null Sun 23 Dec 22:22:56 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 2prx-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prx-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prx-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-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/2prx-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-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 22:23:06 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/2prx-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-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 219 and 0 Target number of residues in the AU: 219 Target solvent content: 0.5968 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-3.4-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: 144 Cell parameters: 38.520 38.520 171.590 90.000 90.000 120.000 Input sequence file: 2prx-3.4-parrot-hancs.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 3.400 Wilson plot Bfac: 51.03 3899 reflections ( 99.57 % complete ) and 0 restraints for refining 2844 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3198 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2358 (Rfree = 0.000) for 2844 atoms. Found 18 (21 requested) and removed 68 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.11 3.51 Search for helices and strands: 0 residues in 0 chains, 2815 seeds are put forward NCS extension: 0 residues added, 2815 seeds are put forward Round 1: 84 peptides, 19 chains. Longest chain 6 peptides. Score 0.222 Round 2: 112 peptides, 22 chains. Longest chain 10 peptides. Score 0.318 Round 3: 106 peptides, 21 chains. Longest chain 10 peptides. Score 0.308 Round 4: 95 peptides, 19 chains. Longest chain 7 peptides. Score 0.292 Round 5: 96 peptides, 20 chains. Longest chain 7 peptides. Score 0.272 Taking the results from Round 2 Chains 22, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5479 restraints for refining 2328 atoms. 5141 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.1934 (Rfree = 0.000) for 2328 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 2: After refmac, R = 0.1764 (Rfree = 0.000) for 2313 atoms. Found 15 (17 requested) and removed 9 (8 requested) atoms. Cycle 3: After refmac, R = 0.1714 (Rfree = 0.000) for 2313 atoms. Found 8 (17 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.1664 (Rfree = 0.000) for 2312 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Cycle 5: After refmac, R = 0.1633 (Rfree = 0.000) for 2307 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 2341 seeds are put forward NCS extension: 0 residues added, 2341 seeds are put forward Round 1: 106 peptides, 22 chains. Longest chain 11 peptides. Score 0.282 Round 2: 116 peptides, 22 chains. Longest chain 11 peptides. Score 0.342 Round 3: 130 peptides, 23 chains. Longest chain 13 peptides. Score 0.396 Round 4: 125 peptides, 21 chains. Longest chain 11 peptides. Score 0.416 Round 5: 124 peptides, 25 chains. Longest chain 10 peptides. Score 0.315 Taking the results from Round 4 Chains 22, Residues 104, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5419 restraints for refining 2328 atoms. 4982 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1880 (Rfree = 0.000) for 2328 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 7: After refmac, R = 0.1667 (Rfree = 0.000) for 2321 atoms. Found 8 (17 requested) and removed 13 (8 requested) atoms. Cycle 8: After refmac, R = 0.1556 (Rfree = 0.000) for 2313 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 9: After refmac, R = 0.1505 (Rfree = 0.000) for 2301 atoms. Found 1 (17 requested) and removed 11 (8 requested) atoms. Cycle 10: After refmac, R = 0.1463 (Rfree = 0.000) for 2287 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 2317 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2330 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 7 peptides. Score 0.265 Round 2: 108 peptides, 21 chains. Longest chain 11 peptides. Score 0.320 Round 3: 113 peptides, 19 chains. Longest chain 11 peptides. Score 0.398 Round 4: 116 peptides, 21 chains. Longest chain 9 peptides. Score 0.366 Round 5: 112 peptides, 21 chains. Longest chain 9 peptides. Score 0.343 Taking the results from Round 3 Chains 19, Residues 94, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5306 restraints for refining 2294 atoms. 4920 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1678 (Rfree = 0.000) for 2294 atoms. Found 14 (17 requested) and removed 13 (8 requested) atoms. Cycle 12: After refmac, R = 0.1508 (Rfree = 0.000) for 2289 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. Cycle 13: After refmac, R = 0.1437 (Rfree = 0.000) for 2280 atoms. Found 2 (17 requested) and removed 12 (8 requested) atoms. Cycle 14: After refmac, R = 0.1458 (Rfree = 0.000) for 2267 atoms. Found 6 (17 requested) and removed 10 (8 requested) atoms. Cycle 15: After refmac, R = 0.1361 (Rfree = 0.000) for 2261 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 2303 seeds are put forward NCS extension: 0 residues added, 2303 seeds are put forward Round 1: 104 peptides, 24 chains. Longest chain 7 peptides. Score 0.218 Round 2: 122 peptides, 22 chains. Longest chain 11 peptides. Score 0.376 Round 3: 122 peptides, 23 chains. Longest chain 9 peptides. Score 0.352 Round 4: 135 peptides, 21 chains. Longest chain 21 peptides. Score 0.468 Round 5: 126 peptides, 23 chains. Longest chain 15 peptides. Score 0.374 Taking the results from Round 4 Chains 22, Residues 114, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5153 restraints for refining 2328 atoms. 4652 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1722 (Rfree = 0.000) for 2328 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 17: After refmac, R = 0.1551 (Rfree = 0.000) for 2323 atoms. Found 7 (17 requested) and removed 11 (8 requested) atoms. Cycle 18: After refmac, R = 0.1514 (Rfree = 0.000) for 2314 atoms. Found 1 (17 requested) and removed 12 (8 requested) atoms. Cycle 19: After refmac, R = 0.1467 (Rfree = 0.000) for 2303 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. Cycle 20: After refmac, R = 0.1443 (Rfree = 0.000) for 2295 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 2339 seeds are put forward NCS extension: 0 residues added, 2339 seeds are put forward Round 1: 108 peptides, 23 chains. Longest chain 7 peptides. Score 0.269 Round 2: 133 peptides, 24 chains. Longest chain 10 peptides. Score 0.389 Round 3: 115 peptides, 20 chains. Longest chain 14 peptides. Score 0.385 Round 4: 115 peptides, 20 chains. Longest chain 10 peptides. Score 0.385 Round 5: 116 peptides, 21 chains. Longest chain 12 peptides. Score 0.366 Taking the results from Round 2 Chains 24, Residues 109, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5171 restraints for refining 2328 atoms. 4702 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1682 (Rfree = 0.000) for 2328 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 22: After refmac, R = 0.1500 (Rfree = 0.000) for 2329 atoms. Found 5 (17 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.1466 (Rfree = 0.000) for 2319 atoms. Found 6 (17 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.1437 (Rfree = 0.000) for 2315 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.1398 (Rfree = 0.000) for 2310 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 2339 seeds are put forward NCS extension: 0 residues added, 2339 seeds are put forward Round 1: 115 peptides, 26 chains. Longest chain 7 peptides. Score 0.236 Round 2: 130 peptides, 26 chains. Longest chain 8 peptides. Score 0.325 Round 3: 132 peptides, 25 chains. Longest chain 9 peptides. Score 0.361 Round 4: 124 peptides, 22 chains. Longest chain 11 peptides. Score 0.387 Round 5: 123 peptides, 21 chains. Longest chain 9 peptides. Score 0.405 Taking the results from Round 5 Chains 21, Residues 102, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5410 restraints for refining 2328 atoms. 5001 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1620 (Rfree = 0.000) for 2328 atoms. Found 10 (17 requested) and removed 12 (8 requested) atoms. Cycle 27: After refmac, R = 0.1461 (Rfree = 0.000) for 2325 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. Cycle 28: After refmac, R = 0.1410 (Rfree = 0.000) for 2317 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.1345 (Rfree = 0.000) for 2314 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.1318 (Rfree = 0.000) for 2305 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.06 3.45 Search for helices and strands: 0 residues in 0 chains, 2334 seeds are put forward NCS extension: 0 residues added, 2334 seeds are put forward Round 1: 112 peptides, 23 chains. Longest chain 6 peptides. Score 0.293 Round 2: 125 peptides, 24 chains. Longest chain 8 peptides. Score 0.345 Round 3: 129 peptides, 25 chains. Longest chain 9 peptides. Score 0.344 Round 4: 134 peptides, 26 chains. Longest chain 9 peptides. Score 0.348 Round 5: 132 peptides, 23 chains. Longest chain 11 peptides. Score 0.407 Taking the results from Round 5 Chains 24, Residues 109, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5323 restraints for refining 2327 atoms. 4854 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1651 (Rfree = 0.000) for 2327 atoms. Found 15 (17 requested) and removed 11 (8 requested) atoms. Cycle 32: After refmac, R = 0.1515 (Rfree = 0.000) for 2324 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. Cycle 33: After refmac, R = 0.1496 (Rfree = 0.000) for 2312 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. Cycle 34: After refmac, R = 0.1455 (Rfree = 0.000) for 2305 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. Cycle 35: After refmac, R = 0.1459 (Rfree = 0.000) for 2296 atoms. Found 1 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 2316 seeds are put forward NCS extension: 0 residues added, 2316 seeds are put forward Round 1: 104 peptides, 21 chains. Longest chain 7 peptides. Score 0.296 Round 2: 110 peptides, 19 chains. Longest chain 10 peptides. Score 0.381 Round 3: 108 peptides, 19 chains. Longest chain 11 peptides. Score 0.369 Round 4: 110 peptides, 21 chains. Longest chain 10 peptides. Score 0.332 Round 5: 122 peptides, 21 chains. Longest chain 11 peptides. Score 0.399 Taking the results from Round 5 Chains 21, Residues 101, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5387 restraints for refining 2317 atoms. 4982 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1696 (Rfree = 0.000) for 2317 atoms. Found 10 (17 requested) and removed 23 (8 requested) atoms. Cycle 37: After refmac, R = 0.1826 (Rfree = 0.000) for 2302 atoms. Found 14 (17 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.1558 (Rfree = 0.000) for 2306 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. Cycle 39: After refmac, R = 0.1575 (Rfree = 0.000) for 2295 atoms. Found 6 (17 requested) and removed 11 (8 requested) atoms. Cycle 40: After refmac, R = 0.1354 (Rfree = 0.000) for 2289 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 2316 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2330 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 7 peptides. Score 0.222 Round 2: 89 peptides, 18 chains. Longest chain 8 peptides. Score 0.281 Round 3: 78 peptides, 15 chains. Longest chain 7 peptides. Score 0.293 Round 4: 95 peptides, 20 chains. Longest chain 7 peptides. Score 0.266 Round 5: 103 peptides, 19 chains. Longest chain 8 peptides. Score 0.341 Taking the results from Round 5 Chains 19, Residues 84, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5669 restraints for refining 2319 atoms. 5338 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1646 (Rfree = 0.000) for 2319 atoms. Found 15 (17 requested) and removed 14 (8 requested) atoms. Cycle 42: After refmac, R = 0.1747 (Rfree = 0.000) for 2318 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 43: After refmac, R = 0.1715 (Rfree = 0.000) for 2325 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 44: After refmac, R = 0.1435 (Rfree = 0.000) for 2327 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. Cycle 45: After refmac, R = 0.1473 (Rfree = 0.000) for 2323 atoms. Found 14 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 2367 seeds are put forward NCS extension: 0 residues added, 2367 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 6 peptides. Score 0.236 Round 2: 86 peptides, 18 chains. Longest chain 7 peptides. Score 0.262 Round 3: 83 peptides, 18 chains. Longest chain 7 peptides. Score 0.242 Round 4: 83 peptides, 16 chains. Longest chain 9 peptides. Score 0.297 Round 5: 76 peptides, 17 chains. Longest chain 8 peptides. Score 0.223 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 67, 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 2prx-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3899 reflections ( 99.57 % complete ) and 5747 restraints for refining 2328 atoms. 5495 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1460 (Rfree = 0.000) for 2328 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1445 (Rfree = 0.000) for 2318 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1400 (Rfree = 0.000) for 2308 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1270 (Rfree = 0.000) for 2299 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:06:18 GMT 2018 Job finished. TimeTaking 43.38 Used memory is bytes: 1956264