Mon 24 Dec 00:02:08 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fqp-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fqp-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fqp-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.6-parrot-mrncs ############### 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 00:02:13 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.6-parrot-mrncs/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-mrncs.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-mrncs.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 3422 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3223 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2726 (Rfree = 0.000) for 3422 atoms. Found 21 (21 requested) and removed 50 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 4.01 Search for helices and strands: 0 residues in 0 chains, 3431 seeds are put forward NCS extension: 0 residues added, 3431 seeds are put forward Round 1: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.257 Round 2: 132 peptides, 22 chains. Longest chain 10 peptides. Score 0.404 Round 3: 137 peptides, 25 chains. Longest chain 10 peptides. Score 0.365 Round 4: 142 peptides, 23 chains. Longest chain 11 peptides. Score 0.430 Round 5: 151 peptides, 26 chains. Longest chain 11 peptides. Score 0.412 Taking the results from Round 4 Chains 23, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6729 restraints for refining 2812 atoms. 6276 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2112 (Rfree = 0.000) for 2812 atoms. Found 11 (18 requested) and removed 22 (9 requested) atoms. Cycle 2: After refmac, R = 0.1893 (Rfree = 0.000) for 2768 atoms. Found 8 (17 requested) and removed 14 (8 requested) atoms. Cycle 3: After refmac, R = 0.1716 (Rfree = 0.000) for 2743 atoms. Found 2 (17 requested) and removed 10 (8 requested) atoms. Cycle 4: After refmac, R = 0.1885 (Rfree = 0.000) for 2721 atoms. Found 8 (17 requested) and removed 11 (8 requested) atoms. Cycle 5: After refmac, R = 0.1714 (Rfree = 0.000) for 2709 atoms. Found 6 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.88 Search for helices and strands: 0 residues in 0 chains, 2777 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2792 seeds are put forward Round 1: 130 peptides, 29 chains. Longest chain 7 peptides. Score 0.244 Round 2: 140 peptides, 26 chains. Longest chain 10 peptides. Score 0.359 Round 3: 154 peptides, 25 chains. Longest chain 13 peptides. Score 0.445 Round 4: 150 peptides, 26 chains. Longest chain 11 peptides. Score 0.407 Round 5: 136 peptides, 25 chains. Longest chain 13 peptides. Score 0.361 Taking the results from Round 3 Chains 25, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 5974 restraints for refining 2577 atoms. 5483 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1614 (Rfree = 0.000) for 2577 atoms. Found 10 (16 requested) and removed 12 (8 requested) atoms. Cycle 7: After refmac, R = 0.1611 (Rfree = 0.000) for 2562 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. Cycle 8: After refmac, R = 0.1404 (Rfree = 0.000) for 2553 atoms. Found 6 (16 requested) and removed 11 (8 requested) atoms. Cycle 9: After refmac, R = 0.1664 (Rfree = 0.000) for 2543 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. Cycle 10: After refmac, R = 0.1353 (Rfree = 0.000) for 2540 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.79 Search for helices and strands: 0 residues in 0 chains, 2597 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2614 seeds are put forward Round 1: 117 peptides, 24 chains. Longest chain 8 peptides. Score 0.285 Round 2: 136 peptides, 24 chains. Longest chain 12 peptides. Score 0.381 Round 3: 140 peptides, 26 chains. Longest chain 13 peptides. Score 0.359 Round 4: 136 peptides, 23 chains. Longest chain 10 peptides. Score 0.402 Round 5: 142 peptides, 26 chains. Longest chain 12 peptides. Score 0.369 Taking the results from Round 4 Chains 23, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6121 restraints for refining 2645 atoms. 5692 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1510 (Rfree = 0.000) for 2645 atoms. Found 12 (16 requested) and removed 15 (8 requested) atoms. Cycle 12: After refmac, R = 0.1417 (Rfree = 0.000) for 2631 atoms. Found 8 (16 requested) and removed 12 (8 requested) atoms. Cycle 13: After refmac, R = 0.1426 (Rfree = 0.000) for 2625 atoms. Found 13 (16 requested) and removed 10 (8 requested) atoms. Cycle 14: After refmac, R = 0.1417 (Rfree = 0.000) for 2626 atoms. Found 11 (16 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.1390 (Rfree = 0.000) for 2622 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.78 Search for helices and strands: 0 residues in 0 chains, 2697 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2708 seeds are put forward Round 1: 136 peptides, 29 chains. Longest chain 8 peptides. Score 0.275 Round 2: 145 peptides, 25 chains. Longest chain 12 peptides. Score 0.404 Round 3: 142 peptides, 27 chains. Longest chain 12 peptides. Score 0.348 Round 4: 137 peptides, 23 chains. Longest chain 11 peptides. Score 0.407 Round 5: 142 peptides, 25 chains. Longest chain 13 peptides. Score 0.390 Taking the results from Round 4 Chains 23, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6315 restraints for refining 2697 atoms. 5882 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1594 (Rfree = 0.000) for 2697 atoms. Found 13 (17 requested) and removed 12 (8 requested) atoms. Cycle 17: After refmac, R = 0.1530 (Rfree = 0.000) for 2689 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 18: After refmac, R = 0.1539 (Rfree = 0.000) for 2690 atoms. Found 14 (17 requested) and removed 13 (8 requested) atoms. Cycle 19: After refmac, R = 0.1394 (Rfree = 0.000) for 2686 atoms. Found 9 (17 requested) and removed 10 (8 requested) atoms. Cycle 20: After refmac, R = 0.0930 (Rfree = 0.000) for 2681 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.87 Search for helices and strands: 0 residues in 0 chains, 2729 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 2742 seeds are put forward Round 1: 111 peptides, 23 chains. Longest chain 9 peptides. Score 0.275 Round 2: 120 peptides, 24 chains. Longest chain 9 peptides. Score 0.301 Round 3: 125 peptides, 24 chains. Longest chain 12 peptides. Score 0.327 Round 4: 128 peptides, 22 chains. Longest chain 14 peptides. Score 0.384 Round 5: 124 peptides, 21 chains. Longest chain 12 peptides. Score 0.386 Taking the results from Round 5 Chains 21, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6567 restraints for refining 2746 atoms. 6176 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1319 (Rfree = 0.000) for 2746 atoms. Found 6 (17 requested) and removed 9 (8 requested) atoms. Cycle 22: After refmac, R = 0.1434 (Rfree = 0.000) for 2732 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.1561 (Rfree = 0.000) for 2735 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 24: After refmac, R = 0.0887 (Rfree = 0.000) for 2734 atoms. Found 8 (17 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.0926 (Rfree = 0.000) for 2731 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.85 Search for helices and strands: 0 residues in 0 chains, 2794 seeds are put forward NCS extension: 9 residues added (2 deleted due to clashes), 2803 seeds are put forward Round 1: 129 peptides, 28 chains. Longest chain 7 peptides. Score 0.260 Round 2: 131 peptides, 25 chains. Longest chain 12 peptides. Score 0.336 Round 3: 139 peptides, 25 chains. Longest chain 16 peptides. Score 0.375 Round 4: 146 peptides, 26 chains. Longest chain 14 peptides. Score 0.388 Round 5: 152 peptides, 25 chains. Longest chain 18 peptides. Score 0.436 Taking the results from Round 5 Chains 25, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6525 restraints for refining 2790 atoms. 6042 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1307 (Rfree = 0.000) for 2790 atoms. Found 11 (17 requested) and removed 10 (8 requested) atoms. Cycle 27: After refmac, R = 0.1261 (Rfree = 0.000) for 2784 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.1378 (Rfree = 0.000) for 2782 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 29: After refmac, R = 0.1137 (Rfree = 0.000) for 2781 atoms. Found 11 (17 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.1222 (Rfree = 0.000) for 2783 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.86 Search for helices and strands: 0 residues in 0 chains, 2844 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2860 seeds are put forward Round 1: 110 peptides, 23 chains. Longest chain 10 peptides. Score 0.270 Round 2: 133 peptides, 25 chains. Longest chain 12 peptides. Score 0.346 Round 3: 133 peptides, 25 chains. Longest chain 12 peptides. Score 0.346 Round 4: 135 peptides, 22 chains. Longest chain 11 peptides. Score 0.418 Round 5: 139 peptides, 22 chains. Longest chain 12 peptides. Score 0.436 Taking the results from Round 5 Chains 23, Residues 117, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6540 restraints for refining 2814 atoms. 6050 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1373 (Rfree = 0.000) for 2814 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 32: After refmac, R = 0.1200 (Rfree = 0.000) for 2814 atoms. Found 8 (18 requested) and removed 9 (9 requested) atoms. Cycle 33: After refmac, R = 0.1156 (Rfree = 0.000) for 2808 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.1108 (Rfree = 0.000) for 2801 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.1129 (Rfree = 0.000) for 2797 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.88 Search for helices and strands: 0 residues in 0 chains, 2856 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2870 seeds are put forward Round 1: 130 peptides, 28 chains. Longest chain 9 peptides. Score 0.266 Round 2: 144 peptides, 28 chains. Longest chain 13 peptides. Score 0.337 Round 3: 144 peptides, 27 chains. Longest chain 11 peptides. Score 0.358 Round 4: 141 peptides, 26 chains. Longest chain 9 peptides. Score 0.364 Round 5: 143 peptides, 28 chains. Longest chain 11 peptides. Score 0.332 Taking the results from Round 4 Chains 26, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6733 restraints for refining 2814 atoms. 6299 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1455 (Rfree = 0.000) for 2814 atoms. Found 13 (18 requested) and removed 11 (9 requested) atoms. Cycle 37: After refmac, R = 0.1382 (Rfree = 0.000) for 2805 atoms. Found 14 (18 requested) and removed 10 (9 requested) atoms. Cycle 38: After refmac, R = 0.1281 (Rfree = 0.000) for 2805 atoms. Found 17 (18 requested) and removed 11 (9 requested) atoms. Cycle 39: After refmac, R = 0.1169 (Rfree = 0.000) for 2807 atoms. Found 13 (18 requested) and removed 11 (9 requested) atoms. Cycle 40: After refmac, R = 0.1094 (Rfree = 0.000) for 2805 atoms. Found 11 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.23 3.80 Search for helices and strands: 0 residues in 0 chains, 2855 seeds are put forward NCS extension: 0 residues added, 2855 seeds are put forward Round 1: 101 peptides, 20 chains. Longest chain 8 peptides. Score 0.290 Round 2: 131 peptides, 22 chains. Longest chain 10 peptides. Score 0.399 Round 3: 117 peptides, 22 chains. Longest chain 8 peptides. Score 0.329 Round 4: 126 peptides, 22 chains. Longest chain 10 peptides. Score 0.375 Round 5: 131 peptides, 23 chains. Longest chain 9 peptides. Score 0.378 Taking the results from Round 2 Chains 22, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6797 restraints for refining 2814 atoms. 6383 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1210 (Rfree = 0.000) for 2814 atoms. Found 12 (18 requested) and removed 9 (9 requested) atoms. Cycle 42: After refmac, R = 0.1109 (Rfree = 0.000) for 2811 atoms. Found 9 (18 requested) and removed 9 (9 requested) atoms. Cycle 43: After refmac, R = 0.1557 (Rfree = 0.000) for 2807 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 44: After refmac, R = 0.1308 (Rfree = 0.000) for 2807 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.1080 (Rfree = 0.000) for 2810 atoms. Found 15 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.78 Search for helices and strands: 0 residues in 0 chains, 2878 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2881 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 8 peptides. Score 0.260 Round 2: 129 peptides, 26 chains. Longest chain 8 peptides. Score 0.304 Round 3: 136 peptides, 25 chains. Longest chain 10 peptides. Score 0.361 Round 4: 134 peptides, 26 chains. Longest chain 8 peptides. Score 0.329 Round 5: 127 peptides, 24 chains. Longest chain 10 peptides. Score 0.337 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 111, 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 6724 restraints for refining 2812 atoms. 6305 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1374 (Rfree = 0.000) for 2812 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1305 (Rfree = 0.000) for 2802 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1363 (Rfree = 0.000) for 2790 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1095 (Rfree = 0.000) for 2780 atoms. TimeTaking 35.33