null 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 2ou6-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ou6-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ou6-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-3.6-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/2ou6-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-3.6-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/2ou6-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-3.6-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 164 and 0 Target number of residues in the AU: 164 Target solvent content: 0.6347 Checking the provided sequence file Detected sequence length: 190 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 190 Adjusted target solvent content: 0.58 Input MTZ file: 2ou6-3.6-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: 179 Cell parameters: 57.933 57.933 250.773 90.000 90.000 120.000 Input sequence file: 2ou6-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1520 target number of atoms Had to go as low as 0.85 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: 50.171 3.601 Wilson plot Bfac: 68.52 3319 reflections ( 99.76 % complete ) and 0 restraints for refining 1682 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3669 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3412 (Rfree = 0.000) for 1682 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.05 Search for helices and strands: 0 residues in 0 chains, 1734 seeds are put forward Round 1: 87 peptides, 17 chains. Longest chain 7 peptides. Score 0.314 Round 2: 115 peptides, 17 chains. Longest chain 18 peptides. Score 0.497 Round 3: 119 peptides, 16 chains. Longest chain 17 peptides. Score 0.545 Round 4: 117 peptides, 15 chains. Longest chain 20 peptides. Score 0.558 Round 5: 125 peptides, 14 chains. Longest chain 15 peptides. Score 0.622 Taking the results from Round 5 Chains 15, Residues 111, Estimated correctness of the model 23.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3319 reflections ( 99.76 % complete ) and 2729 restraints for refining 1377 atoms. 2217 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3131 (Rfree = 0.000) for 1377 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 2: After refmac, R = 0.2793 (Rfree = 0.000) for 1348 atoms. Found 6 (8 requested) and removed 10 (4 requested) atoms. Cycle 3: After refmac, R = 0.2614 (Rfree = 0.000) for 1323 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 4: After refmac, R = 0.2587 (Rfree = 0.000) for 1314 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. Cycle 5: After refmac, R = 0.2659 (Rfree = 0.000) for 1310 atoms. Found 7 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.02 Search for helices and strands: 0 residues in 0 chains, 1374 seeds are put forward Round 1: 121 peptides, 20 chains. Longest chain 17 peptides. Score 0.455 Round 2: 116 peptides, 16 chains. Longest chain 12 peptides. Score 0.528 Round 3: 128 peptides, 16 chains. Longest chain 23 peptides. Score 0.592 Round 4: 125 peptides, 18 chains. Longest chain 15 peptides. Score 0.529 Round 5: 122 peptides, 19 chains. Longest chain 19 peptides. Score 0.487 Taking the results from Round 3 Chains 16, Residues 112, Estimated correctness of the model 11.4 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3319 reflections ( 99.76 % complete ) and 2705 restraints for refining 1377 atoms. 2163 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3035 (Rfree = 0.000) for 1377 atoms. Found 8 (8 requested) and removed 26 (4 requested) atoms. Cycle 7: After refmac, R = 0.2565 (Rfree = 0.000) for 1345 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 8: After refmac, R = 0.2494 (Rfree = 0.000) for 1337 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.2357 (Rfree = 0.000) for 1336 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.2380 (Rfree = 0.000) for 1335 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.04 Search for helices and strands: 0 residues in 0 chains, 1406 seeds are put forward Round 1: 110 peptides, 19 chains. Longest chain 11 peptides. Score 0.413 Round 2: 111 peptides, 17 chains. Longest chain 14 peptides. Score 0.473 Round 3: 108 peptides, 15 chains. Longest chain 15 peptides. Score 0.508 Round 4: 123 peptides, 17 chains. Longest chain 15 peptides. Score 0.542 Round 5: 120 peptides, 13 chains. Longest chain 24 peptides. Score 0.620 Taking the results from Round 5 Chains 13, Residues 107, Estimated correctness of the model 22.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3319 reflections ( 99.76 % complete ) and 3028 restraints for refining 1377 atoms. 2613 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2973 (Rfree = 0.000) for 1377 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 12: After refmac, R = 0.2669 (Rfree = 0.000) for 1368 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. Cycle 13: After refmac, R = 0.2599 (Rfree = 0.000) for 1368 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 14: After refmac, R = 0.2528 (Rfree = 0.000) for 1361 atoms. Found 6 (8 requested) and removed 11 (4 requested) atoms. Cycle 15: After refmac, R = 0.2447 (Rfree = 0.000) for 1355 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.05 Search for helices and strands: 0 residues in 0 chains, 1422 seeds are put forward Round 1: 98 peptides, 18 chains. Longest chain 11 peptides. Score 0.362 Round 2: 102 peptides, 15 chains. Longest chain 16 peptides. Score 0.472 Round 3: 102 peptides, 17 chains. Longest chain 13 peptides. Score 0.417 Round 4: 108 peptides, 16 chains. Longest chain 23 peptides. Score 0.482 Round 5: 115 peptides, 16 chains. Longest chain 22 peptides. Score 0.523 Taking the results from Round 5 Chains 16, Residues 99, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3319 reflections ( 99.76 % complete ) and 3056 restraints for refining 1377 atoms. 2646 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2882 (Rfree = 0.000) for 1377 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 17: After refmac, R = 0.2599 (Rfree = 0.000) for 1359 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 18: After refmac, R = 0.2486 (Rfree = 0.000) for 1355 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 19: After refmac, R = 0.2482 (Rfree = 0.000) for 1348 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2493 (Rfree = 0.000) for 1348 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.06 Search for helices and strands: 0 residues in 0 chains, 1407 seeds are put forward Round 1: 98 peptides, 19 chains. Longest chain 10 peptides. Score 0.332 Round 2: 126 peptides, 16 chains. Longest chain 17 peptides. Score 0.582 Round 3: 129 peptides, 18 chains. Longest chain 17 peptides. Score 0.551 Round 4: 128 peptides, 18 chains. Longest chain 23 peptides. Score 0.545 Round 5: 114 peptides, 14 chains. Longest chain 24 peptides. Score 0.566 Taking the results from Round 2 Chains 16, Residues 110, Estimated correctness of the model 7.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3319 reflections ( 99.76 % complete ) and 2959 restraints for refining 1377 atoms. 2535 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2884 (Rfree = 0.000) for 1377 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 22: After refmac, R = 0.2501 (Rfree = 0.000) for 1375 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.2353 (Rfree = 0.000) for 1374 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.2341 (Rfree = 0.000) for 1372 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.2218 (Rfree = 0.000) for 1372 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.04 Search for helices and strands: 0 residues in 0 chains, 1418 seeds are put forward Round 1: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.334 Round 2: 108 peptides, 15 chains. Longest chain 16 peptides. Score 0.508 Round 3: 111 peptides, 16 chains. Longest chain 17 peptides. Score 0.500 Round 4: 102 peptides, 14 chains. Longest chain 16 peptides. Score 0.499 Round 5: 105 peptides, 15 chains. Longest chain 15 peptides. Score 0.490 Taking the results from Round 2 Chains 17, Residues 93, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3319 reflections ( 99.76 % complete ) and 2999 restraints for refining 1377 atoms. 2596 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2590 (Rfree = 0.000) for 1377 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 27: After refmac, R = 0.2580 (Rfree = 0.000) for 1373 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 28: After refmac, R = 0.2383 (Rfree = 0.000) for 1368 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2340 (Rfree = 0.000) for 1366 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.2291 (Rfree = 0.000) for 1360 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.06 Search for helices and strands: 0 residues in 0 chains, 1411 seeds are put forward Round 1: 91 peptides, 16 chains. Longest chain 12 peptides. Score 0.372 Round 2: 98 peptides, 13 chains. Longest chain 24 peptides. Score 0.502 Round 3: 95 peptides, 15 chains. Longest chain 13 peptides. Score 0.428 Round 4: 91 peptides, 12 chains. Longest chain 18 peptides. Score 0.488 Round 5: 100 peptides, 13 chains. Longest chain 18 peptides. Score 0.514 Taking the results from Round 5 Chains 13, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3319 reflections ( 99.76 % complete ) and 3082 restraints for refining 1377 atoms. 2747 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2909 (Rfree = 0.000) for 1377 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.2986 (Rfree = 0.000) for 1376 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 33: After refmac, R = 0.2777 (Rfree = 0.000) for 1373 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.2870 (Rfree = 0.000) for 1373 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 35: After refmac, R = 0.2729 (Rfree = 0.000) for 1368 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.05 Search for helices and strands: 0 residues in 0 chains, 1406 seeds are put forward Round 1: 96 peptides, 17 chains. Longest chain 12 peptides. Score 0.377 Round 2: 104 peptides, 17 chains. Longest chain 14 peptides. Score 0.430 Round 3: 96 peptides, 13 chains. Longest chain 14 peptides. Score 0.490 Round 4: 105 peptides, 16 chains. Longest chain 15 peptides. Score 0.464 Round 5: 89 peptides, 14 chains. Longest chain 12 peptides. Score 0.418 Taking the results from Round 3 Chains 13, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3319 reflections ( 99.76 % complete ) and 3216 restraints for refining 1377 atoms. 2897 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2813 (Rfree = 0.000) for 1377 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2662 (Rfree = 0.000) for 1376 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.2476 (Rfree = 0.000) for 1374 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.2397 (Rfree = 0.000) for 1372 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.2516 (Rfree = 0.000) for 1368 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.07 Search for helices and strands: 0 residues in 0 chains, 1408 seeds are put forward Round 1: 97 peptides, 16 chains. Longest chain 11 peptides. Score 0.413 Round 2: 109 peptides, 17 chains. Longest chain 12 peptides. Score 0.461 Round 3: 107 peptides, 16 chains. Longest chain 13 peptides. Score 0.476 Round 4: 96 peptides, 16 chains. Longest chain 12 peptides. Score 0.406 Round 5: 103 peptides, 15 chains. Longest chain 14 peptides. Score 0.478 Taking the results from Round 5 Chains 16, Residues 88, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3319 reflections ( 99.76 % complete ) and 3022 restraints for refining 1377 atoms. 2640 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2686 (Rfree = 0.000) for 1377 atoms. Found 6 (8 requested) and removed 14 (4 requested) atoms. Cycle 42: After refmac, R = 0.2667 (Rfree = 0.000) for 1368 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 43: After refmac, R = 0.2596 (Rfree = 0.000) for 1365 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 44: After refmac, R = 0.2586 (Rfree = 0.000) for 1354 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2522 (Rfree = 0.000) for 1357 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.02 Search for helices and strands: 0 residues in 0 chains, 1408 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 8 peptides. Score 0.269 Round 2: 90 peptides, 16 chains. Longest chain 12 peptides. Score 0.366 Round 3: 94 peptides, 14 chains. Longest chain 13 peptides. Score 0.450 Round 4: 108 peptides, 18 chains. Longest chain 12 peptides. Score 0.428 Round 5: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.400 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 80, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2ou6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3319 reflections ( 99.76 % complete ) and 3139 restraints for refining 1377 atoms. 2811 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2708 (Rfree = 0.000) for 1377 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2690 (Rfree = 0.000) for 1364 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2691 (Rfree = 0.000) for 1356 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2669 (Rfree = 0.000) for 1351 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:23 GMT 2018 Job finished. TimeTaking 29.41 Used memory is bytes: 5488120