null Sun 23 Dec 22:23:14 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 2isb-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2isb-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2isb-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-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/2isb-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-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 22:23:22 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/2isb-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-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 139 and 0 Target number of residues in the AU: 139 Target solvent content: 0.6427 Checking the provided sequence file Detected sequence length: 192 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 192 Adjusted target solvent content: 0.51 Input MTZ file: 2isb-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: 96 Cell parameters: 51.664 51.664 157.756 90.000 90.000 90.000 Input sequence file: 2isb-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1536 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 Loops will be built when appropriate and at the last cycle Resolution range: 49.098 3.601 Wilson plot Bfac: 72.46 2785 reflections ( 99.18 % complete ) and 0 restraints for refining 1700 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3352 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3179 (Rfree = 0.000) for 1700 atoms. Found 10 (10 requested) and removed 71 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.44 Search for helices and strands: 0 residues in 0 chains, 1666 seeds are put forward Round 1: 102 peptides, 20 chains. Longest chain 11 peptides. Score 0.350 Round 2: 123 peptides, 19 chains. Longest chain 14 peptides. Score 0.528 Round 3: 123 peptides, 15 chains. Longest chain 20 peptides. Score 0.630 Round 4: 138 peptides, 13 chains. Longest chain 30 peptides. Score 0.741 Round 5: 132 peptides, 12 chains. Longest chain 18 peptides. Score 0.736 Taking the results from Round 4 Chains 15, Residues 125, Estimated correctness of the model 61.4 % 3 chains (29 residues) have been docked in sequence Building loops using Loopy2018 15 chains (125 residues) following loop building 3 chains (29 residues) in sequence following loop building ------------------------------------------------------ 2785 reflections ( 99.18 % complete ) and 2692 restraints for refining 1393 atoms. 2127 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2783 (Rfree = 0.000) for 1393 atoms. Found 4 (8 requested) and removed 9 (4 requested) atoms. Cycle 2: After refmac, R = 0.2633 (Rfree = 0.000) for 1368 atoms. Found 5 (8 requested) and removed 8 (4 requested) atoms. Cycle 3: After refmac, R = 0.2502 (Rfree = 0.000) for 1355 atoms. Found 3 (8 requested) and removed 9 (4 requested) atoms. Cycle 4: After refmac, R = 0.2445 (Rfree = 0.000) for 1344 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.2423 (Rfree = 0.000) for 1331 atoms. Found 2 (7 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 1370 seeds are put forward Round 1: 112 peptides, 16 chains. Longest chain 14 peptides. Score 0.541 Round 2: 122 peptides, 15 chains. Longest chain 25 peptides. Score 0.625 Round 3: 123 peptides, 14 chains. Longest chain 27 peptides. Score 0.653 Round 4: 125 peptides, 15 chains. Longest chain 19 peptides. Score 0.640 Round 5: 132 peptides, 12 chains. Longest chain 34 peptides. Score 0.736 Taking the results from Round 5 Chains 15, Residues 120, Estimated correctness of the model 60.1 % 3 chains (25 residues) have been docked in sequence Building loops using Loopy2018 15 chains (120 residues) following loop building 3 chains (25 residues) in sequence following loop building ------------------------------------------------------ 2785 reflections ( 99.18 % complete ) and 2749 restraints for refining 1393 atoms. 2228 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2732 (Rfree = 0.000) for 1393 atoms. Found 6 (7 requested) and removed 27 (4 requested) atoms. Cycle 7: After refmac, R = 0.2496 (Rfree = 0.000) for 1365 atoms. Found 4 (7 requested) and removed 10 (4 requested) atoms. Cycle 8: After refmac, R = 0.2424 (Rfree = 0.000) for 1353 atoms. Found 1 (7 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.2375 (Rfree = 0.000) for 1343 atoms. Found 5 (7 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.2300 (Rfree = 0.000) for 1341 atoms. Found 3 (7 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.40 Search for helices and strands: 0 residues in 0 chains, 1392 seeds are put forward Round 1: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.386 Round 2: 123 peptides, 18 chains. Longest chain 17 peptides. Score 0.554 Round 3: 121 peptides, 15 chains. Longest chain 17 peptides. Score 0.619 Round 4: 128 peptides, 16 chains. Longest chain 23 peptides. Score 0.632 Round 5: 123 peptides, 13 chains. Longest chain 17 peptides. Score 0.676 Taking the results from Round 5 Chains 13, Residues 110, Estimated correctness of the model 41.9 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2785 reflections ( 99.18 % complete ) and 2894 restraints for refining 1391 atoms. 2421 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2563 (Rfree = 0.000) for 1391 atoms. Found 6 (6 requested) and removed 168 (4 requested) atoms. Cycle 12: After refmac, R = 0.2581 (Rfree = 0.000) for 1216 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 13: After refmac, R = 0.2457 (Rfree = 0.000) for 1216 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.2198 (Rfree = 0.000) for 1211 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 15: After refmac, R = 0.2211 (Rfree = 0.000) for 1204 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 1247 seeds are put forward Round 1: 111 peptides, 18 chains. Longest chain 10 peptides. Score 0.477 Round 2: 123 peptides, 15 chains. Longest chain 19 peptides. Score 0.630 Round 3: 125 peptides, 15 chains. Longest chain 19 peptides. Score 0.640 Round 4: 130 peptides, 16 chains. Longest chain 19 peptides. Score 0.643 Round 5: 124 peptides, 13 chains. Longest chain 19 peptides. Score 0.681 Taking the results from Round 5 Chains 15, Residues 111, Estimated correctness of the model 43.5 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 2785 reflections ( 99.18 % complete ) and 2780 restraints for refining 1380 atoms. 2304 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2646 (Rfree = 0.000) for 1380 atoms. Found 6 (6 requested) and removed 17 (4 requested) atoms. Cycle 17: After refmac, R = 0.2512 (Rfree = 0.000) for 1360 atoms. Found 4 (6 requested) and removed 8 (4 requested) atoms. Cycle 18: After refmac, R = 0.2425 (Rfree = 0.000) for 1355 atoms. Found 1 (6 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.2390 (Rfree = 0.000) for 1348 atoms. Found 2 (6 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2372 (Rfree = 0.000) for 1346 atoms. Found 2 (6 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 1389 seeds are put forward Round 1: 109 peptides, 18 chains. Longest chain 12 peptides. Score 0.464 Round 2: 120 peptides, 15 chains. Longest chain 14 peptides. Score 0.614 Round 3: 114 peptides, 16 chains. Longest chain 18 peptides. Score 0.553 Round 4: 122 peptides, 17 chains. Longest chain 14 peptides. Score 0.575 Round 5: 118 peptides, 16 chains. Longest chain 14 peptides. Score 0.577 Taking the results from Round 2 Chains 15, Residues 105, Estimated correctness of the model 20.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2785 reflections ( 99.18 % complete ) and 3047 restraints for refining 1380 atoms. 2642 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2437 (Rfree = 0.000) for 1380 atoms. Found 6 (6 requested) and removed 12 (4 requested) atoms. Cycle 22: After refmac, R = 0.2246 (Rfree = 0.000) for 1366 atoms. Found 2 (6 requested) and removed 7 (4 requested) atoms. Cycle 23: After refmac, R = 0.2343 (Rfree = 0.000) for 1357 atoms. Found 6 (6 requested) and removed 7 (4 requested) atoms. Cycle 24: After refmac, R = 0.2326 (Rfree = 0.000) for 1355 atoms. Found 6 (6 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.2297 (Rfree = 0.000) for 1355 atoms. Found 6 (6 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 1403 seeds are put forward Round 1: 85 peptides, 17 chains. Longest chain 8 peptides. Score 0.315 Round 2: 115 peptides, 19 chains. Longest chain 13 peptides. Score 0.475 Round 3: 111 peptides, 16 chains. Longest chain 15 peptides. Score 0.534 Round 4: 118 peptides, 17 chains. Longest chain 15 peptides. Score 0.551 Round 5: 105 peptides, 15 chains. Longest chain 16 peptides. Score 0.524 Taking the results from Round 4 Chains 17, Residues 101, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2785 reflections ( 99.18 % complete ) and 2954 restraints for refining 1393 atoms. 2532 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2359 (Rfree = 0.000) for 1393 atoms. Found 6 (6 requested) and removed 4 (4 requested) atoms. Cycle 27: After refmac, R = 0.2161 (Rfree = 0.000) for 1386 atoms. Found 6 (6 requested) and removed 7 (4 requested) atoms. Cycle 28: After refmac, R = 0.2044 (Rfree = 0.000) for 1380 atoms. Found 3 (6 requested) and removed 5 (4 requested) atoms. Cycle 29: After refmac, R = 0.1971 (Rfree = 0.000) for 1374 atoms. Found 0 (6 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.1959 (Rfree = 0.000) for 1367 atoms. Found 3 (6 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.43 Search for helices and strands: 0 residues in 0 chains, 1420 seeds are put forward Round 1: 103 peptides, 18 chains. Longest chain 11 peptides. Score 0.421 Round 2: 113 peptides, 16 chains. Longest chain 15 peptides. Score 0.547 Round 3: 112 peptides, 15 chains. Longest chain 12 peptides. Score 0.568 Round 4: 113 peptides, 15 chains. Longest chain 15 peptides. Score 0.574 Round 5: 126 peptides, 18 chains. Longest chain 17 peptides. Score 0.572 Taking the results from Round 4 Chains 15, Residues 98, Estimated correctness of the model 4.1 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2785 reflections ( 99.18 % complete ) and 3056 restraints for refining 1393 atoms. 2658 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2348 (Rfree = 0.000) for 1393 atoms. Found 6 (6 requested) and removed 6 (4 requested) atoms. Cycle 32: After refmac, R = 0.2184 (Rfree = 0.000) for 1386 atoms. Found 4 (6 requested) and removed 6 (4 requested) atoms. Cycle 33: After refmac, R = 0.2155 (Rfree = 0.000) for 1382 atoms. Found 2 (6 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.2177 (Rfree = 0.000) for 1378 atoms. Found 5 (6 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.2186 (Rfree = 0.000) for 1378 atoms. Found 1 (6 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.40 Search for helices and strands: 0 residues in 0 chains, 1408 seeds are put forward Round 1: 95 peptides, 16 chains. Longest chain 13 peptides. Score 0.425 Round 2: 113 peptides, 17 chains. Longest chain 17 peptides. Score 0.519 Round 3: 121 peptides, 16 chains. Longest chain 19 peptides. Score 0.594 Round 4: 125 peptides, 14 chains. Longest chain 20 peptides. Score 0.663 Round 5: 117 peptides, 13 chains. Longest chain 19 peptides. Score 0.646 Taking the results from Round 4 Chains 14, Residues 111, Estimated correctness of the model 37.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2785 reflections ( 99.18 % complete ) and 3092 restraints for refining 1393 atoms. 2662 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2572 (Rfree = 0.000) for 1393 atoms. Found 6 (6 requested) and removed 8 (4 requested) atoms. Cycle 37: After refmac, R = 0.2404 (Rfree = 0.000) for 1388 atoms. Found 5 (6 requested) and removed 7 (4 requested) atoms. Cycle 38: After refmac, R = 0.2345 (Rfree = 0.000) for 1385 atoms. Found 1 (6 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.2334 (Rfree = 0.000) for 1379 atoms. Found 2 (6 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2329 (Rfree = 0.000) for 1376 atoms. Found 2 (6 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.41 Search for helices and strands: 0 residues in 0 chains, 1406 seeds are put forward Round 1: 104 peptides, 21 chains. Longest chain 11 peptides. Score 0.333 Round 2: 112 peptides, 18 chains. Longest chain 10 peptides. Score 0.484 Round 3: 107 peptides, 18 chains. Longest chain 12 peptides. Score 0.450 Round 4: 113 peptides, 17 chains. Longest chain 24 peptides. Score 0.519 Round 5: 116 peptides, 16 chains. Longest chain 19 peptides. Score 0.565 Taking the results from Round 5 Chains 16, Residues 100, Estimated correctness of the model 0.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2785 reflections ( 99.18 % complete ) and 3208 restraints for refining 1393 atoms. 2824 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2646 (Rfree = 0.000) for 1393 atoms. Found 6 (6 requested) and removed 5 (4 requested) atoms. Cycle 42: After refmac, R = 0.2387 (Rfree = 0.000) for 1390 atoms. Found 2 (6 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2325 (Rfree = 0.000) for 1388 atoms. Found 1 (6 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.2318 (Rfree = 0.000) for 1383 atoms. Found 2 (6 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.2288 (Rfree = 0.000) for 1380 atoms. Found 2 (6 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.43 Search for helices and strands: 0 residues in 0 chains, 1421 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 8 peptides. Score 0.271 Round 2: 95 peptides, 17 chains. Longest chain 12 peptides. Score 0.393 Round 3: 107 peptides, 19 chains. Longest chain 10 peptides. Score 0.419 Round 4: 100 peptides, 15 chains. Longest chain 12 peptides. Score 0.491 Round 5: 108 peptides, 17 chains. Longest chain 19 peptides. Score 0.486 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 85, 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 2isb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2785 reflections ( 99.18 % complete ) and 3313 restraints for refining 1393 atoms. 2988 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2467 (Rfree = 0.000) for 1393 atoms. Found 0 (6 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2310 (Rfree = 0.000) for 1388 atoms. Found 0 (6 requested) and removed 2 (4 requested) atoms. Cycle 48: After refmac, R = 0.2293 (Rfree = 0.000) for 1383 atoms. Found 0 (6 requested) and removed 2 (4 requested) atoms. Cycle 49: After refmac, R = 0.2333 (Rfree = 0.000) for 1378 atoms. Found 0 (6 requested) and removed 1 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:17 GMT 2018 Job finished. TimeTaking 28.05 Used memory is bytes: 1889648