null Sun 23 Dec 22:22:53 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 1zbt-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zbt-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zbt-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-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/1zbt-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-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 ============================================================ Sun 23 Dec 22:23:03 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/1zbt-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-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 329 and 0 Target number of residues in the AU: 329 Target solvent content: 0.6311 Checking the provided sequence file Detected sequence length: 371 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 371 Adjusted target solvent content: 0.58 Input MTZ file: 1zbt-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: 96 Cell parameters: 71.823 71.823 187.134 90.000 90.000 90.000 Input sequence file: 1zbt-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2968 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 Loops will be built when appropriate and at the last cycle Resolution range: 28.608 3.400 Wilson plot Bfac: 66.69 7240 reflections ( 99.72 % complete ) and 0 restraints for refining 3299 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3329 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3627 (Rfree = 0.000) for 3299 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.05 Search for helices and strands: 0 residues in 0 chains, 3345 seeds are put forward Round 1: 131 peptides, 20 chains. Longest chain 15 peptides. Score 0.380 Round 2: 181 peptides, 23 chains. Longest chain 15 peptides. Score 0.500 Round 3: 187 peptides, 19 chains. Longest chain 26 peptides. Score 0.571 Round 4: 188 peptides, 18 chains. Longest chain 36 peptides. Score 0.586 Round 5: 199 peptides, 18 chains. Longest chain 38 peptides. Score 0.615 Taking the results from Round 5 Chains 20, Residues 181, Estimated correctness of the model 33.5 % 3 chains (54 residues) have been docked in sequence ------------------------------------------------------ 7240 reflections ( 99.72 % complete ) and 5293 restraints for refining 2627 atoms. 4372 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3409 (Rfree = 0.000) for 2627 atoms. Found 19 (19 requested) and removed 35 (9 requested) atoms. Cycle 2: After refmac, R = 0.3323 (Rfree = 0.000) for 2502 atoms. Found 19 (19 requested) and removed 38 (9 requested) atoms. Cycle 3: After refmac, R = 0.2954 (Rfree = 0.000) for 2436 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 4: After refmac, R = 0.2889 (Rfree = 0.000) for 2411 atoms. Found 13 (18 requested) and removed 15 (9 requested) atoms. Cycle 5: After refmac, R = 0.3054 (Rfree = 0.000) for 2382 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 2.99 Search for helices and strands: 0 residues in 0 chains, 2463 seeds are put forward Round 1: 187 peptides, 25 chains. Longest chain 18 peptides. Score 0.490 Round 2: 216 peptides, 21 chains. Longest chain 48 peptides. Score 0.621 Round 3: 196 peptides, 22 chains. Longest chain 22 peptides. Score 0.557 Round 4: 197 peptides, 21 chains. Longest chain 28 peptides. Score 0.572 Round 5: 193 peptides, 22 chains. Longest chain 23 peptides. Score 0.548 Taking the results from Round 2 Chains 24, Residues 195, Estimated correctness of the model 35.4 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 7240 reflections ( 99.72 % complete ) and 4634 restraints for refining 2401 atoms. 3723 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3098 (Rfree = 0.000) for 2401 atoms. Found 18 (18 requested) and removed 31 (9 requested) atoms. Cycle 7: After refmac, R = 0.3024 (Rfree = 0.000) for 2356 atoms. Found 12 (18 requested) and removed 19 (9 requested) atoms. Cycle 8: After refmac, R = 0.2960 (Rfree = 0.000) for 2328 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 9: After refmac, R = 0.2836 (Rfree = 0.000) for 2310 atoms. Found 16 (17 requested) and removed 14 (8 requested) atoms. Cycle 10: After refmac, R = 0.2645 (Rfree = 0.000) for 2298 atoms. Found 8 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 2.95 Search for helices and strands: 0 residues in 0 chains, 2375 seeds are put forward Round 1: 180 peptides, 23 chains. Longest chain 26 peptides. Score 0.497 Round 2: 192 peptides, 20 chains. Longest chain 42 peptides. Score 0.571 Round 3: 191 peptides, 22 chains. Longest chain 24 peptides. Score 0.543 Round 4: 195 peptides, 20 chains. Longest chain 50 peptides. Score 0.579 Round 5: 198 peptides, 22 chains. Longest chain 29 peptides. Score 0.562 Taking the results from Round 4 Chains 21, Residues 175, Estimated correctness of the model 21.7 % 4 chains (76 residues) have been docked in sequence ------------------------------------------------------ 7240 reflections ( 99.72 % complete ) and 4622 restraints for refining 2497 atoms. 3667 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2986 (Rfree = 0.000) for 2497 atoms. Found 16 (18 requested) and removed 37 (9 requested) atoms. Cycle 12: After refmac, R = 0.2783 (Rfree = 0.000) for 2446 atoms. Found 8 (18 requested) and removed 22 (9 requested) atoms. Cycle 13: After refmac, R = 0.2686 (Rfree = 0.000) for 2418 atoms. Found 9 (18 requested) and removed 19 (9 requested) atoms. Cycle 14: After refmac, R = 0.2612 (Rfree = 0.000) for 2401 atoms. Found 3 (18 requested) and removed 16 (9 requested) atoms. Cycle 15: After refmac, R = 0.2549 (Rfree = 0.000) for 2375 atoms. Found 8 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 2.95 Search for helices and strands: 0 residues in 0 chains, 2463 seeds are put forward Round 1: 177 peptides, 24 chains. Longest chain 26 peptides. Score 0.474 Round 2: 199 peptides, 22 chains. Longest chain 29 peptides. Score 0.565 Round 3: 193 peptides, 23 chains. Longest chain 41 peptides. Score 0.535 Round 4: 199 peptides, 21 chains. Longest chain 38 peptides. Score 0.577 Round 5: 201 peptides, 22 chains. Longest chain 42 peptides. Score 0.570 Taking the results from Round 4 Chains 21, Residues 178, Estimated correctness of the model 21.0 % 1 chains (37 residues) have been docked in sequence ------------------------------------------------------ 7240 reflections ( 99.72 % complete ) and 4904 restraints for refining 2490 atoms. 4067 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2881 (Rfree = 0.000) for 2490 atoms. Found 10 (18 requested) and removed 39 (9 requested) atoms. Cycle 17: After refmac, R = 0.2738 (Rfree = 0.000) for 2441 atoms. Found 10 (18 requested) and removed 25 (9 requested) atoms. Cycle 18: After refmac, R = 0.2670 (Rfree = 0.000) for 2416 atoms. Found 6 (18 requested) and removed 14 (9 requested) atoms. Cycle 19: After refmac, R = 0.2611 (Rfree = 0.000) for 2402 atoms. Found 2 (18 requested) and removed 12 (9 requested) atoms. Cycle 20: After refmac, R = 0.2547 (Rfree = 0.000) for 2388 atoms. Found 4 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 2.96 Search for helices and strands: 0 residues in 0 chains, 2467 seeds are put forward Round 1: 177 peptides, 24 chains. Longest chain 18 peptides. Score 0.474 Round 2: 197 peptides, 23 chains. Longest chain 46 peptides. Score 0.546 Round 3: 203 peptides, 22 chains. Longest chain 48 peptides. Score 0.576 Round 4: 205 peptides, 24 chains. Longest chain 33 peptides. Score 0.556 Round 5: 195 peptides, 24 chains. Longest chain 26 peptides. Score 0.528 Taking the results from Round 3 Chains 23, Residues 181, Estimated correctness of the model 20.7 % 3 chains (67 residues) have been docked in sequence ------------------------------------------------------ 7240 reflections ( 99.72 % complete ) and 4613 restraints for refining 2560 atoms. 3653 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2860 (Rfree = 0.000) for 2560 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 22: After refmac, R = 0.2706 (Rfree = 0.000) for 2532 atoms. Found 13 (19 requested) and removed 22 (9 requested) atoms. Cycle 23: After refmac, R = 0.2642 (Rfree = 0.000) for 2506 atoms. Found 6 (19 requested) and removed 16 (9 requested) atoms. Cycle 24: After refmac, R = 0.2648 (Rfree = 0.000) for 2487 atoms. Found 4 (18 requested) and removed 12 (9 requested) atoms. Cycle 25: After refmac, R = 0.2667 (Rfree = 0.000) for 2474 atoms. Found 6 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 2.97 Search for helices and strands: 0 residues in 0 chains, 2560 seeds are put forward Round 1: 201 peptides, 27 chains. Longest chain 26 peptides. Score 0.505 Round 2: 213 peptides, 22 chains. Longest chain 28 peptides. Score 0.602 Round 3: 214 peptides, 26 chains. Longest chain 28 peptides. Score 0.555 Round 4: 208 peptides, 22 chains. Longest chain 28 peptides. Score 0.589 Round 5: 214 peptides, 23 chains. Longest chain 36 peptides. Score 0.592 Taking the results from Round 2 Chains 23, Residues 191, Estimated correctness of the model 29.3 % 3 chains (51 residues) have been docked in sequence ------------------------------------------------------ 7240 reflections ( 99.72 % complete ) and 4806 restraints for refining 2614 atoms. 3846 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2860 (Rfree = 0.000) for 2614 atoms. Found 14 (19 requested) and removed 35 (9 requested) atoms. Cycle 27: After refmac, R = 0.2841 (Rfree = 0.000) for 2581 atoms. Found 18 (19 requested) and removed 17 (9 requested) atoms. Cycle 28: After refmac, R = 0.2759 (Rfree = 0.000) for 2571 atoms. Found 10 (19 requested) and removed 23 (9 requested) atoms. Cycle 29: After refmac, R = 0.2681 (Rfree = 0.000) for 2544 atoms. Found 9 (19 requested) and removed 22 (9 requested) atoms. Cycle 30: After refmac, R = 0.2675 (Rfree = 0.000) for 2522 atoms. Found 13 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 2.97 Search for helices and strands: 0 residues in 0 chains, 2626 seeds are put forward Round 1: 191 peptides, 25 chains. Longest chain 38 peptides. Score 0.502 Round 2: 207 peptides, 24 chains. Longest chain 22 peptides. Score 0.561 Round 3: 205 peptides, 22 chains. Longest chain 30 peptides. Score 0.581 Round 4: 214 peptides, 21 chains. Longest chain 51 peptides. Score 0.616 Round 5: 219 peptides, 23 chains. Longest chain 47 peptides. Score 0.605 Taking the results from Round 4 Chains 24, Residues 193, Estimated correctness of the model 33.8 % 5 chains (59 residues) have been docked in sequence ------------------------------------------------------ 7240 reflections ( 99.72 % complete ) and 5102 restraints for refining 2699 atoms. 4135 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2950 (Rfree = 0.000) for 2699 atoms. Found 20 (20 requested) and removed 37 (10 requested) atoms. Cycle 32: After refmac, R = 0.2830 (Rfree = 0.000) for 2660 atoms. Found 15 (20 requested) and removed 24 (10 requested) atoms. Cycle 33: After refmac, R = 0.2752 (Rfree = 0.000) for 2635 atoms. Found 13 (20 requested) and removed 17 (10 requested) atoms. Cycle 34: After refmac, R = 0.2685 (Rfree = 0.000) for 2622 atoms. Found 8 (19 requested) and removed 18 (9 requested) atoms. Cycle 35: After refmac, R = 0.2686 (Rfree = 0.000) for 2598 atoms. Found 12 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 2.97 Search for helices and strands: 0 residues in 0 chains, 2685 seeds are put forward Round 1: 170 peptides, 20 chains. Longest chain 31 peptides. Score 0.509 Round 2: 190 peptides, 22 chains. Longest chain 39 peptides. Score 0.540 Round 3: 185 peptides, 23 chains. Longest chain 20 peptides. Score 0.512 Round 4: 195 peptides, 23 chains. Longest chain 26 peptides. Score 0.541 Round 5: 193 peptides, 24 chains. Longest chain 15 peptides. Score 0.522 Taking the results from Round 4 Chains 25, Residues 172, Estimated correctness of the model 8.3 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7240 reflections ( 99.72 % complete ) and 5463 restraints for refining 2699 atoms. 4669 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2874 (Rfree = 0.000) for 2699 atoms. Found 13 (20 requested) and removed 22 (10 requested) atoms. Cycle 37: After refmac, R = 0.2739 (Rfree = 0.000) for 2670 atoms. Found 14 (20 requested) and removed 22 (10 requested) atoms. Cycle 38: After refmac, R = 0.2754 (Rfree = 0.000) for 2650 atoms. Found 11 (20 requested) and removed 17 (10 requested) atoms. Cycle 39: After refmac, R = 0.2682 (Rfree = 0.000) for 2629 atoms. Found 12 (19 requested) and removed 16 (9 requested) atoms. Cycle 40: After refmac, R = 0.2673 (Rfree = 0.000) for 2613 atoms. Found 13 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.02 Search for helices and strands: 0 residues in 0 chains, 2687 seeds are put forward Round 1: 166 peptides, 25 chains. Longest chain 16 peptides. Score 0.423 Round 2: 193 peptides, 27 chains. Longest chain 35 peptides. Score 0.481 Round 3: 183 peptides, 24 chains. Longest chain 22 peptides. Score 0.492 Round 4: 187 peptides, 26 chains. Longest chain 18 peptides. Score 0.476 Round 5: 185 peptides, 25 chains. Longest chain 23 peptides. Score 0.484 Taking the results from Round 3 Chains 25, Residues 159, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7240 reflections ( 99.72 % complete ) and 5525 restraints for refining 2671 atoms. 4798 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2714 (Rfree = 0.000) for 2671 atoms. Found 18 (20 requested) and removed 32 (10 requested) atoms. Cycle 42: After refmac, R = 0.2547 (Rfree = 0.000) for 2644 atoms. Found 6 (20 requested) and removed 18 (10 requested) atoms. Cycle 43: After refmac, R = 0.2475 (Rfree = 0.000) for 2626 atoms. Found 3 (19 requested) and removed 12 (9 requested) atoms. Cycle 44: After refmac, R = 0.2438 (Rfree = 0.000) for 2610 atoms. Found 3 (19 requested) and removed 11 (9 requested) atoms. Cycle 45: After refmac, R = 0.2441 (Rfree = 0.000) for 2597 atoms. Found 7 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 2.98 Search for helices and strands: 0 residues in 0 chains, 2677 seeds are put forward Round 1: 158 peptides, 28 chains. Longest chain 13 peptides. Score 0.350 Round 2: 177 peptides, 25 chains. Longest chain 16 peptides. Score 0.459 Round 3: 179 peptides, 28 chains. Longest chain 15 peptides. Score 0.422 Round 4: 177 peptides, 24 chains. Longest chain 25 peptides. Score 0.474 Round 5: 168 peptides, 23 chains. Longest chain 20 peptides. Score 0.460 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 153, Estimated correctness of the model 0.0 % 3 chains (40 residues) have been docked in sequence Sequence coverage is 25 % Consider running further cycles of model building using 1zbt-3_warpNtrace.pdb as input Building loops using Loopy2018 26 chains (153 residues) following loop building 3 chains (40 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7240 reflections ( 99.72 % complete ) and 5517 restraints for refining 2699 atoms. 4772 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2655 (Rfree = 0.000) for 2699 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2663 (Rfree = 0.000) for 2674 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2532 (Rfree = 0.000) for 2661 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2488 (Rfree = 0.000) for 2649 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:13:26 GMT 2018 Job finished. TimeTaking 50.55 Used memory is bytes: 10256592