Mon 24 Dec 08:00:33 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 1vlu-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vlu-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vlu-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.2-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/1vlu-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.2-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 08:00:37 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/1vlu-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.2-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 1033 and 0 Target number of residues in the AU: 1033 Target solvent content: 0.6196 Checking the provided sequence file Detected sequence length: 468 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 936 Adjusted target solvent content: 0.66 Input MTZ file: 1vlu-3.2-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: 20 Cell parameters: 123.109 190.784 125.153 90.000 90.000 90.000 Input sequence file: 1vlu-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 7488 target number of atoms Had to go as low as 0.85 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: 44.569 3.200 Wilson plot Bfac: 61.18 24672 reflections ( 99.89 % complete ) and 0 restraints for refining 8318 atoms. Observations/parameters ratio is 0.74 ------------------------------------------------------ Starting model: R = 0.3423 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3019 (Rfree = 0.000) for 8318 atoms. Found 74 (74 requested) and removed 167 (37 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.13 2.51 Search for helices and strands: 0 residues in 0 chains, 8421 seeds are put forward NCS extension: 0 residues added, 8421 seeds are put forward Round 1: 460 peptides, 64 chains. Longest chain 27 peptides. Score 0.434 Round 2: 560 peptides, 69 chains. Longest chain 30 peptides. Score 0.513 Round 3: 571 peptides, 68 chains. Longest chain 26 peptides. Score 0.528 Round 4: 590 peptides, 65 chains. Longest chain 40 peptides. Score 0.559 Round 5: 601 peptides, 66 chains. Longest chain 46 peptides. Score 0.565 Taking the results from Round 5 Chains 71, Residues 535, Estimated correctness of the model 31.3 % 7 chains (79 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 14065 restraints for refining 6831 atoms. 11753 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2713 (Rfree = 0.000) for 6831 atoms. Found 61 (61 requested) and removed 78 (30 requested) atoms. Cycle 2: After refmac, R = 0.2515 (Rfree = 0.000) for 6730 atoms. Found 52 (61 requested) and removed 52 (30 requested) atoms. Cycle 3: After refmac, R = 0.2413 (Rfree = 0.000) for 6688 atoms. Found 37 (60 requested) and removed 43 (30 requested) atoms. Cycle 4: After refmac, R = 0.2346 (Rfree = 0.000) for 6657 atoms. Found 21 (59 requested) and removed 35 (29 requested) atoms. Cycle 5: After refmac, R = 0.2298 (Rfree = 0.000) for 6629 atoms. Found 23 (59 requested) and removed 33 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 2.51 Search for helices and strands: 0 residues in 0 chains, 6880 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 6911 seeds are put forward Round 1: 562 peptides, 59 chains. Longest chain 32 peptides. Score 0.559 Round 2: 593 peptides, 58 chains. Longest chain 39 peptides. Score 0.591 Round 3: 602 peptides, 54 chains. Longest chain 47 peptides. Score 0.615 Round 4: 595 peptides, 58 chains. Longest chain 41 peptides. Score 0.592 Round 5: 605 peptides, 60 chains. Longest chain 34 peptides. Score 0.593 Taking the results from Round 3 Chains 56, Residues 548, Estimated correctness of the model 45.0 % 5 chains (136 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13278 restraints for refining 6835 atoms. 10639 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2659 (Rfree = 0.000) for 6835 atoms. Found 61 (61 requested) and removed 75 (30 requested) atoms. Cycle 7: After refmac, R = 0.2483 (Rfree = 0.000) for 6783 atoms. Found 49 (61 requested) and removed 40 (30 requested) atoms. Cycle 8: After refmac, R = 0.2392 (Rfree = 0.000) for 6764 atoms. Found 18 (60 requested) and removed 42 (30 requested) atoms. Cycle 9: After refmac, R = 0.2290 (Rfree = 0.000) for 6724 atoms. Found 24 (60 requested) and removed 34 (30 requested) atoms. Cycle 10: After refmac, R = 0.2249 (Rfree = 0.000) for 6697 atoms. Found 17 (60 requested) and removed 34 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 2.50 Search for helices and strands: 0 residues in 0 chains, 6912 seeds are put forward NCS extension: 34 residues added (14 deleted due to clashes), 6946 seeds are put forward Round 1: 585 peptides, 63 chains. Longest chain 33 peptides. Score 0.563 Round 2: 590 peptides, 56 chains. Longest chain 45 peptides. Score 0.596 Round 3: 607 peptides, 56 chains. Longest chain 33 peptides. Score 0.611 Round 4: 619 peptides, 55 chains. Longest chain 45 peptides. Score 0.624 Round 5: 615 peptides, 57 chains. Longest chain 47 peptides. Score 0.613 Taking the results from Round 4 Chains 61, Residues 564, Estimated correctness of the model 47.4 % 13 chains (207 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 12390 restraints for refining 6833 atoms. 9442 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2666 (Rfree = 0.000) for 6833 atoms. Found 61 (61 requested) and removed 66 (30 requested) atoms. Cycle 12: After refmac, R = 0.2495 (Rfree = 0.000) for 6781 atoms. Found 47 (61 requested) and removed 40 (30 requested) atoms. Cycle 13: After refmac, R = 0.2416 (Rfree = 0.000) for 6773 atoms. Found 34 (60 requested) and removed 35 (30 requested) atoms. Cycle 14: After refmac, R = 0.2357 (Rfree = 0.000) for 6752 atoms. Found 19 (60 requested) and removed 33 (30 requested) atoms. Cycle 15: After refmac, R = 0.2313 (Rfree = 0.000) for 6728 atoms. Found 21 (60 requested) and removed 34 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 2.51 Search for helices and strands: 0 residues in 0 chains, 6925 seeds are put forward NCS extension: 18 residues added (18 deleted due to clashes), 6943 seeds are put forward Round 1: 564 peptides, 64 chains. Longest chain 26 peptides. Score 0.539 Round 2: 600 peptides, 53 chains. Longest chain 45 peptides. Score 0.617 Round 3: 610 peptides, 58 chains. Longest chain 34 peptides. Score 0.605 Round 4: 588 peptides, 55 chains. Longest chain 32 peptides. Score 0.599 Round 5: 594 peptides, 61 chains. Longest chain 27 peptides. Score 0.579 Taking the results from Round 2 Chains 58, Residues 547, Estimated correctness of the model 45.6 % 14 chains (240 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 12364 restraints for refining 6833 atoms. 9379 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2633 (Rfree = 0.000) for 6833 atoms. Found 58 (61 requested) and removed 71 (30 requested) atoms. Cycle 17: After refmac, R = 0.2443 (Rfree = 0.000) for 6793 atoms. Found 32 (61 requested) and removed 43 (30 requested) atoms. Cycle 18: After refmac, R = 0.2378 (Rfree = 0.000) for 6764 atoms. Found 20 (60 requested) and removed 30 (30 requested) atoms. Cycle 19: After refmac, R = 0.2339 (Rfree = 0.000) for 6742 atoms. Found 10 (60 requested) and removed 30 (30 requested) atoms. Cycle 20: After refmac, R = 0.2312 (Rfree = 0.000) for 6710 atoms. Found 26 (60 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 2.53 Search for helices and strands: 0 residues in 0 chains, 6956 seeds are put forward NCS extension: 49 residues added (35 deleted due to clashes), 7005 seeds are put forward Round 1: 569 peptides, 58 chains. Longest chain 66 peptides. Score 0.570 Round 2: 592 peptides, 57 chains. Longest chain 44 peptides. Score 0.594 Round 3: 579 peptides, 58 chains. Longest chain 33 peptides. Score 0.579 Round 4: 588 peptides, 65 chains. Longest chain 33 peptides. Score 0.557 Round 5: 600 peptides, 60 chains. Longest chain 43 peptides. Score 0.589 Taking the results from Round 2 Chains 64, Residues 535, Estimated correctness of the model 39.4 % 11 chains (185 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 12871 restraints for refining 6835 atoms. 10104 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2592 (Rfree = 0.000) for 6835 atoms. Found 57 (61 requested) and removed 59 (30 requested) atoms. Cycle 22: After refmac, R = 0.2425 (Rfree = 0.000) for 6807 atoms. Found 38 (61 requested) and removed 36 (30 requested) atoms. Cycle 23: After refmac, R = 0.2344 (Rfree = 0.000) for 6795 atoms. Found 17 (61 requested) and removed 36 (30 requested) atoms. Cycle 24: After refmac, R = 0.2310 (Rfree = 0.000) for 6769 atoms. Found 13 (60 requested) and removed 33 (30 requested) atoms. Cycle 25: After refmac, R = 0.2268 (Rfree = 0.000) for 6745 atoms. Found 14 (60 requested) and removed 31 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 2.53 Search for helices and strands: 0 residues in 0 chains, 6956 seeds are put forward NCS extension: 9 residues added (15 deleted due to clashes), 6965 seeds are put forward Round 1: 541 peptides, 68 chains. Longest chain 24 peptides. Score 0.499 Round 2: 577 peptides, 63 chains. Longest chain 29 peptides. Score 0.556 Round 3: 591 peptides, 66 chains. Longest chain 34 peptides. Score 0.556 Round 4: 615 peptides, 62 chains. Longest chain 40 peptides. Score 0.593 Round 5: 578 peptides, 60 chains. Longest chain 45 peptides. Score 0.569 Taking the results from Round 4 Chains 67, Residues 553, Estimated correctness of the model 39.2 % 8 chains (136 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13336 restraints for refining 6835 atoms. 10698 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2705 (Rfree = 0.000) for 6835 atoms. Found 61 (61 requested) and removed 62 (30 requested) atoms. Cycle 27: After refmac, R = 0.2472 (Rfree = 0.000) for 6814 atoms. Found 50 (61 requested) and removed 36 (30 requested) atoms. Cycle 28: After refmac, R = 0.2408 (Rfree = 0.000) for 6819 atoms. Found 26 (61 requested) and removed 31 (30 requested) atoms. Cycle 29: After refmac, R = 0.2376 (Rfree = 0.000) for 6803 atoms. Found 21 (61 requested) and removed 32 (30 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2357 (Rfree = 0.000) for 6783 atoms. Found 20 (60 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 2.55 Search for helices and strands: 0 residues in 0 chains, 6989 seeds are put forward NCS extension: 29 residues added (18 deleted due to clashes), 7018 seeds are put forward Round 1: 535 peptides, 67 chains. Longest chain 23 peptides. Score 0.498 Round 2: 556 peptides, 57 chains. Longest chain 36 peptides. Score 0.562 Round 3: 569 peptides, 61 chains. Longest chain 37 peptides. Score 0.557 Round 4: 549 peptides, 60 chains. Longest chain 32 peptides. Score 0.543 Round 5: 560 peptides, 62 chains. Longest chain 34 peptides. Score 0.544 Taking the results from Round 2 Chains 64, Residues 499, Estimated correctness of the model 30.4 % 10 chains (162 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13322 restraints for refining 6836 atoms. 10780 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2606 (Rfree = 0.000) for 6836 atoms. Found 61 (61 requested) and removed 58 (30 requested) atoms. Cycle 32: After refmac, R = 0.2486 (Rfree = 0.000) for 6816 atoms. Found 35 (61 requested) and removed 36 (30 requested) atoms. Cycle 33: After refmac, R = 0.2465 (Rfree = 0.000) for 6807 atoms. Found 23 (61 requested) and removed 32 (30 requested) atoms. Cycle 34: After refmac, R = 0.2453 (Rfree = 0.000) for 6795 atoms. Found 16 (60 requested) and removed 35 (30 requested) atoms. Cycle 35: After refmac, R = 0.2433 (Rfree = 0.000) for 6773 atoms. Found 12 (60 requested) and removed 31 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 2.57 Search for helices and strands: 0 residues in 0 chains, 6975 seeds are put forward NCS extension: 17 residues added (8 deleted due to clashes), 6992 seeds are put forward Round 1: 534 peptides, 65 chains. Longest chain 28 peptides. Score 0.506 Round 2: 549 peptides, 61 chains. Longest chain 22 peptides. Score 0.538 Round 3: 567 peptides, 65 chains. Longest chain 24 peptides. Score 0.538 Round 4: 571 peptides, 59 chains. Longest chain 36 peptides. Score 0.567 Round 5: 566 peptides, 60 chains. Longest chain 21 peptides. Score 0.559 Taking the results from Round 4 Chains 65, Residues 512, Estimated correctness of the model 31.9 % 10 chains (128 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13695 restraints for refining 6836 atoms. 11265 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2674 (Rfree = 0.000) for 6836 atoms. Found 61 (61 requested) and removed 47 (30 requested) atoms. Cycle 37: After refmac, R = 0.2530 (Rfree = 0.000) for 6828 atoms. Found 38 (61 requested) and removed 41 (30 requested) atoms. Cycle 38: After refmac, R = 0.2455 (Rfree = 0.000) for 6816 atoms. Found 17 (61 requested) and removed 33 (30 requested) atoms. Cycle 39: After refmac, R = 0.2448 (Rfree = 0.000) for 6796 atoms. Found 13 (61 requested) and removed 30 (30 requested) atoms. Cycle 40: After refmac, R = 0.2446 (Rfree = 0.000) for 6775 atoms. Found 12 (60 requested) and removed 31 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 2.54 Search for helices and strands: 0 residues in 0 chains, 7002 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 7016 seeds are put forward Round 1: 530 peptides, 65 chains. Longest chain 36 peptides. Score 0.502 Round 2: 570 peptides, 63 chains. Longest chain 25 peptides. Score 0.549 Round 3: 575 peptides, 62 chains. Longest chain 28 peptides. Score 0.558 Round 4: 567 peptides, 56 chains. Longest chain 30 peptides. Score 0.577 Round 5: 580 peptides, 64 chains. Longest chain 27 peptides. Score 0.554 Taking the results from Round 4 Chains 58, Residues 511, Estimated correctness of the model 34.7 % 4 chains (75 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 14215 restraints for refining 6835 atoms. 11956 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2677 (Rfree = 0.000) for 6835 atoms. Found 61 (61 requested) and removed 44 (30 requested) atoms. Cycle 42: After refmac, R = 0.2517 (Rfree = 0.000) for 6830 atoms. Found 31 (61 requested) and removed 33 (30 requested) atoms. Cycle 43: After refmac, R = 0.2451 (Rfree = 0.000) for 6815 atoms. Found 24 (61 requested) and removed 30 (30 requested) atoms. Cycle 44: After refmac, R = 0.2451 (Rfree = 0.000) for 6801 atoms. Found 15 (61 requested) and removed 30 (30 requested) atoms. Cycle 45: After refmac, R = 0.2408 (Rfree = 0.000) for 6779 atoms. Found 15 (60 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.55 Search for helices and strands: 0 residues in 0 chains, 7004 seeds are put forward NCS extension: 18 residues added (9 deleted due to clashes), 7022 seeds are put forward Round 1: 469 peptides, 59 chains. Longest chain 22 peptides. Score 0.468 Round 2: 537 peptides, 58 chains. Longest chain 22 peptides. Score 0.541 Round 3: 539 peptides, 64 chains. Longest chain 21 peptides. Score 0.515 Round 4: 537 peptides, 60 chains. Longest chain 41 peptides. Score 0.532 Round 5: 548 peptides, 63 chains. Longest chain 25 peptides. Score 0.529 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 479, Estimated correctness of the model 24.2 % 5 chains (76 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input Building loops using Loopy2018 61 chains (479 residues) following loop building 5 chains (76 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 24672 reflections ( 99.89 % complete ) and 14363 restraints for refining 6836 atoms. 12223 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2563 (Rfree = 0.000) for 6836 atoms. Found 0 (61 requested) and removed 8 (30 requested) atoms. Cycle 47: After refmac, R = 0.2520 (Rfree = 0.000) for 6811 atoms. Found 0 (61 requested) and removed 4 (30 requested) atoms. Cycle 48: After refmac, R = 0.2524 (Rfree = 0.000) for 6799 atoms. Found 0 (61 requested) and removed 3 (30 requested) atoms. Cycle 49: After refmac, R = 0.2475 (Rfree = 0.000) for 6793 atoms. Found 0 (60 requested) and removed 3 (30 requested) atoms. Writing output files ... TimeTaking 91.32