Mon 24 Dec 07:32:24 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1ztc-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1ztc-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.8-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-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.8-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 07:32:29 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.8-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 1095 and 0 Target number of residues in the AU: 1095 Target solvent content: 0.6595 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-3.8-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-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 7072 target number of atoms Had to go as low as 1.15 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 3.800 Wilson plot Bfac: 84.57 17528 reflections ( 98.52 % complete ) and 0 restraints for refining 7781 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.3567 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3279 (Rfree = 0.000) for 7781 atoms. Found 42 (42 requested) and removed 52 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 2.60 Search for helices and strands: 0 residues in 0 chains, 7928 seeds are put forward NCS extension: 0 residues added, 7928 seeds are put forward Round 1: 503 peptides, 72 chains. Longest chain 18 peptides. Score 0.411 Round 2: 592 peptides, 65 chains. Longest chain 27 peptides. Score 0.519 Round 3: 599 peptides, 61 chains. Longest chain 27 peptides. Score 0.540 Round 4: 612 peptides, 62 chains. Longest chain 30 peptides. Score 0.547 Round 5: 612 peptides, 56 chains. Longest chain 38 peptides. Score 0.569 Taking the results from Round 5 Chains 56, Residues 556, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13594 restraints for refining 6395 atoms. 11426 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2868 (Rfree = 0.000) for 6395 atoms. Found 35 (35 requested) and removed 27 (17 requested) atoms. Cycle 2: After refmac, R = 0.2618 (Rfree = 0.000) for 6344 atoms. Found 35 (35 requested) and removed 30 (17 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2419 (Rfree = 0.000) for 6318 atoms. Found 33 (34 requested) and removed 27 (17 requested) atoms. Cycle 4: After refmac, R = 0.2510 (Rfree = 0.000) for 6303 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. Cycle 5: After refmac, R = 0.2412 (Rfree = 0.000) for 6290 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 2.64 Search for helices and strands: 0 residues in 0 chains, 6540 seeds are put forward NCS extension: 18 residues added (10 deleted due to clashes), 6558 seeds are put forward Round 1: 590 peptides, 71 chains. Longest chain 33 peptides. Score 0.494 Round 2: 604 peptides, 56 chains. Longest chain 39 peptides. Score 0.563 Round 3: 615 peptides, 63 chains. Longest chain 29 peptides. Score 0.545 Round 4: 616 peptides, 55 chains. Longest chain 34 peptides. Score 0.576 Round 5: 609 peptides, 59 chains. Longest chain 28 peptides. Score 0.556 Taking the results from Round 4 Chains 57, Residues 561, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13764 restraints for refining 6394 atoms. 11531 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2736 (Rfree = 0.000) for 6394 atoms. Found 35 (35 requested) and removed 27 (17 requested) atoms. Cycle 7: After refmac, R = 0.2530 (Rfree = 0.000) for 6324 atoms. Found 35 (35 requested) and removed 24 (17 requested) atoms. Cycle 8: After refmac, R = 0.2579 (Rfree = 0.000) for 6295 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. Cycle 9: After refmac, R = 0.2490 (Rfree = 0.000) for 6281 atoms. Found 34 (34 requested) and removed 45 (17 requested) atoms. Cycle 10: After refmac, R = 0.2467 (Rfree = 0.000) for 6255 atoms. Found 34 (34 requested) and removed 36 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 2.63 Search for helices and strands: 0 residues in 0 chains, 6513 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 6533 seeds are put forward Round 1: 592 peptides, 69 chains. Longest chain 23 peptides. Score 0.503 Round 2: 619 peptides, 62 chains. Longest chain 29 peptides. Score 0.552 Round 3: 617 peptides, 55 chains. Longest chain 33 peptides. Score 0.577 Round 4: 604 peptides, 51 chains. Longest chain 37 peptides. Score 0.582 Round 5: 603 peptides, 54 chains. Longest chain 40 peptides. Score 0.570 Taking the results from Round 4 Chains 53, Residues 553, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13899 restraints for refining 6394 atoms. 11674 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2790 (Rfree = 0.000) for 6394 atoms. Found 35 (35 requested) and removed 29 (17 requested) atoms. Cycle 12: After refmac, R = 0.2566 (Rfree = 0.000) for 6354 atoms. Found 35 (35 requested) and removed 25 (17 requested) atoms. Cycle 13: After refmac, R = 0.2444 (Rfree = 0.000) for 6342 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 14: After refmac, R = 0.2397 (Rfree = 0.000) for 6337 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 15: After refmac, R = 0.2309 (Rfree = 0.000) for 6333 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 2.64 Search for helices and strands: 0 residues in 0 chains, 6573 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 6599 seeds are put forward Round 1: 558 peptides, 64 chains. Longest chain 25 peptides. Score 0.495 Round 2: 612 peptides, 66 chains. Longest chain 26 peptides. Score 0.532 Round 3: 620 peptides, 62 chains. Longest chain 29 peptides. Score 0.553 Round 4: 607 peptides, 56 chains. Longest chain 51 peptides. Score 0.566 Round 5: 620 peptides, 61 chains. Longest chain 41 peptides. Score 0.557 Taking the results from Round 4 Chains 56, Residues 551, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13901 restraints for refining 6395 atoms. 11753 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2856 (Rfree = 0.000) for 6395 atoms. Found 35 (35 requested) and removed 21 (17 requested) atoms. Cycle 17: After refmac, R = 0.2622 (Rfree = 0.000) for 6369 atoms. Found 35 (35 requested) and removed 21 (17 requested) atoms. Cycle 18: After refmac, R = 0.2473 (Rfree = 0.000) for 6350 atoms. Found 32 (35 requested) and removed 21 (17 requested) atoms. Cycle 19: After refmac, R = 0.2445 (Rfree = 0.000) for 6346 atoms. Found 29 (34 requested) and removed 22 (17 requested) atoms. Cycle 20: After refmac, R = 0.2366 (Rfree = 0.000) for 6338 atoms. Found 21 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 2.63 Search for helices and strands: 0 residues in 0 chains, 6586 seeds are put forward NCS extension: 24 residues added (15 deleted due to clashes), 6610 seeds are put forward Round 1: 582 peptides, 68 chains. Longest chain 35 peptides. Score 0.499 Round 2: 610 peptides, 60 chains. Longest chain 38 peptides. Score 0.553 Round 3: 608 peptides, 64 chains. Longest chain 38 peptides. Score 0.536 Round 4: 612 peptides, 61 chains. Longest chain 33 peptides. Score 0.551 Round 5: 609 peptides, 58 chains. Longest chain 35 peptides. Score 0.560 Taking the results from Round 5 Chains 61, Residues 551, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13741 restraints for refining 6395 atoms. 11497 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2530 (Rfree = 0.000) for 6395 atoms. Found 35 (35 requested) and removed 29 (17 requested) atoms. Cycle 22: After refmac, R = 0.2617 (Rfree = 0.000) for 6341 atoms. Found 35 (35 requested) and removed 30 (17 requested) atoms. Cycle 23: After refmac, R = 0.2391 (Rfree = 0.000) for 6325 atoms. Found 29 (34 requested) and removed 22 (17 requested) atoms. Cycle 24: After refmac, R = 0.2354 (Rfree = 0.000) for 6311 atoms. Found 25 (34 requested) and removed 27 (17 requested) atoms. Cycle 25: After refmac, R = 0.2280 (Rfree = 0.000) for 6299 atoms. Found 26 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 2.66 Search for helices and strands: 0 residues in 0 chains, 6519 seeds are put forward NCS extension: 21 residues added (9 deleted due to clashes), 6540 seeds are put forward Round 1: 540 peptides, 69 chains. Longest chain 24 peptides. Score 0.458 Round 2: 585 peptides, 62 chains. Longest chain 32 peptides. Score 0.525 Round 3: 608 peptides, 58 chains. Longest chain 35 peptides. Score 0.559 Round 4: 593 peptides, 52 chains. Longest chain 35 peptides. Score 0.570 Round 5: 605 peptides, 58 chains. Longest chain 31 peptides. Score 0.557 Taking the results from Round 4 Chains 53, Residues 541, Estimated correctness of the model 0.0 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13658 restraints for refining 6397 atoms. 11438 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2552 (Rfree = 0.000) for 6397 atoms. Found 35 (35 requested) and removed 65 (17 requested) atoms. Cycle 27: After refmac, R = 0.2488 (Rfree = 0.000) for 6315 atoms. Found 35 (35 requested) and removed 53 (17 requested) atoms. Cycle 28: After refmac, R = 0.2437 (Rfree = 0.000) for 6272 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. Cycle 29: After refmac, R = 0.2306 (Rfree = 0.000) for 6271 atoms. Found 22 (34 requested) and removed 20 (17 requested) atoms. Cycle 30: After refmac, R = 0.2287 (Rfree = 0.000) for 6268 atoms. Found 17 (34 requested) and removed 45 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 2.63 Search for helices and strands: 0 residues in 0 chains, 6397 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 6419 seeds are put forward Round 1: 566 peptides, 71 chains. Longest chain 22 peptides. Score 0.473 Round 2: 605 peptides, 62 chains. Longest chain 41 peptides. Score 0.541 Round 3: 629 peptides, 60 chains. Longest chain 41 peptides. Score 0.568 Round 4: 608 peptides, 62 chains. Longest chain 45 peptides. Score 0.544 Round 5: 590 peptides, 65 chains. Longest chain 31 peptides. Score 0.518 Taking the results from Round 3 Chains 63, Residues 569, Estimated correctness of the model 0.0 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13358 restraints for refining 6395 atoms. 11010 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2721 (Rfree = 0.000) for 6395 atoms. Found 35 (35 requested) and removed 27 (17 requested) atoms. Cycle 32: After refmac, R = 0.2476 (Rfree = 0.000) for 6352 atoms. Found 35 (35 requested) and removed 27 (17 requested) atoms. Cycle 33: After refmac, R = 0.2408 (Rfree = 0.000) for 6328 atoms. Found 34 (34 requested) and removed 26 (17 requested) atoms. Cycle 34: After refmac, R = 0.2399 (Rfree = 0.000) for 6308 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 35: After refmac, R = 0.2352 (Rfree = 0.000) for 6300 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 2.62 Search for helices and strands: 0 residues in 0 chains, 6519 seeds are put forward NCS extension: 45 residues added (12 deleted due to clashes), 6564 seeds are put forward Round 1: 573 peptides, 72 chains. Longest chain 30 peptides. Score 0.475 Round 2: 620 peptides, 66 chains. Longest chain 25 peptides. Score 0.538 Round 3: 641 peptides, 62 chains. Longest chain 28 peptides. Score 0.569 Round 4: 605 peptides, 68 chains. Longest chain 22 peptides. Score 0.518 Round 5: 607 peptides, 63 chains. Longest chain 26 peptides. Score 0.539 Taking the results from Round 3 Chains 65, Residues 579, Estimated correctness of the model 0.0 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13440 restraints for refining 6396 atoms. 11054 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2585 (Rfree = 0.000) for 6396 atoms. Found 35 (35 requested) and removed 30 (17 requested) atoms. Cycle 37: After refmac, R = 0.2403 (Rfree = 0.000) for 6344 atoms. Found 24 (35 requested) and removed 18 (17 requested) atoms. Cycle 38: After refmac, R = 0.2365 (Rfree = 0.000) for 6324 atoms. Found 25 (34 requested) and removed 19 (17 requested) atoms. Cycle 39: After refmac, R = 0.2294 (Rfree = 0.000) for 6317 atoms. Found 32 (34 requested) and removed 23 (17 requested) atoms. Cycle 40: After refmac, R = 0.2250 (Rfree = 0.000) for 6309 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 2.63 Search for helices and strands: 0 residues in 0 chains, 6530 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 6549 seeds are put forward Round 1: 561 peptides, 81 chains. Longest chain 20 peptides. Score 0.427 Round 2: 588 peptides, 68 chains. Longest chain 31 peptides. Score 0.504 Round 3: 608 peptides, 72 chains. Longest chain 28 peptides. Score 0.505 Round 4: 613 peptides, 63 chains. Longest chain 29 peptides. Score 0.544 Round 5: 597 peptides, 64 chains. Longest chain 26 peptides. Score 0.527 Taking the results from Round 4 Chains 63, Residues 550, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 14064 restraints for refining 6394 atoms. 11927 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2597 (Rfree = 0.000) for 6394 atoms. Found 35 (35 requested) and removed 31 (17 requested) atoms. Cycle 42: After refmac, R = 0.2422 (Rfree = 0.000) for 6358 atoms. Found 35 (35 requested) and removed 24 (17 requested) atoms. Cycle 43: After refmac, R = 0.2376 (Rfree = 0.000) for 6351 atoms. Found 35 (35 requested) and removed 27 (17 requested) atoms. Cycle 44: After refmac, R = 0.2245 (Rfree = 0.000) for 6350 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 45: After refmac, R = 0.2221 (Rfree = 0.000) for 6350 atoms. Found 31 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 2.63 Search for helices and strands: 0 residues in 0 chains, 6611 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 6628 seeds are put forward Round 1: 540 peptides, 77 chains. Longest chain 20 peptides. Score 0.424 Round 2: 578 peptides, 67 chains. Longest chain 28 peptides. Score 0.500 Round 3: 584 peptides, 61 chains. Longest chain 32 peptides. Score 0.528 Round 4: 564 peptides, 60 chains. Longest chain 36 peptides. Score 0.516 Round 5: 554 peptides, 59 chains. Longest chain 29 peptides. Score 0.512 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 523, 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 1ztc-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17528 reflections ( 98.52 % complete ) and 14263 restraints for refining 6397 atoms. 12232 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2460 (Rfree = 0.000) for 6397 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2287 (Rfree = 0.000) for 6339 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.2199 (Rfree = 0.000) for 6305 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.2150 (Rfree = 0.000) for 6278 atoms. TimeTaking 82.08