null Sun 23 Dec 22:22:52 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 2fqp-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fqp-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fqp-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-3.2-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/2fqp-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-3.2-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 22:23:02 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/2fqp-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-3.2-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 252 and 0 Target number of residues in the AU: 252 Target solvent content: 0.5972 Checking the provided sequence file Detected sequence length: 97 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 388 Adjusted target solvent content: 0.38 Input MTZ file: 2fqp-3.2-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: 4 Cell parameters: 35.909 92.640 53.056 90.000 106.409 90.000 Input sequence file: 2fqp-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3104 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 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: 50.895 3.200 Wilson plot Bfac: 51.11 4635 reflections ( 83.48 % complete ) and 0 restraints for refining 3445 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3219 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2518 (Rfree = 0.000) for 3445 atoms. Found 30 (30 requested) and removed 55 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.95 3.47 Search for helices and strands: 0 residues in 0 chains, 3451 seeds are put forward NCS extension: 0 residues added, 3451 seeds are put forward Round 1: 111 peptides, 24 chains. Longest chain 8 peptides. Score 0.253 Round 2: 134 peptides, 24 chains. Longest chain 12 peptides. Score 0.372 Round 3: 142 peptides, 24 chains. Longest chain 14 peptides. Score 0.410 Round 4: 145 peptides, 24 chains. Longest chain 11 peptides. Score 0.424 Round 5: 154 peptides, 25 chains. Longest chain 15 peptides. Score 0.445 Taking the results from Round 5 Chains 25, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6601 restraints for refining 2834 atoms. 6110 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2190 (Rfree = 0.000) for 2834 atoms. Found 21 (25 requested) and removed 17 (12 requested) atoms. Cycle 2: After refmac, R = 0.2028 (Rfree = 0.000) for 2814 atoms. Found 11 (25 requested) and removed 13 (12 requested) atoms. Cycle 3: After refmac, R = 0.1947 (Rfree = 0.000) for 2806 atoms. Found 3 (25 requested) and removed 14 (12 requested) atoms. Cycle 4: After refmac, R = 0.2011 (Rfree = 0.000) for 2791 atoms. Found 4 (25 requested) and removed 13 (12 requested) atoms. Cycle 5: After refmac, R = 0.2006 (Rfree = 0.000) for 2776 atoms. Found 6 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.91 3.43 Search for helices and strands: 0 residues in 0 chains, 2796 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 2821 seeds are put forward Round 1: 143 peptides, 29 chains. Longest chain 9 peptides. Score 0.311 Round 2: 180 peptides, 31 chains. Longest chain 11 peptides. Score 0.446 Round 3: 172 peptides, 31 chains. Longest chain 12 peptides. Score 0.410 Round 4: 187 peptides, 32 chains. Longest chain 14 peptides. Score 0.458 Round 5: 166 peptides, 26 chains. Longest chain 13 peptides. Score 0.479 Taking the results from Round 5 Chains 26, Residues 140, Estimated correctness of the model 4.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6414 restraints for refining 2736 atoms. 5880 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2223 (Rfree = 0.000) for 2736 atoms. Found 22 (24 requested) and removed 17 (12 requested) atoms. Cycle 7: After refmac, R = 0.1989 (Rfree = 0.000) for 2734 atoms. Found 11 (24 requested) and removed 15 (12 requested) atoms. Cycle 8: After refmac, R = 0.2094 (Rfree = 0.000) for 2726 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. Cycle 9: After refmac, R = 0.1844 (Rfree = 0.000) for 2716 atoms. Found 8 (24 requested) and removed 15 (12 requested) atoms. Cycle 10: After refmac, R = 0.1715 (Rfree = 0.000) for 2707 atoms. Found 5 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.87 3.38 Search for helices and strands: 0 residues in 0 chains, 2741 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2755 seeds are put forward Round 1: 172 peptides, 34 chains. Longest chain 10 peptides. Score 0.351 Round 2: 190 peptides, 34 chains. Longest chain 13 peptides. Score 0.434 Round 3: 185 peptides, 31 chains. Longest chain 19 peptides. Score 0.468 Round 4: 175 peptides, 29 chains. Longest chain 14 peptides. Score 0.462 Round 5: 185 peptides, 28 chains. Longest chain 14 peptides. Score 0.521 Taking the results from Round 5 Chains 28, Residues 157, Estimated correctness of the model 18.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6268 restraints for refining 2766 atoms. 5668 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2193 (Rfree = 0.000) for 2766 atoms. Found 21 (24 requested) and removed 29 (12 requested) atoms. Cycle 12: After refmac, R = 0.1958 (Rfree = 0.000) for 2748 atoms. Found 18 (24 requested) and removed 13 (12 requested) atoms. Cycle 13: After refmac, R = 0.1874 (Rfree = 0.000) for 2748 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. Cycle 14: After refmac, R = 0.1817 (Rfree = 0.000) for 2737 atoms. Found 6 (24 requested) and removed 14 (12 requested) atoms. Cycle 15: After refmac, R = 0.1696 (Rfree = 0.000) for 2726 atoms. Found 2 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.93 3.45 Search for helices and strands: 0 residues in 0 chains, 2776 seeds are put forward NCS extension: 0 residues added, 2776 seeds are put forward Round 1: 146 peptides, 31 chains. Longest chain 7 peptides. Score 0.284 Round 2: 162 peptides, 31 chains. Longest chain 10 peptides. Score 0.364 Round 3: 162 peptides, 28 chains. Longest chain 17 peptides. Score 0.423 Round 4: 156 peptides, 28 chains. Longest chain 13 peptides. Score 0.395 Round 5: 167 peptides, 26 chains. Longest chain 13 peptides. Score 0.483 Taking the results from Round 5 Chains 26, Residues 141, Estimated correctness of the model 5.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6530 restraints for refining 2824 atoms. 5992 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2145 (Rfree = 0.000) for 2824 atoms. Found 18 (25 requested) and removed 40 (12 requested) atoms. Cycle 17: After refmac, R = 0.1888 (Rfree = 0.000) for 2799 atoms. Found 16 (25 requested) and removed 13 (12 requested) atoms. Cycle 18: After refmac, R = 0.1803 (Rfree = 0.000) for 2795 atoms. Found 9 (25 requested) and removed 13 (12 requested) atoms. Cycle 19: After refmac, R = 0.1750 (Rfree = 0.000) for 2787 atoms. Found 8 (25 requested) and removed 13 (12 requested) atoms. Cycle 20: After refmac, R = 0.1661 (Rfree = 0.000) for 2781 atoms. Found 10 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.89 3.40 Search for helices and strands: 0 residues in 0 chains, 2821 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2836 seeds are put forward Round 1: 153 peptides, 30 chains. Longest chain 14 peptides. Score 0.340 Round 2: 155 peptides, 27 chains. Longest chain 13 peptides. Score 0.410 Round 3: 164 peptides, 27 chains. Longest chain 17 peptides. Score 0.451 Round 4: 156 peptides, 25 chains. Longest chain 13 peptides. Score 0.454 Round 5: 162 peptides, 21 chains. Longest chain 19 peptides. Score 0.552 Taking the results from Round 5 Chains 21, Residues 141, Estimated correctness of the model 27.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6399 restraints for refining 2792 atoms. 5856 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1977 (Rfree = 0.000) for 2792 atoms. Found 25 (25 requested) and removed 15 (12 requested) atoms. Cycle 22: After refmac, R = 0.1708 (Rfree = 0.000) for 2797 atoms. Found 21 (25 requested) and removed 12 (12 requested) atoms. Cycle 23: After refmac, R = 0.1386 (Rfree = 0.000) for 2797 atoms. Found 10 (25 requested) and removed 12 (12 requested) atoms. Cycle 24: After refmac, R = 0.1317 (Rfree = 0.000) for 2790 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.1330 (Rfree = 0.000) for 2778 atoms. Found 2 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.93 3.45 Search for helices and strands: 0 residues in 0 chains, 2816 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 2838 seeds are put forward Round 1: 145 peptides, 27 chains. Longest chain 12 peptides. Score 0.363 Round 2: 165 peptides, 28 chains. Longest chain 15 peptides. Score 0.436 Round 3: 153 peptides, 28 chains. Longest chain 12 peptides. Score 0.381 Round 4: 154 peptides, 25 chains. Longest chain 14 peptides. Score 0.445 Round 5: 154 peptides, 25 chains. Longest chain 13 peptides. Score 0.445 Taking the results from Round 5 Chains 25, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6342 restraints for refining 2773 atoms. 5851 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1659 (Rfree = 0.000) for 2773 atoms. Found 18 (24 requested) and removed 13 (12 requested) atoms. Cycle 27: After refmac, R = 0.1552 (Rfree = 0.000) for 2771 atoms. Found 9 (24 requested) and removed 14 (12 requested) atoms. Cycle 28: After refmac, R = 0.1457 (Rfree = 0.000) for 2758 atoms. Found 11 (24 requested) and removed 12 (12 requested) atoms. Cycle 29: After refmac, R = 0.1392 (Rfree = 0.000) for 2753 atoms. Found 8 (24 requested) and removed 12 (12 requested) atoms. Cycle 30: After refmac, R = 0.1350 (Rfree = 0.000) for 2748 atoms. Found 13 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.93 3.45 Search for helices and strands: 0 residues in 0 chains, 2780 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2795 seeds are put forward Round 1: 147 peptides, 29 chains. Longest chain 10 peptides. Score 0.331 Round 2: 159 peptides, 28 chains. Longest chain 11 peptides. Score 0.409 Round 3: 163 peptides, 29 chains. Longest chain 11 peptides. Score 0.408 Round 4: 165 peptides, 28 chains. Longest chain 12 peptides. Score 0.436 Round 5: 162 peptides, 26 chains. Longest chain 14 peptides. Score 0.461 Taking the results from Round 5 Chains 26, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6274 restraints for refining 2779 atoms. 5756 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1585 (Rfree = 0.000) for 2779 atoms. Found 17 (24 requested) and removed 13 (12 requested) atoms. Cycle 32: After refmac, R = 0.1431 (Rfree = 0.000) for 2780 atoms. Found 11 (24 requested) and removed 13 (12 requested) atoms. Cycle 33: After refmac, R = 0.1382 (Rfree = 0.000) for 2775 atoms. Found 9 (24 requested) and removed 13 (12 requested) atoms. Cycle 34: After refmac, R = 0.1323 (Rfree = 0.000) for 2766 atoms. Found 8 (24 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.1266 (Rfree = 0.000) for 2758 atoms. Found 9 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.92 3.44 Search for helices and strands: 0 residues in 0 chains, 2793 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2804 seeds are put forward Round 1: 138 peptides, 29 chains. Longest chain 8 peptides. Score 0.286 Round 2: 151 peptides, 24 chains. Longest chain 10 peptides. Score 0.451 Round 3: 146 peptides, 23 chains. Longest chain 11 peptides. Score 0.448 Round 4: 144 peptides, 21 chains. Longest chain 13 peptides. Score 0.478 Round 5: 150 peptides, 22 chains. Longest chain 12 peptides. Score 0.485 Taking the results from Round 5 Chains 22, Residues 128, Estimated correctness of the model 6.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6268 restraints for refining 2764 atoms. 5778 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1593 (Rfree = 0.000) for 2764 atoms. Found 22 (24 requested) and removed 14 (12 requested) atoms. Cycle 37: After refmac, R = 0.1402 (Rfree = 0.000) for 2770 atoms. Found 6 (24 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.1716 (Rfree = 0.000) for 2756 atoms. Found 24 (24 requested) and removed 13 (12 requested) atoms. Cycle 39: After refmac, R = 0.1224 (Rfree = 0.000) for 2764 atoms. Found 7 (24 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.1386 (Rfree = 0.000) for 2757 atoms. Found 18 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.88 3.39 Search for helices and strands: 0 residues in 0 chains, 2794 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2807 seeds are put forward Round 1: 122 peptides, 25 chains. Longest chain 11 peptides. Score 0.289 Round 2: 135 peptides, 24 chains. Longest chain 11 peptides. Score 0.377 Round 3: 133 peptides, 23 chains. Longest chain 11 peptides. Score 0.388 Round 4: 140 peptides, 23 chains. Longest chain 11 peptides. Score 0.421 Round 5: 133 peptides, 23 chains. Longest chain 11 peptides. Score 0.388 Taking the results from Round 4 Chains 23, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6167 restraints for refining 2744 atoms. 5722 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1479 (Rfree = 0.000) for 2744 atoms. Found 17 (24 requested) and removed 12 (12 requested) atoms. Cycle 42: After refmac, R = 0.1456 (Rfree = 0.000) for 2747 atoms. Found 11 (24 requested) and removed 14 (12 requested) atoms. Cycle 43: After refmac, R = 0.1697 (Rfree = 0.000) for 2741 atoms. Found 24 (24 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.1499 (Rfree = 0.000) for 2749 atoms. Found 14 (24 requested) and removed 15 (12 requested) atoms. Cycle 45: After refmac, R = 0.1459 (Rfree = 0.000) for 2748 atoms. Found 10 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.85 3.35 Search for helices and strands: 0 residues in 0 chains, 2784 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2797 seeds are put forward Round 1: 124 peptides, 27 chains. Longest chain 8 peptides. Score 0.256 Round 2: 136 peptides, 25 chains. Longest chain 10 peptides. Score 0.361 Round 3: 140 peptides, 25 chains. Longest chain 10 peptides. Score 0.380 Round 4: 129 peptides, 25 chains. Longest chain 10 peptides. Score 0.326 Round 5: 146 peptides, 27 chains. Longest chain 9 peptides. Score 0.368 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 115, 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 2fqp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4635 reflections ( 83.48 % complete ) and 6078 restraints for refining 2725 atoms. 5643 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1566 (Rfree = 0.000) for 2725 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1609 (Rfree = 0.000) for 2708 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1480 (Rfree = 0.000) for 2694 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1794 (Rfree = 0.000) for 2681 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:10:11 GMT 2018 Job finished. TimeTaking 47.31 Used memory is bytes: 12959344