null Mon 24 Dec 07:32:54 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1ztc-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1ztc-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1ztc-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.4-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:32:59 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/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.4-parrot-noncs/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 1148 and 0 Target number of residues in the AU: 1148 Target solvent content: 0.6430 Checking the provided sequence file Detected sequence length: 221 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 884 Adjusted target solvent content: 0.73 Input MTZ file: 1ztc-3.4-parrot-noncs.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: 89.783 127.343 152.224 90.000 90.000 90.000 Input sequence file: 1ztc-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 7072 target number of atoms Had to go as low as 1.10 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: 97.673 3.400 Wilson plot Bfac: 73.76 24384 reflections ( 98.85 % complete ) and 0 restraints for refining 7848 atoms. Observations/parameters ratio is 0.78 ------------------------------------------------------ Starting model: R = 0.3506 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3047 (Rfree = 0.000) for 7848 atoms. Found 59 (59 requested) and removed 54 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 2.41 Search for helices and strands: 0 residues in 0 chains, 7983 seeds are put forward NCS extension: 0 residues added, 7983 seeds are put forward Round 1: 604 peptides, 71 chains. Longest chain 24 peptides. Score 0.506 Round 2: 669 peptides, 64 chains. Longest chain 39 peptides. Score 0.583 Round 3: 679 peptides, 54 chains. Longest chain 55 peptides. Score 0.625 Round 4: 682 peptides, 56 chains. Longest chain 52 peptides. Score 0.620 Round 5: 680 peptides, 58 chains. Longest chain 56 peptides. Score 0.612 Taking the results from Round 3 Chains 55, Residues 625, Estimated correctness of the model 36.6 % 2 chains (98 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 12445 restraints for refining 6549 atoms. 9589 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2720 (Rfree = 0.000) for 6549 atoms. Found 49 (49 requested) and removed 51 (24 requested) atoms. Cycle 2: After refmac, R = 0.2549 (Rfree = 0.000) for 6425 atoms. Found 49 (49 requested) and removed 37 (24 requested) atoms. Cycle 3: After refmac, R = 0.2422 (Rfree = 0.000) for 6388 atoms. Found 48 (48 requested) and removed 30 (24 requested) atoms. Cycle 4: After refmac, R = 0.2373 (Rfree = 0.000) for 6384 atoms. Found 33 (48 requested) and removed 41 (24 requested) atoms. Cycle 5: After refmac, R = 0.2292 (Rfree = 0.000) for 6361 atoms. Found 20 (48 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 2.41 Search for helices and strands: 0 residues in 0 chains, 6586 seeds are put forward NCS extension: 29 residues added (19 deleted due to clashes), 6615 seeds are put forward Round 1: 683 peptides, 66 chains. Longest chain 53 peptides. Score 0.586 Round 2: 688 peptides, 55 chains. Longest chain 55 peptides. Score 0.628 Round 3: 684 peptides, 58 chains. Longest chain 56 peptides. Score 0.615 Round 4: 677 peptides, 52 chains. Longest chain 44 peptides. Score 0.630 Round 5: 683 peptides, 56 chains. Longest chain 55 peptides. Score 0.621 Taking the results from Round 4 Chains 57, Residues 625, Estimated correctness of the model 38.2 % 6 chains (166 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11600 restraints for refining 6430 atoms. 8403 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2732 (Rfree = 0.000) for 6430 atoms. Found 48 (48 requested) and removed 58 (24 requested) atoms. Cycle 7: After refmac, R = 0.2476 (Rfree = 0.000) for 6368 atoms. Found 48 (48 requested) and removed 39 (24 requested) atoms. Cycle 8: After refmac, R = 0.2360 (Rfree = 0.000) for 6348 atoms. Found 43 (48 requested) and removed 34 (24 requested) atoms. Cycle 9: After refmac, R = 0.2276 (Rfree = 0.000) for 6343 atoms. Found 27 (47 requested) and removed 29 (23 requested) atoms. Cycle 10: After refmac, R = 0.2223 (Rfree = 0.000) for 6327 atoms. Found 15 (47 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 2.42 Search for helices and strands: 0 residues in 0 chains, 6503 seeds are put forward NCS extension: 12 residues added (16 deleted due to clashes), 6515 seeds are put forward Round 1: 669 peptides, 68 chains. Longest chain 44 peptides. Score 0.569 Round 2: 688 peptides, 56 chains. Longest chain 56 peptides. Score 0.624 Round 3: 676 peptides, 54 chains. Longest chain 50 peptides. Score 0.623 Round 4: 667 peptides, 59 chains. Longest chain 29 peptides. Score 0.599 Round 5: 661 peptides, 60 chains. Longest chain 40 peptides. Score 0.591 Taking the results from Round 2 Chains 64, Residues 632, Estimated correctness of the model 36.3 % 7 chains (200 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11300 restraints for refining 6428 atoms. 7970 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2595 (Rfree = 0.000) for 6428 atoms. Found 48 (48 requested) and removed 60 (24 requested) atoms. Cycle 12: After refmac, R = 0.2399 (Rfree = 0.000) for 6375 atoms. Found 48 (48 requested) and removed 37 (24 requested) atoms. Cycle 13: After refmac, R = 0.2281 (Rfree = 0.000) for 6360 atoms. Found 31 (48 requested) and removed 34 (24 requested) atoms. Cycle 14: After refmac, R = 0.2204 (Rfree = 0.000) for 6341 atoms. Found 19 (47 requested) and removed 23 (23 requested) atoms. Cycle 15: After refmac, R = 0.2151 (Rfree = 0.000) for 6326 atoms. Found 17 (47 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 2.41 Search for helices and strands: 0 residues in 0 chains, 6520 seeds are put forward NCS extension: 23 residues added (23 deleted due to clashes), 6543 seeds are put forward Round 1: 673 peptides, 66 chains. Longest chain 32 peptides. Score 0.579 Round 2: 693 peptides, 54 chains. Longest chain 59 peptides. Score 0.634 Round 3: 681 peptides, 56 chains. Longest chain 39 peptides. Score 0.619 Round 4: 673 peptides, 60 chains. Longest chain 30 peptides. Score 0.600 Round 5: 677 peptides, 59 chains. Longest chain 35 peptides. Score 0.606 Taking the results from Round 2 Chains 57, Residues 639, Estimated correctness of the model 39.4 % 6 chains (141 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 12027 restraints for refining 6426 atoms. 8921 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2548 (Rfree = 0.000) for 6426 atoms. Found 48 (48 requested) and removed 59 (24 requested) atoms. Cycle 17: After refmac, R = 0.2405 (Rfree = 0.000) for 6384 atoms. Found 48 (48 requested) and removed 41 (24 requested) atoms. Cycle 18: After refmac, R = 0.2285 (Rfree = 0.000) for 6369 atoms. Found 21 (48 requested) and removed 27 (24 requested) atoms. Cycle 19: After refmac, R = 0.2240 (Rfree = 0.000) for 6347 atoms. Found 21 (48 requested) and removed 25 (24 requested) atoms. Cycle 20: After refmac, R = 0.2194 (Rfree = 0.000) for 6332 atoms. Found 17 (47 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 2.42 Search for helices and strands: 0 residues in 0 chains, 6508 seeds are put forward NCS extension: 11 residues added (13 deleted due to clashes), 6519 seeds are put forward Round 1: 671 peptides, 63 chains. Longest chain 32 peptides. Score 0.588 Round 2: 690 peptides, 56 chains. Longest chain 42 peptides. Score 0.626 Round 3: 693 peptides, 58 chains. Longest chain 39 peptides. Score 0.621 Round 4: 683 peptides, 63 chains. Longest chain 37 peptides. Score 0.597 Round 5: 695 peptides, 55 chains. Longest chain 41 peptides. Score 0.632 Taking the results from Round 5 Chains 59, Residues 640, Estimated correctness of the model 38.8 % 5 chains (120 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 12150 restraints for refining 6428 atoms. 9081 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2551 (Rfree = 0.000) for 6428 atoms. Found 48 (48 requested) and removed 40 (24 requested) atoms. Cycle 22: After refmac, R = 0.2350 (Rfree = 0.000) for 6403 atoms. Found 48 (48 requested) and removed 35 (24 requested) atoms. Cycle 23: After refmac, R = 0.2249 (Rfree = 0.000) for 6397 atoms. Found 26 (48 requested) and removed 26 (24 requested) atoms. Cycle 24: After refmac, R = 0.2193 (Rfree = 0.000) for 6390 atoms. Found 24 (48 requested) and removed 27 (24 requested) atoms. Cycle 25: After refmac, R = 0.2147 (Rfree = 0.000) for 6379 atoms. Found 26 (48 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 2.43 Search for helices and strands: 0 residues in 0 chains, 6588 seeds are put forward NCS extension: 12 residues added (19 deleted due to clashes), 6600 seeds are put forward Round 1: 667 peptides, 64 chains. Longest chain 43 peptides. Score 0.582 Round 2: 696 peptides, 51 chains. Longest chain 48 peptides. Score 0.646 Round 3: 686 peptides, 53 chains. Longest chain 58 peptides. Score 0.633 Round 4: 678 peptides, 52 chains. Longest chain 49 peptides. Score 0.631 Round 5: 680 peptides, 53 chains. Longest chain 49 peptides. Score 0.629 Taking the results from Round 2 Chains 58, Residues 645, Estimated correctness of the model 43.0 % 8 chains (164 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11641 restraints for refining 6428 atoms. 8371 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2464 (Rfree = 0.000) for 6428 atoms. Found 48 (48 requested) and removed 49 (24 requested) atoms. Cycle 27: After refmac, R = 0.2311 (Rfree = 0.000) for 6397 atoms. Found 39 (48 requested) and removed 28 (24 requested) atoms. Cycle 28: After refmac, R = 0.2204 (Rfree = 0.000) for 6394 atoms. Found 16 (48 requested) and removed 25 (24 requested) atoms. Cycle 29: After refmac, R = 0.2146 (Rfree = 0.000) for 6376 atoms. Found 14 (48 requested) and removed 24 (24 requested) atoms. Cycle 30: After refmac, R = 0.2102 (Rfree = 0.000) for 6363 atoms. Found 15 (48 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 2.43 Search for helices and strands: 0 residues in 0 chains, 6533 seeds are put forward NCS extension: 14 residues added (23 deleted due to clashes), 6547 seeds are put forward Round 1: 657 peptides, 63 chains. Longest chain 48 peptides. Score 0.578 Round 2: 678 peptides, 52 chains. Longest chain 39 peptides. Score 0.631 Round 3: 667 peptides, 58 chains. Longest chain 39 peptides. Score 0.603 Round 4: 650 peptides, 59 chains. Longest chain 40 peptides. Score 0.587 Round 5: 667 peptides, 55 chains. Longest chain 46 peptides. Score 0.613 Taking the results from Round 2 Chains 58, Residues 626, Estimated correctness of the model 38.5 % 10 chains (200 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11468 restraints for refining 6430 atoms. 8117 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2437 (Rfree = 0.000) for 6430 atoms. Found 48 (48 requested) and removed 38 (24 requested) atoms. Cycle 32: After refmac, R = 0.2254 (Rfree = 0.000) for 6419 atoms. Found 36 (48 requested) and removed 27 (24 requested) atoms. Cycle 33: After refmac, R = 0.2167 (Rfree = 0.000) for 6421 atoms. Found 21 (48 requested) and removed 26 (24 requested) atoms. Cycle 34: After refmac, R = 0.2143 (Rfree = 0.000) for 6408 atoms. Found 21 (48 requested) and removed 27 (24 requested) atoms. Cycle 35: After refmac, R = 0.2094 (Rfree = 0.000) for 6398 atoms. Found 13 (48 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 2.43 Search for helices and strands: 0 residues in 0 chains, 6568 seeds are put forward NCS extension: 27 residues added (18 deleted due to clashes), 6595 seeds are put forward Round 1: 647 peptides, 67 chains. Longest chain 48 peptides. Score 0.555 Round 2: 679 peptides, 59 chains. Longest chain 48 peptides. Score 0.608 Round 3: 654 peptides, 55 chains. Longest chain 41 peptides. Score 0.604 Round 4: 674 peptides, 53 chains. Longest chain 44 peptides. Score 0.625 Round 5: 678 peptides, 55 chains. Longest chain 42 peptides. Score 0.621 Taking the results from Round 4 Chains 58, Residues 621, Estimated correctness of the model 36.6 % 9 chains (228 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11455 restraints for refining 6448 atoms. 8055 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2505 (Rfree = 0.000) for 6448 atoms. Found 48 (48 requested) and removed 57 (24 requested) atoms. Cycle 37: After refmac, R = 0.2292 (Rfree = 0.000) for 6408 atoms. Found 47 (48 requested) and removed 34 (24 requested) atoms. Cycle 38: After refmac, R = 0.2187 (Rfree = 0.000) for 6410 atoms. Found 22 (48 requested) and removed 24 (24 requested) atoms. Cycle 39: After refmac, R = 0.2132 (Rfree = 0.000) for 6404 atoms. Found 13 (48 requested) and removed 26 (24 requested) atoms. Cycle 40: After refmac, R = 0.2109 (Rfree = 0.000) for 6387 atoms. Found 13 (48 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 2.43 Search for helices and strands: 0 residues in 0 chains, 6571 seeds are put forward NCS extension: 20 residues added (12 deleted due to clashes), 6591 seeds are put forward Round 1: 622 peptides, 69 chains. Longest chain 26 peptides. Score 0.528 Round 2: 671 peptides, 62 chains. Longest chain 44 peptides. Score 0.592 Round 3: 675 peptides, 54 chains. Longest chain 52 peptides. Score 0.622 Round 4: 677 peptides, 57 chains. Longest chain 40 peptides. Score 0.613 Round 5: 674 peptides, 57 chains. Longest chain 40 peptides. Score 0.611 Taking the results from Round 3 Chains 62, Residues 621, Estimated correctness of the model 35.7 % 11 chains (252 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11332 restraints for refining 6559 atoms. 7799 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2598 (Rfree = 0.000) for 6559 atoms. Found 49 (49 requested) and removed 51 (24 requested) atoms. Cycle 42: After refmac, R = 0.2379 (Rfree = 0.000) for 6524 atoms. Found 49 (49 requested) and removed 32 (24 requested) atoms. Cycle 43: After refmac, R = 0.2265 (Rfree = 0.000) for 6528 atoms. Found 13 (49 requested) and removed 26 (24 requested) atoms. Cycle 44: After refmac, R = 0.2223 (Rfree = 0.000) for 6500 atoms. Found 22 (49 requested) and removed 27 (24 requested) atoms. Cycle 45: After refmac, R = 0.2188 (Rfree = 0.000) for 6485 atoms. Found 14 (49 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 2.43 Search for helices and strands: 0 residues in 0 chains, 6630 seeds are put forward NCS extension: 24 residues added (36 deleted due to clashes), 6654 seeds are put forward Round 1: 615 peptides, 67 chains. Longest chain 37 peptides. Score 0.530 Round 2: 642 peptides, 53 chains. Longest chain 50 peptides. Score 0.603 Round 3: 658 peptides, 63 chains. Longest chain 43 peptides. Score 0.578 Round 4: 661 peptides, 54 chains. Longest chain 43 peptides. Score 0.612 Round 5: 664 peptides, 58 chains. Longest chain 33 peptides. Score 0.601 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 607, Estimated correctness of the model 32.5 % 8 chains (203 residues) have been docked in sequence Sequence coverage is 33 % Consider running further cycles of model building using 1ztc-3_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (607 residues) following loop building 8 chains (203 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 24384 reflections ( 98.85 % complete ) and 11668 restraints for refining 6430 atoms. 8391 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2583 (Rfree = 0.000) for 6430 atoms. Found 0 (48 requested) and removed 13 (24 requested) atoms. Cycle 47: After refmac, R = 0.2462 (Rfree = 0.000) for 6390 atoms. Found 0 (48 requested) and removed 10 (24 requested) atoms. Cycle 48: After refmac, R = 0.2397 (Rfree = 0.000) for 6371 atoms. Found 0 (48 requested) and removed 5 (24 requested) atoms. Cycle 49: After refmac, R = 0.2336 (Rfree = 0.000) for 6356 atoms. Found 0 (48 requested) and removed 3 (24 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:52:54 GMT 2018 Job finished. TimeTaking 80 Used memory is bytes: 15117896