Sun 23 Dec 22:22:50 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 1zko-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zko-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zko-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-3.8-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/1zko-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-3.8-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 22:22:59 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/1zko-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-3.8-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 172 and 0 Target number of residues in the AU: 172 Target solvent content: 0.6187 Checking the provided sequence file Detected sequence length: 136 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 272 Adjusted target solvent content: 0.40 Input MTZ file: 1zko-3.8-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: 19 Cell parameters: 54.005 65.321 69.197 90.000 90.000 90.000 Input sequence file: 1zko-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2176 target number of atoms Had to go as low as 0.60 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: 47.500 3.801 Wilson plot Bfac: 60.61 2442 reflections ( 92.68 % complete ) and 0 restraints for refining 2424 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3691 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3599 (Rfree = 0.000) for 2424 atoms. Found 13 (13 requested) and removed 38 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 4.09 Search for helices and strands: 0 residues in 0 chains, 2414 seeds are put forward NCS extension: 0 residues added, 2414 seeds are put forward Round 1: 41 peptides, 10 chains. Longest chain 5 peptides. Score 0.177 Round 2: 56 peptides, 12 chains. Longest chain 6 peptides. Score 0.237 Round 3: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.297 Round 4: 50 peptides, 10 chains. Longest chain 8 peptides. Score 0.259 Round 5: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.273 Taking the results from Round 3 Chains 11, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 4809 restraints for refining 1968 atoms. 4628 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3758 (Rfree = 0.000) for 1968 atoms. Found 10 (10 requested) and removed 29 (5 requested) atoms. Cycle 2: After refmac, R = 0.3591 (Rfree = 0.000) for 1934 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 3: After refmac, R = 0.3071 (Rfree = 0.000) for 1915 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 4: After refmac, R = 0.2734 (Rfree = 0.000) for 1893 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 5: After refmac, R = 0.3213 (Rfree = 0.000) for 1876 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.85 Search for helices and strands: 0 residues in 0 chains, 1896 seeds are put forward NCS extension: 0 residues added, 1896 seeds are put forward Round 1: 39 peptides, 9 chains. Longest chain 7 peptides. Score 0.197 Round 2: 41 peptides, 9 chains. Longest chain 7 peptides. Score 0.216 Round 3: 40 peptides, 8 chains. Longest chain 7 peptides. Score 0.247 Round 4: 43 peptides, 9 chains. Longest chain 9 peptides. Score 0.235 Round 5: 46 peptides, 8 chains. Longest chain 9 peptides. Score 0.299 Taking the results from Round 5 Chains 8, Residues 38, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3576 restraints for refining 1545 atoms. 3432 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3090 (Rfree = 0.000) for 1545 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 7: After refmac, R = 0.2925 (Rfree = 0.000) for 1533 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.2488 (Rfree = 0.000) for 1525 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 9: After refmac, R = 0.3344 (Rfree = 0.000) for 1525 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 10: After refmac, R = 0.2705 (Rfree = 0.000) for 1519 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.86 Search for helices and strands: 0 residues in 0 chains, 1545 seeds are put forward NCS extension: 0 residues added, 1545 seeds are put forward Round 1: 70 peptides, 17 chains. Longest chain 5 peptides. Score 0.183 Round 2: 94 peptides, 18 chains. Longest chain 10 peptides. Score 0.333 Round 3: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.344 Round 4: 94 peptides, 17 chains. Longest chain 9 peptides. Score 0.363 Round 5: 84 peptides, 14 chains. Longest chain 13 peptides. Score 0.383 Taking the results from Round 5 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3256 restraints for refining 1498 atoms. 2990 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2907 (Rfree = 0.000) for 1498 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 12: After refmac, R = 0.2506 (Rfree = 0.000) for 1466 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.2530 (Rfree = 0.000) for 1459 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 14: After refmac, R = 0.2908 (Rfree = 0.000) for 1456 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 15: After refmac, R = 0.2464 (Rfree = 0.000) for 1446 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 4.01 Search for helices and strands: 0 residues in 0 chains, 1474 seeds are put forward NCS extension: 0 residues added, 1474 seeds are put forward Round 1: 60 peptides, 12 chains. Longest chain 7 peptides. Score 0.270 Round 2: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.344 Round 3: 85 peptides, 13 chains. Longest chain 15 peptides. Score 0.420 Round 4: 83 peptides, 14 chains. Longest chain 10 peptides. Score 0.377 Round 5: 89 peptides, 14 chains. Longest chain 13 peptides. Score 0.417 Taking the results from Round 3 Chains 13, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3242 restraints for refining 1497 atoms. 2967 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2871 (Rfree = 0.000) for 1497 atoms. Found 8 (8 requested) and removed 26 (4 requested) atoms. Cycle 17: After refmac, R = 0.2716 (Rfree = 0.000) for 1467 atoms. Found 7 (8 requested) and removed 16 (4 requested) atoms. Cycle 18: After refmac, R = 0.2489 (Rfree = 0.000) for 1454 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.2578 (Rfree = 0.000) for 1454 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. Cycle 20: After refmac, R = 0.2471 (Rfree = 0.000) for 1454 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 1481 seeds are put forward NCS extension: 0 residues added, 1481 seeds are put forward Round 1: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.305 Round 2: 80 peptides, 14 chains. Longest chain 14 peptides. Score 0.356 Round 3: 86 peptides, 15 chains. Longest chain 18 peptides. Score 0.367 Round 4: 94 peptides, 16 chains. Longest chain 18 peptides. Score 0.392 Round 5: 93 peptides, 14 chains. Longest chain 18 peptides. Score 0.443 Taking the results from Round 5 Chains 14, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3521 restraints for refining 1590 atoms. 3219 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3166 (Rfree = 0.000) for 1590 atoms. Found 8 (8 requested) and removed 31 (4 requested) atoms. Cycle 22: After refmac, R = 0.2913 (Rfree = 0.000) for 1545 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 23: After refmac, R = 0.3104 (Rfree = 0.000) for 1518 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 24: After refmac, R = 0.3177 (Rfree = 0.000) for 1496 atoms. Found 8 (8 requested) and removed 31 (4 requested) atoms. Cycle 25: After refmac, R = 0.2559 (Rfree = 0.000) for 1464 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.75 Search for helices and strands: 0 residues in 0 chains, 1488 seeds are put forward NCS extension: 0 residues added, 1488 seeds are put forward Round 1: 71 peptides, 17 chains. Longest chain 6 peptides. Score 0.191 Round 2: 70 peptides, 14 chains. Longest chain 8 peptides. Score 0.282 Round 3: 75 peptides, 15 chains. Longest chain 11 peptides. Score 0.288 Round 4: 66 peptides, 14 chains. Longest chain 7 peptides. Score 0.251 Round 5: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.297 Taking the results from Round 5 Chains 14, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 2967 restraints for refining 1400 atoms. 2749 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3028 (Rfree = 0.000) for 1400 atoms. Found 7 (7 requested) and removed 18 (3 requested) atoms. Cycle 27: After refmac, R = 0.3107 (Rfree = 0.000) for 1383 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 28: After refmac, R = 0.2591 (Rfree = 0.000) for 1370 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 29: After refmac, R = 0.2558 (Rfree = 0.000) for 1365 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 30: After refmac, R = 0.2505 (Rfree = 0.000) for 1359 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.80 Search for helices and strands: 0 residues in 0 chains, 1383 seeds are put forward NCS extension: 0 residues added, 1383 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 8 peptides. Score 0.226 Round 2: 73 peptides, 14 chains. Longest chain 10 peptides. Score 0.305 Round 3: 70 peptides, 14 chains. Longest chain 8 peptides. Score 0.282 Round 4: 76 peptides, 15 chains. Longest chain 11 peptides. Score 0.295 Round 5: 72 peptides, 15 chains. Longest chain 8 peptides. Score 0.265 Taking the results from Round 2 Chains 14, Residues 59, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 2688 restraints for refining 1362 atoms. 2438 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2839 (Rfree = 0.000) for 1362 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 32: After refmac, R = 0.2475 (Rfree = 0.000) for 1346 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 33: After refmac, R = 0.2624 (Rfree = 0.000) for 1337 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 34: After refmac, R = 0.2609 (Rfree = 0.000) for 1336 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 35: After refmac, R = 0.2413 (Rfree = 0.000) for 1333 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 1370 seeds are put forward NCS extension: 0 residues added, 1370 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 7 peptides. Score 0.226 Round 2: 79 peptides, 15 chains. Longest chain 8 peptides. Score 0.317 Round 3: 84 peptides, 17 chains. Longest chain 8 peptides. Score 0.292 Round 4: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.305 Round 5: 75 peptides, 14 chains. Longest chain 8 peptides. Score 0.320 Taking the results from Round 5 Chains 14, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3049 restraints for refining 1426 atoms. 2819 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3009 (Rfree = 0.000) for 1426 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. Cycle 37: After refmac, R = 0.2627 (Rfree = 0.000) for 1405 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.2935 (Rfree = 0.000) for 1401 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 39: After refmac, R = 0.2381 (Rfree = 0.000) for 1398 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.2654 (Rfree = 0.000) for 1398 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.81 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, 11 chains. Longest chain 7 peptides. Score 0.281 Round 2: 77 peptides, 16 chains. Longest chain 8 peptides. Score 0.271 Round 3: 84 peptides, 15 chains. Longest chain 13 peptides. Score 0.353 Round 4: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.360 Round 5: 76 peptides, 14 chains. Longest chain 8 peptides. Score 0.327 Taking the results from Round 4 Chains 15, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3130 restraints for refining 1459 atoms. 2865 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2788 (Rfree = 0.000) for 1459 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 42: After refmac, R = 0.2645 (Rfree = 0.000) for 1441 atoms. Found 7 (7 requested) and removed 25 (3 requested) atoms. Cycle 43: After refmac, R = 0.2821 (Rfree = 0.000) for 1416 atoms. Found 7 (7 requested) and removed 24 (3 requested) atoms. Cycle 44: After refmac, R = 0.2634 (Rfree = 0.000) for 1396 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.2723 (Rfree = 0.000) for 1391 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 3.96 Search for helices and strands: 0 residues in 0 chains, 1419 seeds are put forward NCS extension: 0 residues added, 1419 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 7 peptides. Score 0.239 Round 2: 62 peptides, 12 chains. Longest chain 7 peptides. Score 0.286 Round 3: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.344 Round 4: 72 peptides, 13 chains. Longest chain 9 peptides. Score 0.329 Round 5: 76 peptides, 13 chains. Longest chain 8 peptides. Score 0.358 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 63, 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 1zko-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2442 reflections ( 92.68 % complete ) and 2973 restraints for refining 1409 atoms. 2734 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3040 (Rfree = 0.000) for 1409 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2607 (Rfree = 0.000) for 1398 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3046 (Rfree = 0.000) for 1393 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2696 (Rfree = 0.000) for 1388 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... TimeTaking 27.33