Mon 24 Dec 07:27:46 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 2hx1-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hx1-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hx1-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.4-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/2hx1-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.4-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 07:27:51 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/2hx1-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.4-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 868 and 0 Target number of residues in the AU: 868 Target solvent content: 0.6039 Checking the provided sequence file Detected sequence length: 284 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1136 Adjusted target solvent content: 0.48 Input MTZ file: 2hx1-3.4-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: 65.624 119.462 151.274 90.000 90.000 90.000 Input sequence file: 2hx1-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 9088 target number of atoms Had to go as low as 0.75 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: 93.753 3.400 Wilson plot Bfac: 54.11 16942 reflections ( 99.75 % complete ) and 0 restraints for refining 10096 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3316 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3085 (Rfree = 0.000) for 10096 atoms. Found 76 (76 requested) and removed 94 (38 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 3.18 Search for helices and strands: 0 residues in 0 chains, 10270 seeds are put forward NCS extension: 0 residues added, 10270 seeds are put forward Round 1: 464 peptides, 87 chains. Longest chain 15 peptides. Score 0.347 Round 2: 652 peptides, 103 chains. Longest chain 22 peptides. Score 0.501 Round 3: 712 peptides, 103 chains. Longest chain 20 peptides. Score 0.568 Round 4: 714 peptides, 93 chains. Longest chain 24 peptides. Score 0.614 Round 5: 751 peptides, 91 chains. Longest chain 27 peptides. Score 0.656 Taking the results from Round 5 Chains 95, Residues 660, Estimated correctness of the model 45.9 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17500 restraints for refining 8258 atoms. 14811 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2769 (Rfree = 0.000) for 8258 atoms. Found 62 (62 requested) and removed 60 (31 requested) atoms. Cycle 2: After refmac, R = 0.2582 (Rfree = 0.000) for 8150 atoms. Found 46 (62 requested) and removed 46 (31 requested) atoms. Cycle 3: After refmac, R = 0.2525 (Rfree = 0.000) for 8112 atoms. Found 55 (61 requested) and removed 43 (30 requested) atoms. Cycle 4: After refmac, R = 0.2398 (Rfree = 0.000) for 8094 atoms. Found 45 (61 requested) and removed 39 (30 requested) atoms. Cycle 5: After refmac, R = 0.2430 (Rfree = 0.000) for 8082 atoms. Found 39 (61 requested) and removed 38 (30 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 8376 seeds are put forward NCS extension: 14 residues added (8 deleted due to clashes), 8390 seeds are put forward Round 1: 659 peptides, 102 chains. Longest chain 17 peptides. Score 0.514 Round 2: 719 peptides, 88 chains. Longest chain 25 peptides. Score 0.640 Round 3: 732 peptides, 87 chains. Longest chain 24 peptides. Score 0.655 Round 4: 738 peptides, 77 chains. Longest chain 41 peptides. Score 0.699 Round 5: 747 peptides, 83 chains. Longest chain 24 peptides. Score 0.684 Taking the results from Round 4 Chains 80, Residues 661, Estimated correctness of the model 57.6 % 3 chains (50 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17736 restraints for refining 8260 atoms. 14996 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2633 (Rfree = 0.000) for 8260 atoms. Found 62 (62 requested) and removed 57 (31 requested) atoms. Cycle 7: After refmac, R = 0.2569 (Rfree = 0.000) for 8219 atoms. Found 58 (62 requested) and removed 46 (31 requested) atoms. Cycle 8: After refmac, R = 0.2493 (Rfree = 0.000) for 8204 atoms. Found 29 (62 requested) and removed 40 (31 requested) atoms. Cycle 9: After refmac, R = 0.2333 (Rfree = 0.000) for 8180 atoms. Found 16 (61 requested) and removed 34 (30 requested) atoms. Cycle 10: After refmac, R = 0.2432 (Rfree = 0.000) for 8146 atoms. Found 28 (61 requested) and removed 39 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.32 Search for helices and strands: 0 residues in 0 chains, 8392 seeds are put forward NCS extension: 15 residues added (5 deleted due to clashes), 8407 seeds are put forward Round 1: 613 peptides, 85 chains. Longest chain 25 peptides. Score 0.546 Round 2: 724 peptides, 78 chains. Longest chain 36 peptides. Score 0.684 Round 3: 711 peptides, 83 chains. Longest chain 29 peptides. Score 0.653 Round 4: 716 peptides, 81 chains. Longest chain 29 peptides. Score 0.665 Round 5: 716 peptides, 86 chains. Longest chain 26 peptides. Score 0.645 Taking the results from Round 2 Chains 83, Residues 646, Estimated correctness of the model 53.7 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17588 restraints for refining 8261 atoms. 14929 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2567 (Rfree = 0.000) for 8261 atoms. Found 62 (62 requested) and removed 55 (31 requested) atoms. Cycle 12: After refmac, R = 0.2504 (Rfree = 0.000) for 8238 atoms. Found 44 (62 requested) and removed 43 (31 requested) atoms. Cycle 13: After refmac, R = 0.2502 (Rfree = 0.000) for 8218 atoms. Found 48 (62 requested) and removed 43 (31 requested) atoms. Cycle 14: After refmac, R = 0.2463 (Rfree = 0.000) for 8209 atoms. Found 50 (62 requested) and removed 49 (31 requested) atoms. Cycle 15: After refmac, R = 0.2446 (Rfree = 0.000) for 8194 atoms. Found 36 (61 requested) and removed 38 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 8436 seeds are put forward NCS extension: 24 residues added (12 deleted due to clashes), 8460 seeds are put forward Round 1: 619 peptides, 94 chains. Longest chain 20 peptides. Score 0.508 Round 2: 675 peptides, 83 chains. Longest chain 36 peptides. Score 0.620 Round 3: 676 peptides, 74 chains. Longest chain 29 peptides. Score 0.659 Round 4: 694 peptides, 80 chains. Longest chain 51 peptides. Score 0.650 Round 5: 704 peptides, 84 chains. Longest chain 30 peptides. Score 0.643 Taking the results from Round 3 Chains 74, Residues 602, Estimated correctness of the model 46.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 18714 restraints for refining 8263 atoms. 16380 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2587 (Rfree = 0.000) for 8263 atoms. Found 62 (62 requested) and removed 37 (31 requested) atoms. Cycle 17: After refmac, R = 0.2545 (Rfree = 0.000) for 8267 atoms. Found 61 (62 requested) and removed 44 (31 requested) atoms. Cycle 18: After refmac, R = 0.2509 (Rfree = 0.000) for 8269 atoms. Found 62 (62 requested) and removed 44 (31 requested) atoms. Cycle 19: After refmac, R = 0.2487 (Rfree = 0.000) for 8272 atoms. Found 60 (62 requested) and removed 40 (31 requested) atoms. Cycle 20: After refmac, R = 0.2436 (Rfree = 0.000) for 8284 atoms. Found 47 (62 requested) and removed 42 (31 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 8566 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 8595 seeds are put forward Round 1: 607 peptides, 92 chains. Longest chain 32 peptides. Score 0.504 Round 2: 665 peptides, 84 chains. Longest chain 25 peptides. Score 0.606 Round 3: 712 peptides, 76 chains. Longest chain 33 peptides. Score 0.682 Round 4: 696 peptides, 78 chains. Longest chain 31 peptides. Score 0.660 Round 5: 707 peptides, 87 chains. Longest chain 24 peptides. Score 0.633 Taking the results from Round 3 Chains 80, Residues 636, Estimated correctness of the model 53.1 % 5 chains (54 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17801 restraints for refining 8261 atoms. 15102 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2559 (Rfree = 0.000) for 8261 atoms. Found 59 (62 requested) and removed 45 (31 requested) atoms. Cycle 22: After refmac, R = 0.2434 (Rfree = 0.000) for 8245 atoms. Found 39 (62 requested) and removed 35 (31 requested) atoms. Cycle 23: After refmac, R = 0.2365 (Rfree = 0.000) for 8223 atoms. Found 42 (62 requested) and removed 32 (31 requested) atoms. Cycle 24: After refmac, R = 0.2304 (Rfree = 0.000) for 8209 atoms. Found 37 (62 requested) and removed 38 (31 requested) atoms. Cycle 25: After refmac, R = 0.2238 (Rfree = 0.000) for 8193 atoms. Found 33 (61 requested) and removed 35 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 8457 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 8468 seeds are put forward Round 1: 611 peptides, 91 chains. Longest chain 22 peptides. Score 0.514 Round 2: 695 peptides, 86 chains. Longest chain 28 peptides. Score 0.626 Round 3: 705 peptides, 94 chains. Longest chain 18 peptides. Score 0.601 Round 4: 712 peptides, 85 chains. Longest chain 38 peptides. Score 0.646 Round 5: 700 peptides, 86 chains. Longest chain 26 peptides. Score 0.630 Taking the results from Round 4 Chains 85, Residues 627, Estimated correctness of the model 43.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 18470 restraints for refining 8262 atoms. 16047 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2540 (Rfree = 0.000) for 8262 atoms. Found 62 (62 requested) and removed 42 (31 requested) atoms. Cycle 27: After refmac, R = 0.2454 (Rfree = 0.000) for 8256 atoms. Found 58 (62 requested) and removed 39 (31 requested) atoms. Cycle 28: After refmac, R = 0.2421 (Rfree = 0.000) for 8263 atoms. Found 54 (62 requested) and removed 39 (31 requested) atoms. Cycle 29: After refmac, R = 0.2353 (Rfree = 0.000) for 8262 atoms. Found 56 (62 requested) and removed 34 (31 requested) atoms. Cycle 30: After refmac, R = 0.2345 (Rfree = 0.000) for 8271 atoms. Found 56 (62 requested) and removed 36 (31 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 8555 seeds are put forward NCS extension: 34 residues added (14 deleted due to clashes), 8589 seeds are put forward Round 1: 565 peptides, 99 chains. Longest chain 14 peptides. Score 0.415 Round 2: 644 peptides, 84 chains. Longest chain 30 peptides. Score 0.584 Round 3: 632 peptides, 88 chains. Longest chain 24 peptides. Score 0.553 Round 4: 630 peptides, 82 chains. Longest chain 25 peptides. Score 0.579 Round 5: 672 peptides, 91 chains. Longest chain 25 peptides. Score 0.581 Taking the results from Round 2 Chains 84, Residues 560, Estimated correctness of the model 23.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 18814 restraints for refining 8262 atoms. 16658 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2377 (Rfree = 0.000) for 8262 atoms. Found 60 (62 requested) and removed 35 (31 requested) atoms. Cycle 32: After refmac, R = 0.2310 (Rfree = 0.000) for 8268 atoms. Found 59 (62 requested) and removed 39 (31 requested) atoms. Cycle 33: After refmac, R = 0.2278 (Rfree = 0.000) for 8281 atoms. Found 43 (62 requested) and removed 36 (31 requested) atoms. Cycle 34: After refmac, R = 0.2297 (Rfree = 0.000) for 8278 atoms. Found 44 (62 requested) and removed 37 (31 requested) atoms. Cycle 35: After refmac, R = 0.2345 (Rfree = 0.000) for 8278 atoms. Found 42 (62 requested) and removed 34 (31 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 8495 seeds are put forward NCS extension: 13 residues added (6 deleted due to clashes), 8508 seeds are put forward Round 1: 548 peptides, 93 chains. Longest chain 14 peptides. Score 0.426 Round 2: 620 peptides, 80 chains. Longest chain 28 peptides. Score 0.578 Round 3: 626 peptides, 85 chains. Longest chain 18 peptides. Score 0.561 Round 4: 645 peptides, 86 chains. Longest chain 27 peptides. Score 0.576 Round 5: 642 peptides, 85 chains. Longest chain 22 peptides. Score 0.578 Taking the results from Round 5 Chains 85, Residues 557, Estimated correctness of the model 21.3 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 18520 restraints for refining 8263 atoms. 16210 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2502 (Rfree = 0.000) for 8263 atoms. Found 62 (62 requested) and removed 41 (31 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2412 (Rfree = 0.000) for 8257 atoms. Found 42 (62 requested) and removed 35 (31 requested) atoms. Cycle 38: After refmac, R = 0.2390 (Rfree = 0.000) for 8247 atoms. Found 28 (62 requested) and removed 41 (31 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2405 (Rfree = 0.000) for 8225 atoms. Found 39 (62 requested) and removed 38 (31 requested) atoms. Cycle 40: After refmac, R = 0.2361 (Rfree = 0.000) for 8211 atoms. Found 33 (62 requested) and removed 33 (31 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 8419 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 8434 seeds are put forward Round 1: 519 peptides, 85 chains. Longest chain 16 peptides. Score 0.433 Round 2: 590 peptides, 78 chains. Longest chain 31 peptides. Score 0.555 Round 3: 587 peptides, 79 chains. Longest chain 20 peptides. Score 0.547 Round 4: 603 peptides, 77 chains. Longest chain 31 peptides. Score 0.574 Round 5: 567 peptides, 78 chains. Longest chain 21 peptides. Score 0.530 Taking the results from Round 4 Chains 79, Residues 526, Estimated correctness of the model 20.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 18819 restraints for refining 8263 atoms. 16748 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2432 (Rfree = 0.000) for 8263 atoms. Found 48 (62 requested) and removed 38 (31 requested) atoms. Cycle 42: After refmac, R = 0.2308 (Rfree = 0.000) for 8257 atoms. Found 31 (62 requested) and removed 35 (31 requested) atoms. Cycle 43: After refmac, R = 0.2293 (Rfree = 0.000) for 8236 atoms. Found 47 (62 requested) and removed 35 (31 requested) atoms. Cycle 44: After refmac, R = 0.2271 (Rfree = 0.000) for 8237 atoms. Found 62 (62 requested) and removed 37 (31 requested) atoms. Cycle 45: After refmac, R = 0.2271 (Rfree = 0.000) for 8249 atoms. Found 38 (62 requested) and removed 36 (31 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 8455 seeds are put forward NCS extension: 21 residues added (6 deleted due to clashes), 8476 seeds are put forward Round 1: 491 peptides, 87 chains. Longest chain 13 peptides. Score 0.384 Round 2: 562 peptides, 80 chains. Longest chain 22 peptides. Score 0.514 Round 3: 544 peptides, 83 chains. Longest chain 18 peptides. Score 0.476 Round 4: 576 peptides, 79 chains. Longest chain 23 peptides. Score 0.535 Round 5: 552 peptides, 81 chains. Longest chain 18 peptides. Score 0.496 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 79, Residues 497, Estimated correctness of the model 6.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2hx1-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16942 reflections ( 99.75 % complete ) and 19131 restraints for refining 8262 atoms. 17222 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2605 (Rfree = 0.000) for 8262 atoms. Found 0 (62 requested) and removed 31 (31 requested) atoms. Cycle 47: After refmac, R = 0.2587 (Rfree = 0.000) for 8210 atoms. Found 0 (62 requested) and removed 31 (31 requested) atoms. Cycle 48: After refmac, R = 0.2462 (Rfree = 0.000) for 8160 atoms. Found 0 (61 requested) and removed 30 (30 requested) atoms. Cycle 49: After refmac, R = 0.2431 (Rfree = 0.000) for 8111 atoms. TimeTaking 81.12