 Round 2: 118 peptides, 19 chains. Longest chain 13 peptides. Score 0.425 Round 3: 121 peptides, 21 chains. Longest chain 14 peptides. Score 0.394 Round 4: 115 peptides, 17 chains. Longest chain 15 peptides. Score 0.456 Round 5: 94 peptides, 16 chains. Longest chain 15 peptides. Score 0.364 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 98, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence Sequence coverage is 22 % Consider running further cycles of model building using 2prx-3_warpNtrace.pdb as input Building loops using Loopy2018 18 chains (98 residues) following loop building 4 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4648 reflections ( 99.64 % complete ) and 5191 restraints for refining 2337 atoms. 4750 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1452 (Rfree = 0.000) for 2337 atoms. Found 0 (20 requested) and removed 5 (10 requested) atoms. Cycle 47: After refmac, R = 0.1439 (Rfree = 0.000) for 2332 atoms. Found 0 (20 requested) and removed 3 (10 requested) atoms. Cycle 48: After refmac, R = 0.1311 (Rfree = 0.000) for 2327 atoms. Found 0 (20 requested) and removed 7 (10 requested) atoms. Cycle 49: After refmac, R = 0.1272 (Rfree = 0.000) for 2318 atoms. TimeTaking 27.95