null Tue 25 Dec 19:27:55 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 1ztc-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1ztc-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1ztc-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1ztc-3.4-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/1ztc-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1ztc-3.4-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 ============================================================ Tue 25 Dec 19:28:05 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/1ztc-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1ztc-3.4-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 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-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: 89.783 127.343 152.224 90.000 90.000 90.000 Input sequence file: 1ztc-3.4-parrot-hancs.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 7914 atoms. Observations/parameters ratio is 0.77 ------------------------------------------------------ Starting model: R = 0.3257 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2875 (Rfree = 0.000) for 7914 atoms. Found 59 (59 requested) and removed 47 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 2.41 Search for helices and strands: 0 residues in 0 chains, 8090 seeds are put forward NCS extension: 0 residues added, 8090 seeds are put forward Round 1: 608 peptides, 69 chains. Longest chain 23 peptides. Score 0.517 Round 2: 669 peptides, 58 chains. Longest chain 51 peptides. Score 0.604 Round 3: 660 peptides, 58 chains. Longest chain 29 peptides. Score 0.598 Round 4: 674 peptides, 58 chains. Longest chain 51 peptides. Score 0.608 Round 5: 669 peptides, 54 chains. Longest chain 34 peptides. Score 0.618 Taking the results from Round 5 Chains 56, Residues 615, Estimated correctness of the model 34.4 % 4 chains (75 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 12661 restraints for refining 6428 atoms. 9937 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2678 (Rfree = 0.000) for 6428 atoms. Found 48 (48 requested) and removed 36 (24 requested) atoms. Cycle 2: After refmac, R = 0.2527 (Rfree = 0.000) for 6352 atoms. Found 48 (48 requested) and removed 39 (24 requested) atoms. Cycle 3: After refmac, R = 0.2459 (Rfree = 0.000) for 6324 atoms. Found 48 (48 requested) and removed 37 (24 requested) atoms. Cycle 4: After refmac, R = 0.2402 (Rfree = 0.000) for 6314 atoms. Found 33 (47 requested) and removed 33 (23 requested) atoms. Cycle 5: After refmac, R = 0.2348 (Rfree = 0.000) for 6304 atoms. Found 34 (47 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 2.43 Search for helices and strands: 0 residues in 0 chains, 6487 seeds are put forward NCS extension: 15 residues added (16 deleted due to clashes), 6502 seeds are put forward Round 1: 675 peptides, 62 chains. Longest chain 30 peptides. Score 0.594 Round 2: 687 peptides, 51 chains. Longest chain 44 peptides. Score 0.640 Round 3: 697 peptides, 56 chains. Longest chain 51 peptides. Score 0.630 Round 4: 667 peptides, 51 chains. Longest chain 49 peptides. Score 0.627 Round 5: 675 peptides, 53 chains. Longest chain 57 peptides. Score 0.626 Taking the results from Round 2 Chains 55, Residues 636, Estimated correctness of the model 41.2 % 6 chains (107 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 12239 restraints for refining 6428 atoms. 9310 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2605 (Rfree = 0.000) for 6428 atoms. Found 48 (48 requested) and removed 43 (24 requested) atoms. Cycle 7: After refmac, R = 0.2407 (Rfree = 0.000) for 6388 atoms. Found 48 (48 requested) and removed 31 (24 requested) atoms. Cycle 8: After refmac, R = 0.2291 (Rfree = 0.000) for 6378 atoms. Found 48 (48 requested) and removed 34 (24 requested) atoms. Cycle 9: After refmac, R = 0.2211 (Rfree = 0.000) for 6372 atoms. Found 34 (48 requested) and removed 29 (24 requested) atoms. Cycle 10: After refmac, R = 0.2160 (Rfree = 0.000) for 6364 atoms. Found 28 (48 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 2.42 Search for helices and strands: 0 residues in 0 chains, 6536 seeds are put forward NCS extension: 25 residues added (31 deleted due to clashes), 6561 seeds are put forward Round 1: 658 peptides, 60 chains. Longest chain 32 peptides. Score 0.589 Round 2: 686 peptides, 49 chains. Longest chain 44 peptides. Score 0.646 Round 3: 686 peptides, 56 chains. Longest chain 45 peptides. Score 0.623 Round 4: 662 peptides, 49 chains. Longest chain 50 peptides. Score 0.630 Round 5: 679 peptides, 56 chains. Longest chain 51 peptides. Score 0.618 Taking the results from Round 2 Chains 49, Residues 637, Estimated correctness of the model 43.0 % 3 chains (94 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 12369 restraints for refining 6430 atoms. 9458 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2497 (Rfree = 0.000) for 6430 atoms. Found 48 (48 requested) and removed 39 (24 requested) atoms. Cycle 12: After refmac, R = 0.2299 (Rfree = 0.000) for 6400 atoms. Found 45 (48 requested) and removed 27 (24 requested) atoms. Cycle 13: After refmac, R = 0.2181 (Rfree = 0.000) for 6401 atoms. Found 33 (48 requested) and removed 32 (24 requested) atoms. Cycle 14: After refmac, R = 0.2193 (Rfree = 0.000) for 6387 atoms. Found 36 (48 requested) and removed 34 (24 requested) atoms. Cycle 15: After refmac, R = 0.2141 (Rfree = 0.000) for 6378 atoms. Found 22 (48 requested) and removed 28 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 2.41 Search for helices and strands: 0 residues in 0 chains, 6569 seeds are put forward NCS extension: 20 residues added (13 deleted due to clashes), 6589 seeds are put forward Round 1: 661 peptides, 63 chains. Longest chain 44 peptides. Score 0.581 Round 2: 681 peptides, 51 chains. Longest chain 51 peptides. Score 0.636 Round 3: 688 peptides, 60 chains. Longest chain 43 peptides. Score 0.611 Round 4: 701 peptides, 53 chains. Longest chain 45 peptides. Score 0.643 Round 5: 686 peptides, 62 chains. Longest chain 34 peptides. Score 0.602 Taking the results from Round 4 Chains 56, Residues 648, Estimated correctness of the model 42.1 % 5 chains (96 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 12222 restraints for refining 6430 atoms. 9256 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2555 (Rfree = 0.000) for 6430 atoms. Found 48 (48 requested) and removed 53 (24 requested) atoms. Cycle 17: After refmac, R = 0.2316 (Rfree = 0.000) for 6397 atoms. Found 48 (48 requested) and removed 35 (24 requested) atoms. Cycle 18: After refmac, R = 0.2187 (Rfree = 0.000) for 6392 atoms. Found 36 (48 requested) and removed 29 (24 requested) atoms. Cycle 19: After refmac, R = 0.2124 (Rfree = 0.000) for 6387 atoms. Found 20 (48 requested) and removed 26 (24 requested) atoms. Cycle 20: After refmac, R = 0.2246 (Rfree = 0.000) for 6371 atoms. Found 44 (48 requested) and removed 39 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 2.40 Search for helices and strands: 0 residues in 0 chains, 6538 seeds are put forward NCS extension: 15 residues added (29 deleted due to clashes), 6553 seeds are put forward Round 1: 658 peptides, 63 chains. Longest chain 27 peptides. Score 0.578 Round 2: 694 peptides, 64 chains. Longest chain 30 peptides. Score 0.601 Round 3: 693 peptides, 55 chains. Longest chain 32 peptides. Score 0.631 Round 4: 682 peptides, 50 chains. Longest chain 45 peptides. Score 0.640 Round 5: 684 peptides, 59 chains. Longest chain 39 peptides. Score 0.611 Taking the results from Round 4 Chains 57, Residues 632, Estimated correctness of the model 41.2 % 8 chains (179 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11625 restraints for refining 6430 atoms. 8377 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2564 (Rfree = 0.000) for 6430 atoms. Found 48 (48 requested) and removed 61 (24 requested) atoms. Cycle 22: After refmac, R = 0.2358 (Rfree = 0.000) for 6376 atoms. Found 48 (48 requested) and removed 39 (24 requested) atoms. Cycle 23: After refmac, R = 0.2206 (Rfree = 0.000) for 6377 atoms. Found 22 (48 requested) and removed 32 (24 requested) atoms. Cycle 24: After refmac, R = 0.2120 (Rfree = 0.000) for 6356 atoms. Found 15 (48 requested) and removed 27 (24 requested) atoms. Cycle 25: After refmac, R = 0.2083 (Rfree = 0.000) for 6332 atoms. Found 23 (47 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 2.43 Search for helices and strands: 0 residues in 0 chains, 6503 seeds are put forward NCS extension: 22 residues added (22 deleted due to clashes), 6525 seeds are put forward Round 1: 654 peptides, 64 chains. Longest chain 45 peptides. Score 0.572 Round 2: 682 peptides, 62 chains. Longest chain 31 peptides. Score 0.599 Round 3: 693 peptides, 57 chains. Longest chain 42 peptides. Score 0.624 Round 4: 716 peptides, 53 chains. Longest chain 46 peptides. Score 0.653 Round 5: 700 peptides, 55 chains. Longest chain 41 peptides. Score 0.636 Taking the results from Round 4 Chains 60, Residues 663, Estimated correctness of the model 45.0 % 7 chains (172 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11538 restraints for refining 6430 atoms. 8202 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2560 (Rfree = 0.000) for 6430 atoms. Found 48 (48 requested) and removed 59 (24 requested) atoms. Cycle 27: After refmac, R = 0.2339 (Rfree = 0.000) for 6385 atoms. Found 48 (48 requested) and removed 32 (24 requested) atoms. Cycle 28: After refmac, R = 0.2205 (Rfree = 0.000) for 6386 atoms. Found 21 (48 requested) and removed 28 (24 requested) atoms. Cycle 29: After refmac, R = 0.2132 (Rfree = 0.000) for 6367 atoms. Found 21 (48 requested) and removed 25 (24 requested) atoms. Cycle 30: After refmac, R = 0.2096 (Rfree = 0.000) for 6349 atoms. Found 18 (48 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 2.43 Search for helices and strands: 0 residues in 0 chains, 6543 seeds are put forward NCS extension: 26 residues added (21 deleted due to clashes), 6569 seeds are put forward Round 1: 657 peptides, 61 chains. Longest chain 29 peptides. Score 0.585 Round 2: 695 peptides, 57 chains. Longest chain 45 peptides. Score 0.626 Round 3: 709 peptides, 51 chains. Longest chain 46 peptides. Score 0.655 Round 4: 667 peptides, 60 chains. Longest chain 42 peptides. Score 0.596 Round 5: 688 peptides, 58 chains. Longest chain 46 peptides. Score 0.617 Taking the results from Round 3 Chains 56, Residues 658, Estimated correctness of the model 45.6 % 8 chains (210 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11282 restraints for refining 6429 atoms. 7794 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2634 (Rfree = 0.000) for 6429 atoms. Found 48 (48 requested) and removed 45 (24 requested) atoms. Cycle 32: After refmac, R = 0.2413 (Rfree = 0.000) for 6396 atoms. Found 48 (48 requested) and removed 36 (24 requested) atoms. Cycle 33: After refmac, R = 0.2274 (Rfree = 0.000) for 6380 atoms. Found 33 (48 requested) and removed 27 (24 requested) atoms. Cycle 34: After refmac, R = 0.2202 (Rfree = 0.000) for 6367 atoms. Found 26 (48 requested) and removed 29 (24 requested) atoms. Cycle 35: After refmac, R = 0.2143 (Rfree = 0.000) for 6354 atoms. Found 24 (48 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 2.44 Search for helices and strands: 0 residues in 0 chains, 6530 seeds are put forward NCS extension: 14 residues added (26 deleted due to clashes), 6544 seeds are put forward Round 1: 646 peptides, 62 chains. Longest chain 36 peptides. Score 0.573 Round 2: 694 peptides, 62 chains. Longest chain 41 peptides. Score 0.608 Round 3: 683 peptides, 63 chains. Longest chain 32 peptides. Score 0.597 Round 4: 669 peptides, 56 chains. Longest chain 58 peptides. Score 0.611 Round 5: 684 peptides, 58 chains. Longest chain 44 peptides. Score 0.615 Taking the results from Round 5 Chains 65, Residues 626, Estimated correctness of the model 33.5 % 9 chains (187 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11588 restraints for refining 6429 atoms. 8312 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2561 (Rfree = 0.000) for 6429 atoms. Found 48 (48 requested) and removed 44 (24 requested) atoms. Cycle 37: After refmac, R = 0.2344 (Rfree = 0.000) for 6404 atoms. Found 47 (48 requested) and removed 26 (24 requested) atoms. Cycle 38: After refmac, R = 0.2241 (Rfree = 0.000) for 6411 atoms. Found 20 (48 requested) and removed 24 (24 requested) atoms. Cycle 39: After refmac, R = 0.2209 (Rfree = 0.000) for 6387 atoms. Found 21 (48 requested) and removed 25 (24 requested) atoms. Cycle 40: After refmac, R = 0.2169 (Rfree = 0.000) for 6376 atoms. Found 11 (48 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 2.44 Search for helices and strands: 0 residues in 0 chains, 6543 seeds are put forward NCS extension: 12 residues added (19 deleted due to clashes), 6555 seeds are put forward Round 1: 632 peptides, 64 chains. Longest chain 33 peptides. Score 0.555 Round 2: 675 peptides, 53 chains. Longest chain 44 peptides. Score 0.626 Round 3: 663 peptides, 59 chains. Longest chain 51 peptides. Score 0.596 Round 4: 671 peptides, 57 chains. Longest chain 31 peptides. Score 0.609 Round 5: 675 peptides, 56 chains. Longest chain 49 peptides. Score 0.615 Taking the results from Round 2 Chains 59, Residues 622, Estimated correctness of the model 36.9 % 10 chains (230 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11313 restraints for refining 6430 atoms. 7873 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2494 (Rfree = 0.000) for 6430 atoms. Found 48 (48 requested) and removed 51 (24 requested) atoms. Cycle 42: After refmac, R = 0.2300 (Rfree = 0.000) for 6392 atoms. Found 48 (48 requested) and removed 29 (24 requested) atoms. Cycle 43: After refmac, R = 0.2161 (Rfree = 0.000) for 6396 atoms. Found 17 (48 requested) and removed 30 (24 requested) atoms. Cycle 44: After refmac, R = 0.2103 (Rfree = 0.000) for 6376 atoms. Found 19 (48 requested) and removed 26 (24 requested) atoms. Cycle 45: After refmac, R = 0.2055 (Rfree = 0.000) for 6358 atoms. Found 13 (48 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 2.41 Search for helices and strands: 0 residues in 0 chains, 6541 seeds are put forward NCS extension: 28 residues added (33 deleted due to clashes), 6569 seeds are put forward Round 1: 666 peptides, 65 chains. Longest chain 35 peptides. Score 0.577 Round 2: 677 peptides, 58 chains. Longest chain 47 peptides. Score 0.610 Round 3: 678 peptides, 54 chains. Longest chain 44 peptides. Score 0.624 Round 4: 668 peptides, 50 chains. Longest chain 69 peptides. Score 0.631 Round 5: 663 peptides, 60 chains. Longest chain 31 peptides. Score 0.593 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 54, Residues 618, Estimated correctness of the model 38.5 % 9 chains (223 residues) have been docked in sequence Sequence coverage is 36 % Consider running further cycles of model building using 1ztc-3_warpNtrace.pdb as input Building loops using Loopy2018 54 chains (618 residues) following loop building 9 chains (223 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 24384 reflections ( 98.85 % complete ) and 11401 restraints for refining 6430 atoms. 7982 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2562 (Rfree = 0.000) for 6430 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.2390 (Rfree = 0.000) for 6374 atoms. Found 0 (48 requested) and removed 11 (24 requested) atoms. Cycle 48: After refmac, R = 0.2305 (Rfree = 0.000) for 6347 atoms. Found 0 (48 requested) and removed 7 (24 requested) atoms. Cycle 49: After refmac, R = 0.2265 (Rfree = 0.000) for 6336 atoms. Found 0 (47 requested) and removed 5 (23 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:20:33 GMT 2018 Job finished. TimeTaking 112.62 Used memory is bytes: 10716072