Mon 24 Dec 07:28:55 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 2ouw-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ouw-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ouw-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-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/2ouw-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-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 07:29:00 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/2ouw-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-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 153 and 0 Target number of residues in the AU: 153 Target solvent content: 0.6631 Checking the provided sequence file Detected sequence length: 138 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 276 Adjusted target solvent content: 0.39 Input MTZ file: 2ouw-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: 182 Cell parameters: 62.683 62.683 216.710 90.000 90.000 120.000 Input sequence file: 2ouw-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 2208 target number of atoms Had to go as low as 0.70 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: 108.355 3.800 Wilson plot Bfac: 87.14 2882 reflections ( 99.76 % complete ) and 0 restraints for refining 2456 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3822 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3568 (Rfree = 0.000) for 2456 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 4.34 Search for helices and strands: 0 residues in 0 chains, 2508 seeds are put forward NCS extension: 0 residues added, 2508 seeds are put forward Round 1: 94 peptides, 18 chains. Longest chain 11 peptides. Score 0.332 Round 2: 114 peptides, 19 chains. Longest chain 14 peptides. Score 0.436 Round 3: 121 peptides, 19 chains. Longest chain 14 peptides. Score 0.478 Round 4: 132 peptides, 21 chains. Longest chain 12 peptides. Score 0.491 Round 5: 140 peptides, 19 chains. Longest chain 21 peptides. Score 0.581 Taking the results from Round 5 Chains 21, Residues 121, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 4466 restraints for refining 1992 atoms. 3961 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2970 (Rfree = 0.000) for 1992 atoms. Found 10 (10 requested) and removed 40 (5 requested) atoms. Cycle 2: After refmac, R = 0.2867 (Rfree = 0.000) for 1915 atoms. Found 10 (10 requested) and removed 31 (5 requested) atoms. Cycle 3: After refmac, R = 0.2731 (Rfree = 0.000) for 1863 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 4: After refmac, R = 0.2720 (Rfree = 0.000) for 1833 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 5: After refmac, R = 0.2199 (Rfree = 0.000) for 1813 atoms. Found 7 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 4.27 Search for helices and strands: 0 residues in 0 chains, 1867 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1884 seeds are put forward Round 1: 86 peptides, 15 chains. Longest chain 9 peptides. Score 0.366 Round 2: 102 peptides, 18 chains. Longest chain 10 peptides. Score 0.387 Round 3: 111 peptides, 19 chains. Longest chain 11 peptides. Score 0.417 Round 4: 110 peptides, 19 chains. Longest chain 12 peptides. Score 0.411 Round 5: 113 peptides, 18 chains. Longest chain 11 peptides. Score 0.456 Taking the results from Round 5 Chains 18, Residues 95, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 4210 restraints for refining 1810 atoms. 3811 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2833 (Rfree = 0.000) for 1810 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 7: After refmac, R = 0.2825 (Rfree = 0.000) for 1775 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 8: After refmac, R = 0.2769 (Rfree = 0.000) for 1748 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 9: After refmac, R = 0.2629 (Rfree = 0.000) for 1732 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 10: After refmac, R = 0.2143 (Rfree = 0.000) for 1724 atoms. Found 7 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 4.32 Search for helices and strands: 0 residues in 0 chains, 1785 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1799 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.287 Round 2: 101 peptides, 17 chains. Longest chain 9 peptides. Score 0.408 Round 3: 108 peptides, 17 chains. Longest chain 11 peptides. Score 0.452 Round 4: 118 peptides, 17 chains. Longest chain 10 peptides. Score 0.511 Round 5: 115 peptides, 18 chains. Longest chain 10 peptides. Score 0.468 Taking the results from Round 4 Chains 17, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3944 restraints for refining 1741 atoms. 3557 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2751 (Rfree = 0.000) for 1741 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 12: After refmac, R = 0.2736 (Rfree = 0.000) for 1721 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 13: After refmac, R = 0.2833 (Rfree = 0.000) for 1704 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 14: After refmac, R = 0.2823 (Rfree = 0.000) for 1692 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 15: After refmac, R = 0.2718 (Rfree = 0.000) for 1674 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.65 4.24 Search for helices and strands: 0 residues in 0 chains, 1765 seeds are put forward NCS extension: 0 residues added, 1765 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 7 peptides. Score 0.276 Round 2: 111 peptides, 18 chains. Longest chain 19 peptides. Score 0.444 Round 3: 100 peptides, 19 chains. Longest chain 11 peptides. Score 0.344 Round 4: 107 peptides, 18 chains. Longest chain 10 peptides. Score 0.419 Round 5: 97 peptides, 15 chains. Longest chain 10 peptides. Score 0.438 Taking the results from Round 2 Chains 20, Residues 93, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3521 restraints for refining 1624 atoms. 3132 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2742 (Rfree = 0.000) for 1624 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 17: After refmac, R = 0.2846 (Rfree = 0.000) for 1612 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 18: After refmac, R = 0.2941 (Rfree = 0.000) for 1597 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 19: After refmac, R = 0.2789 (Rfree = 0.000) for 1575 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 20: After refmac, R = 0.2665 (Rfree = 0.000) for 1568 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 4.24 Search for helices and strands: 0 residues in 0 chains, 1666 seeds are put forward NCS extension: 0 residues added, 1666 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 8 peptides. Score 0.247 Round 2: 107 peptides, 19 chains. Longest chain 10 peptides. Score 0.391 Round 3: 110 peptides, 19 chains. Longest chain 11 peptides. Score 0.411 Round 4: 113 peptides, 20 chains. Longest chain 9 peptides. Score 0.402 Round 5: 109 peptides, 19 chains. Longest chain 10 peptides. Score 0.404 Taking the results from Round 3 Chains 19, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3415 restraints for refining 1593 atoms. 3070 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2760 (Rfree = 0.000) for 1593 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 22: After refmac, R = 0.2706 (Rfree = 0.000) for 1567 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 23: After refmac, R = 0.2772 (Rfree = 0.000) for 1557 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 24: After refmac, R = 0.2525 (Rfree = 0.000) for 1544 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 25: After refmac, R = 0.2755 (Rfree = 0.000) for 1538 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 4.28 Search for helices and strands: 0 residues in 0 chains, 1664 seeds are put forward NCS extension: 0 residues added, 1664 seeds are put forward Round 1: 83 peptides, 18 chains. Longest chain 8 peptides. Score 0.253 Round 2: 98 peptides, 17 chains. Longest chain 10 peptides. Score 0.389 Round 3: 102 peptides, 19 chains. Longest chain 11 peptides. Score 0.358 Round 4: 103 peptides, 20 chains. Longest chain 13 peptides. Score 0.336 Round 5: 112 peptides, 20 chains. Longest chain 10 peptides. Score 0.396 Taking the results from Round 5 Chains 20, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3608 restraints for refining 1630 atoms. 3260 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2868 (Rfree = 0.000) for 1630 atoms. Found 8 (8 requested) and removed 30 (4 requested) atoms. Cycle 27: After refmac, R = 0.2828 (Rfree = 0.000) for 1594 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 28: After refmac, R = 0.2628 (Rfree = 0.000) for 1569 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 29: After refmac, R = 0.2917 (Rfree = 0.000) for 1555 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 30: After refmac, R = 0.2613 (Rfree = 0.000) for 1547 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 4.13 Search for helices and strands: 0 residues in 0 chains, 1639 seeds are put forward NCS extension: 0 residues added, 1639 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 7 peptides. Score 0.233 Round 2: 89 peptides, 19 chains. Longest chain 7 peptides. Score 0.266 Round 3: 84 peptides, 15 chains. Longest chain 11 peptides. Score 0.352 Round 4: 83 peptides, 14 chains. Longest chain 10 peptides. Score 0.375 Round 5: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.331 Taking the results from Round 4 Chains 14, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3627 restraints for refining 1601 atoms. 3365 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2875 (Rfree = 0.000) for 1601 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 32: After refmac, R = 0.2594 (Rfree = 0.000) for 1581 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 33: After refmac, R = 0.2885 (Rfree = 0.000) for 1566 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 34: After refmac, R = 0.2554 (Rfree = 0.000) for 1556 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.2915 (Rfree = 0.000) for 1543 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 4.27 Search for helices and strands: 0 residues in 0 chains, 1626 seeds are put forward NCS extension: 0 residues added, 1626 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 7 peptides. Score 0.242 Round 2: 91 peptides, 19 chains. Longest chain 12 peptides. Score 0.281 Round 3: 86 peptides, 17 chains. Longest chain 11 peptides. Score 0.306 Round 4: 88 peptides, 16 chains. Longest chain 17 peptides. Score 0.350 Round 5: 88 peptides, 16 chains. Longest chain 8 peptides. Score 0.350 Taking the results from Round 5 Chains 16, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3383 restraints for refining 1534 atoms. 3111 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2863 (Rfree = 0.000) for 1534 atoms. Found 8 (8 requested) and removed 35 (4 requested) atoms. Cycle 37: After refmac, R = 0.2775 (Rfree = 0.000) for 1492 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 38: After refmac, R = 0.2604 (Rfree = 0.000) for 1481 atoms. Found 4 (8 requested) and removed 23 (4 requested) atoms. Cycle 39: After refmac, R = 0.2599 (Rfree = 0.000) for 1459 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 40: After refmac, R = 0.2791 (Rfree = 0.000) for 1453 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 4.27 Search for helices and strands: 0 residues in 0 chains, 1510 seeds are put forward NCS extension: 0 residues added, 1510 seeds are put forward Round 1: 45 peptides, 11 chains. Longest chain 5 peptides. Score 0.176 Round 2: 58 peptides, 13 chains. Longest chain 5 peptides. Score 0.219 Round 3: 56 peptides, 10 chains. Longest chain 9 peptides. Score 0.307 Round 4: 65 peptides, 11 chains. Longest chain 12 peptides. Score 0.341 Round 5: 60 peptides, 11 chains. Longest chain 7 peptides. Score 0.304 Taking the results from Round 4 Chains 11, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3224 restraints for refining 1469 atoms. 3019 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2716 (Rfree = 0.000) for 1469 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 42: After refmac, R = 0.2801 (Rfree = 0.000) for 1463 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 43: After refmac, R = 0.2812 (Rfree = 0.000) for 1454 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 44: After refmac, R = 0.2790 (Rfree = 0.000) for 1449 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.2819 (Rfree = 0.000) for 1444 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 4.21 Search for helices and strands: 0 residues in 0 chains, 1519 seeds are put forward NCS extension: 0 residues added, 1519 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 7 peptides. Score 0.214 Round 2: 57 peptides, 11 chains. Longest chain 9 peptides. Score 0.280 Round 3: 48 peptides, 9 chains. Longest chain 8 peptides. Score 0.278 Round 4: 48 peptides, 9 chains. Longest chain 9 peptides. Score 0.278 Round 5: 45 peptides, 8 chains. Longest chain 9 peptides. Score 0.290 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 37, 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 2ouw-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2882 reflections ( 99.76 % complete ) and 2853 restraints for refining 1345 atoms. 2713 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2959 (Rfree = 0.000) for 1345 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3070 (Rfree = 0.000) for 1337 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3080 (Rfree = 0.000) for 1329 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3275 (Rfree = 0.000) for 1325 atoms. TimeTaking 31.05