null Tue 25 Dec 19:27:55 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fqp-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fqp-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-3.6-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 ============================================================ Tue 25 Dec 19:28:05 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-3.6-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 232 and 0 Target number of residues in the AU: 232 Target solvent content: 0.6292 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-3.6-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-3.6-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 3.601 Wilson plot Bfac: 65.51 3216 reflections ( 82.48 % complete ) and 0 restraints for refining 3441 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3254 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3053 (Rfree = 0.000) for 3441 atoms. Found 22 (22 requested) and removed 86 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.98 Search for helices and strands: 0 residues in 0 chains, 3394 seeds are put forward NCS extension: 0 residues added, 3394 seeds are put forward Round 1: 71 peptides, 17 chains. Longest chain 5 peptides. Score 0.186 Round 2: 106 peptides, 22 chains. Longest chain 7 peptides. Score 0.271 Round 3: 131 peptides, 26 chains. Longest chain 12 peptides. Score 0.314 Round 4: 137 peptides, 26 chains. Longest chain 12 peptides. Score 0.344 Round 5: 136 peptides, 24 chains. Longest chain 14 peptides. Score 0.381 Taking the results from Round 5 Chains 24, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6987 restraints for refining 2814 atoms. 6563 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2168 (Rfree = 0.000) for 2814 atoms. Found 10 (18 requested) and removed 116 (9 requested) atoms. Cycle 2: After refmac, R = 0.2044 (Rfree = 0.000) for 2679 atoms. Found 13 (17 requested) and removed 14 (8 requested) atoms. Cycle 3: After refmac, R = 0.1994 (Rfree = 0.000) for 2658 atoms. Found 12 (17 requested) and removed 14 (8 requested) atoms. Cycle 4: After refmac, R = 0.1932 (Rfree = 0.000) for 2648 atoms. Found 15 (17 requested) and removed 15 (8 requested) atoms. Cycle 5: After refmac, R = 0.1860 (Rfree = 0.000) for 2636 atoms. Found 12 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.75 Search for helices and strands: 0 residues in 0 chains, 2699 seeds are put forward NCS extension: 0 residues added, 2699 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 8 peptides. Score 0.238 Round 2: 123 peptides, 25 chains. Longest chain 8 peptides. Score 0.294 Round 3: 133 peptides, 26 chains. Longest chain 10 peptides. Score 0.324 Round 4: 124 peptides, 23 chains. Longest chain 10 peptides. Score 0.343 Round 5: 135 peptides, 25 chains. Longest chain 10 peptides. Score 0.356 Taking the results from Round 5 Chains 25, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6402 restraints for refining 2669 atoms. 5987 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1653 (Rfree = 0.000) for 2669 atoms. Found 9 (17 requested) and removed 34 (8 requested) atoms. Cycle 7: After refmac, R = 0.1566 (Rfree = 0.000) for 2630 atoms. Found 12 (16 requested) and removed 12 (8 requested) atoms. Cycle 8: After refmac, R = 0.1549 (Rfree = 0.000) for 2620 atoms. Found 6 (16 requested) and removed 31 (8 requested) atoms. Cycle 9: After refmac, R = 0.1445 (Rfree = 0.000) for 2587 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.1433 (Rfree = 0.000) for 2579 atoms. Found 7 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.77 Search for helices and strands: 0 residues in 0 chains, 2636 seeds are put forward NCS extension: 0 residues added, 2636 seeds are put forward Round 1: 115 peptides, 25 chains. Longest chain 8 peptides. Score 0.252 Round 2: 126 peptides, 27 chains. Longest chain 7 peptides. Score 0.266 Round 3: 140 peptides, 28 chains. Longest chain 9 peptides. Score 0.317 Round 4: 141 peptides, 27 chains. Longest chain 8 peptides. Score 0.343 Round 5: 145 peptides, 25 chains. Longest chain 11 peptides. Score 0.404 Taking the results from Round 5 Chains 26, Residues 120, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6064 restraints for refining 2680 atoms. 5534 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1603 (Rfree = 0.000) for 2680 atoms. Found 15 (17 requested) and removed 29 (8 requested) atoms. Cycle 12: After refmac, R = 0.1464 (Rfree = 0.000) for 2655 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 13: After refmac, R = 0.1441 (Rfree = 0.000) for 2649 atoms. Found 9 (17 requested) and removed 27 (8 requested) atoms. Cycle 14: After refmac, R = 0.1552 (Rfree = 0.000) for 2629 atoms. Found 12 (16 requested) and removed 23 (8 requested) atoms. Cycle 15: After refmac, R = 0.1281 (Rfree = 0.000) for 2614 atoms. Found 5 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.86 Search for helices and strands: 0 residues in 0 chains, 2686 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 2694 seeds are put forward Round 1: 109 peptides, 24 chains. Longest chain 8 peptides. Score 0.241 Round 2: 152 peptides, 28 chains. Longest chain 9 peptides. Score 0.376 Round 3: 140 peptides, 26 chains. Longest chain 10 peptides. Score 0.359 Round 4: 148 peptides, 27 chains. Longest chain 11 peptides. Score 0.377 Round 5: 154 peptides, 24 chains. Longest chain 16 peptides. Score 0.464 Taking the results from Round 5 Chains 26, Residues 130, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6362 restraints for refining 2792 atoms. 5784 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1713 (Rfree = 0.000) for 2792 atoms. Found 11 (17 requested) and removed 28 (8 requested) atoms. Cycle 17: After refmac, R = 0.1539 (Rfree = 0.000) for 2755 atoms. Found 12 (17 requested) and removed 17 (8 requested) atoms. Cycle 18: After refmac, R = 0.1580 (Rfree = 0.000) for 2738 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 19: After refmac, R = 0.1473 (Rfree = 0.000) for 2734 atoms. Found 13 (17 requested) and removed 10 (8 requested) atoms. Cycle 20: After refmac, R = 0.1416 (Rfree = 0.000) for 2732 atoms. Found 7 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.83 Search for helices and strands: 0 residues in 0 chains, 2781 seeds are put forward NCS extension: 0 residues added, 2781 seeds are put forward Round 1: 118 peptides, 27 chains. Longest chain 7 peptides. Score 0.223 Round 2: 142 peptides, 30 chains. Longest chain 9 peptides. Score 0.285 Round 3: 152 peptides, 27 chains. Longest chain 11 peptides. Score 0.396 Round 4: 146 peptides, 26 chains. Longest chain 13 peptides. Score 0.388 Round 5: 140 peptides, 25 chains. Longest chain 10 peptides. Score 0.380 Taking the results from Round 3 Chains 27, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6617 restraints for refining 2764 atoms. 6144 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1616 (Rfree = 0.000) for 2764 atoms. Found 9 (17 requested) and removed 28 (8 requested) atoms. Cycle 22: After refmac, R = 0.1636 (Rfree = 0.000) for 2735 atoms. Found 8 (17 requested) and removed 17 (8 requested) atoms. Cycle 23: After refmac, R = 0.1578 (Rfree = 0.000) for 2721 atoms. Found 13 (17 requested) and removed 12 (8 requested) atoms. Cycle 24: After refmac, R = 0.1571 (Rfree = 0.000) for 2716 atoms. Found 13 (17 requested) and removed 16 (8 requested) atoms. Cycle 25: After refmac, R = 0.1313 (Rfree = 0.000) for 2708 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.77 Search for helices and strands: 0 residues in 0 chains, 2754 seeds are put forward NCS extension: 0 residues added, 2754 seeds are put forward Round 1: 123 peptides, 27 chains. Longest chain 10 peptides. Score 0.250 Round 2: 119 peptides, 22 chains. Longest chain 11 peptides. Score 0.340 Round 3: 111 peptides, 19 chains. Longest chain 10 peptides. Score 0.365 Round 4: 106 peptides, 19 chains. Longest chain 9 peptides. Score 0.339 Round 5: 110 peptides, 19 chains. Longest chain 10 peptides. Score 0.360 Taking the results from Round 3 Chains 19, Residues 92, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6855 restraints for refining 2791 atoms. 6481 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1426 (Rfree = 0.000) for 2791 atoms. Found 11 (17 requested) and removed 18 (8 requested) atoms. Cycle 27: After refmac, R = 0.1421 (Rfree = 0.000) for 2777 atoms. Found 5 (17 requested) and removed 12 (8 requested) atoms. Cycle 28: After refmac, R = 0.1352 (Rfree = 0.000) for 2768 atoms. Found 7 (17 requested) and removed 13 (8 requested) atoms. Cycle 29: After refmac, R = 0.1291 (Rfree = 0.000) for 2758 atoms. Found 13 (17 requested) and removed 13 (8 requested) atoms. Cycle 30: After refmac, R = 0.1256 (Rfree = 0.000) for 2755 atoms. Found 8 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 3.72 Search for helices and strands: 0 residues in 0 chains, 2792 seeds are put forward NCS extension: 0 residues added, 2792 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 6 peptides. Score 0.241 Round 2: 99 peptides, 21 chains. Longest chain 8 peptides. Score 0.255 Round 3: 116 peptides, 22 chains. Longest chain 10 peptides. Score 0.324 Round 4: 119 peptides, 22 chains. Longest chain 10 peptides. Score 0.340 Round 5: 118 peptides, 21 chains. Longest chain 9 peptides. Score 0.356 Taking the results from Round 5 Chains 21, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6979 restraints for refining 2814 atoms. 6612 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1342 (Rfree = 0.000) for 2814 atoms. Found 10 (18 requested) and removed 12 (9 requested) atoms. Cycle 32: After refmac, R = 0.1306 (Rfree = 0.000) for 2805 atoms. Found 11 (18 requested) and removed 12 (9 requested) atoms. Cycle 33: After refmac, R = 0.1436 (Rfree = 0.000) for 2801 atoms. Found 11 (17 requested) and removed 11 (8 requested) atoms. Cycle 34: After refmac, R = 0.1103 (Rfree = 0.000) for 2796 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.0785 (Rfree = 0.000) for 2791 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.11 3.66 Search for helices and strands: 0 residues in 0 chains, 2826 seeds are put forward NCS extension: 0 residues added, 2826 seeds are put forward Round 1: 100 peptides, 22 chains. Longest chain 7 peptides. Score 0.237 Round 2: 116 peptides, 24 chains. Longest chain 7 peptides. Score 0.280 Round 3: 128 peptides, 24 chains. Longest chain 12 peptides. Score 0.342 Round 4: 140 peptides, 30 chains. Longest chain 8 peptides. Score 0.275 Round 5: 115 peptides, 23 chains. Longest chain 12 peptides. Score 0.297 Taking the results from Round 3 Chains 24, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6786 restraints for refining 2814 atoms. 6394 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1438 (Rfree = 0.000) for 2814 atoms. Found 7 (18 requested) and removed 10 (9 requested) atoms. Cycle 37: After refmac, R = 0.1436 (Rfree = 0.000) for 2800 atoms. Found 15 (18 requested) and removed 12 (9 requested) atoms. Cycle 38: After refmac, R = 0.1413 (Rfree = 0.000) for 2798 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.1182 (Rfree = 0.000) for 2800 atoms. Found 12 (17 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.1249 (Rfree = 0.000) for 2799 atoms. Found 10 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 3.64 Search for helices and strands: 0 residues in 0 chains, 2856 seeds are put forward NCS extension: 0 residues added, 2856 seeds are put forward Round 1: 87 peptides, 20 chains. Longest chain 6 peptides. Score 0.210 Round 2: 76 peptides, 15 chains. Longest chain 10 peptides. Score 0.269 Round 3: 82 peptides, 17 chains. Longest chain 7 peptides. Score 0.254 Round 4: 82 peptides, 15 chains. Longest chain 18 peptides. Score 0.304 Round 5: 80 peptides, 16 chains. Longest chain 10 peptides. Score 0.267 Taking the results from Round 4 Chains 15, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6932 restraints for refining 2814 atoms. 6679 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1249 (Rfree = 0.000) for 2814 atoms. Found 17 (18 requested) and removed 10 (9 requested) atoms. Cycle 42: After refmac, R = 0.1283 (Rfree = 0.000) for 2818 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 43: After refmac, R = 0.0808 (Rfree = 0.000) for 2819 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. Cycle 44: After refmac, R = 0.0856 (Rfree = 0.000) for 2812 atoms. Found 15 (18 requested) and removed 10 (9 requested) atoms. Cycle 45: After refmac, R = 0.0711 (Rfree = 0.000) for 2817 atoms. Found 3 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 3.65 Search for helices and strands: 0 residues in 0 chains, 2840 seeds are put forward NCS extension: 0 residues added, 2840 seeds are put forward Round 1: 73 peptides, 18 chains. Longest chain 5 peptides. Score 0.173 Round 2: 81 peptides, 18 chains. Longest chain 7 peptides. Score 0.223 Round 3: 70 peptides, 15 chains. Longest chain 7 peptides. Score 0.233 Round 4: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.306 Round 5: 78 peptides, 17 chains. Longest chain 10 peptides. Score 0.230 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 64, 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. 3216 reflections ( 82.48 % complete ) and 6772 restraints for refining 2788 atoms. 6530 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1647 (Rfree = 0.000) for 2788 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1413 (Rfree = 0.000) for 2777 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.0784 (Rfree = 0.000) for 2767 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.0689 (Rfree = 0.000) for 2756 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:14:54 GMT 2018 Job finished. TimeTaking 46.98 Used memory is bytes: 14545152